WO1996033267A1 - Cyclomaltodextrin glucanotransferase variants - Google Patents

Cyclomaltodextrin glucanotransferase variants Download PDF

Info

Publication number
WO1996033267A1
WO1996033267A1 PCT/DK1996/000179 DK9600179W WO9633267A1 WO 1996033267 A1 WO1996033267 A1 WO 1996033267A1 DK 9600179 W DK9600179 W DK 9600179W WO 9633267 A1 WO9633267 A1 WO 9633267A1
Authority
WO
WIPO (PCT)
Prior art keywords
residue
strain
variant
cgtase
holds
Prior art date
Application number
PCT/DK1996/000179
Other languages
French (fr)
Inventor
Lubbert Dijkhuizen
Bauke W. Dijkstra
Carsten Andersen
Claus Von Der Osten
Original Assignee
Novo Nordisk A/S
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Novo Nordisk A/S filed Critical Novo Nordisk A/S
Priority to EP96910915A priority Critical patent/EP0822982B1/en
Priority to DE69635515T priority patent/DE69635515T2/en
Priority to AT96910915T priority patent/ATE311439T1/en
Priority to JP53141396A priority patent/JP4057055B2/en
Priority to AU53968/96A priority patent/AU5396896A/en
Publication of WO1996033267A1 publication Critical patent/WO1996033267A1/en

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/1048—Glycosyltransferases (2.4)
    • C12N9/1051—Hexosyltransferases (2.4.1)
    • C12N9/1074—Cyclomaltodextrin glucanotransferase (2.4.1.19)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/24—Hydrolases (3) acting on glycosyl compounds (3.2)
    • C12N9/2402—Hydrolases (3) acting on glycosyl compounds (3.2) hydrolysing O- and S- glycosyl compounds (3.2.1)
    • C12N9/2405—Glucanases
    • C12N9/2408—Glucanases acting on alpha -1,4-glucosidic bonds
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12P—FERMENTATION OR ENZYME-USING PROCESSES TO SYNTHESISE A DESIRED CHEMICAL COMPOUND OR COMPOSITION OR TO SEPARATE OPTICAL ISOMERS FROM A RACEMIC MIXTURE
    • C12P19/00—Preparation of compounds containing saccharide radicals
    • C12P19/18—Preparation of compounds containing saccharide radicals produced by the action of a glycosyl transferase, e.g. alpha-, beta- or gamma-cyclodextrins
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y204/00—Glycosyltransferases (2.4)
    • C12Y204/01—Hexosyltransferases (2.4.1)
    • C12Y204/01019—Cyclomaltodextrin glucanotransferase (2.4.1.19)

Definitions

  • the present invention relates to variants of cyclomaltodextrin glucanotransferase. More specifically the invention relates to a method of modifying the substrate binding and/or product selectivity of a precursor CGTase enzyme, and CGTase variants derived from a precursor CGTase enzyme by substitution, insertion and/or deletion of one or more amino acid residue(s), which amino acid residue(s) holds a position close to the substrate. Moreover, the invention relates to DNA constructs encoding the CGTase variants, expression vectors, host cells and methods of producing the CGTase variants of the invention.
  • Cyclomaltodextrin glucanotransferase (E.C. 2.4.1.19), also designated cyclodextrin glucanotransferase or cyclodextrin glycosyltransferase, in the following termed CGTase, catalyses the conversion of starch and similar substrates into cydomaltodextrins via an intramolecular transglycosylation reaction, thereby forming cydomaltodextrins, in the following termed cyclodexthns (or CD), of various sizes.
  • CGTase Cyclomaltodextrin glucanotransferase
  • CGTase catalyses the conversion of starch and similar substrates into cydomaltodextrins via an intramolecular transglycosylation reaction, thereby forming cydomaltodextrins, in the following termed cyclodexthns (or CD), of various sizes
  • cyclodexthns of 6, 7 and 8 glucose units which are termed ⁇ -, ⁇ - and ⁇ -cyclodextrins, respectively.
  • cyclodexthns of 9, 10, and 11 glucose units which are termed ⁇ -, ⁇ -, and ⁇ - cyclodexthns, respectively.
  • Cyclodexthns are thus cyclic glucose oligomers with a hydrophobic internal cavity. They are able to form inclusion complexes with many small hydrophobic molecules in aqueous solutions, resulting in changes in physical properties, e.g. increased solubility and stability and decreased chemical reactivity and volatility. Cyclodexthns find applications particularly in the food, cosmetic, chemical and pharmaceutical industries.
  • CGTases have both starch-degrading activity and transglycosylation activity. Although some CGTases produce mainly ⁇ -cyclodextrins and some CGTases produce mainly ⁇ -cyclodextrins, CGTases usually form a mixture of ⁇ -, ⁇ - and ⁇ -cyclodextrins. Selective precipitation steps with organic solvents may be used for the isolation of separate ⁇ -, ⁇ - and ⁇ -cydodexthns. To avoid expensive and environmentally harmful procedures, the availability of CGTases capable of producing an increased ratio of one particular type of cyclodextrin is desirable.
  • CGTases from different bacterial sources including CGTases obtained from Bacillus, Brevibacterium, Clostridi ⁇ m, Corynebactehum, Klebsiella, Micrococcus, Thermoanaerobacter and Thermoanaerobacterium have been described in the literature.
  • EP 614971 describes a Brevibacterium CGTase, Haeckel & Bahl [Haeckel K, Bahl H; FEMS Microbiol. Lett. 1989 60 333-338] describe Clostridium thermos ⁇ lfurogenes CGTase, Podkovyrov & Zeik ⁇ s [Podkovyrov S M, Zeikus J G; J. Bacteriol. 1992 174 5400-5405] describe a Clostridium thermohydrosulfuricum CGTase, JP 7000183 describes a Corynebacterium CGTase, Binder et al.
  • thermophilic Actinomycetes have been reported [Abelian V A, Afyan K B, Avakian Z G, Melkumyan A G and Afrikian E G; Biochemistry (Moscow) 1995 60 (10) 1223-1229].
  • CGTases are functionally related to ⁇ -amylases. CGTases and ⁇ - amylases both degrade starch by hydrolysis of the ⁇ -(1 ,4)-glycosidic bonds, but produce virtually exclusively cyclic and linear products, respectively.
  • CGTases and ⁇ -amylases possess a high overall amino acid sequence identity, more than 60 %.
  • CGTases and ⁇ -amylases share about 30% amino acid sequence identity.
  • the active site clefts of CGTases and ⁇ - amylases, located between the A and B domain are rather similar.
  • the catalytic site of CGTases is located in the A domain, and has three catalytic residues (in Bacillus circulans strain 251 these are Asp229, Glu257 and Asp328, respectively, cf. Strokopytov et al. 1995, op cit.).
  • a central amino acid residue is located in the B domain, around which residue the cyclodextrins are formed, i.e. the cyclization axis. Substitution of this central residue, e.g.
  • Nakamura et al. [Nakamura A, Haga K and Yamane K; Biochemistry 1994 33 9929-9936] describe the effects on substrate binding and cyclization characteristics by replacements carried out at four residues in the active center of a Bacillus sp. Strain 1011 CGTase.
  • a phenylalanine at position 183 has been replaced by leucine
  • a tyrosine at position 195 has been replaced by alanine
  • phenylalanine, leucine, threonine, valine, and tryptophan respectively
  • a phenylalanine at position 259 has been replaced by leucine
  • a phenylalanine at position 283 has been replaced by leucine.
  • Fujiware et al. [F ⁇ jiwara S, Kakihara H, Sakaguchi K and Imanaka T; J. Bacteriol. 1992 174 (22) 7478-7481] describe CGTase variants derived from Bacillus stearothermophilus, in which a tyrosine residue at position 191 (corresponding to position 195 CGTase numbering) has been replaced by phenylalanine, a tryptophan residue at position 254 (corresponding to position 258, CGTase numbering) has been replaced by valine, a phenylalanine at position 255 (corresponding to position 259, CGTase numbering) has been replaced by phenylalanine and isoleucine, respectively, a threonine residue at position 591 (corresponding to position 598, CGTase numbering) has been replaced by phenylalanine, and a tryptophan residue at position 629 (corresponding to position 636, CGTase numbering)
  • JP-A-7023781 describes CGTase variants derived from Bacillus sp. 1011 , in which a tyrosine residue at position 195 has been replaced by leucine, valine, phenylalanine and isoleucine, respectively.
  • JP-A-5244945 describes CGTase variants derived from Bacillus stearothermophilus TC-91 , in which tyrosine residues at positions 222 and 286
  • JP-A-5041985 describes CGTase variants derived from Bacillus sp. #1011 , in which histidine at residue 140 in region A, histidine at residue 233 in region B, and histidine at residue 327 in region C, respectively, have been replaced by arginine and asparagine residues, respectively.
  • EP 630,967 describes CGTase variants in which a tyrosine residue at position 211 of a Bacillus sp.290-3 CGTase (corresponding to position 195, CGTase numbering), at position 217 of a Bacillus sp. 1-1 CGTase (corresponding to position 195, CGTase numbering), and at position 229 of a Bacillus circulans CGTase (corresponding to position 195, CGTase numbering), have been substituted for tryptophan and serine.
  • the invention provides a method of modifying the substrate binding and/or product selectivity of a precursor CGTase enzyme, which method comprises substitution, insertion and/or deletion of one or more amino acid residue(s) of the precursor enzyme, which amino acid residue(s) holds a position close to the substrate.
  • the invention provides a CGTase variant derived from a precursor CGTase enzyme by substitution, insertion and/or deletion of one or more amino acid residue(s), which amino acid residue(s) holds a position close to the substrate.
  • the invention provides a DNA construct encoding a CGTase variant of the invention.
  • the invention provides a recombinant expression vector comprising the DNA construct of the invention.
  • the invention provides a host cell comprising the DNA construct of the invention, or the recombinant expression vector of the invention.
  • the invention provides a method of producing a CGTase variant of the invention, which method comprises culturing the host cell of the invention under conditions permitting the production of the CGTase variant, and recovering the enzyme from the culture.
  • the invention provides CGTase variants for use in processes for the manufacture of cyclodextrins, in processes for the manufacture of linear oligosaccharides, and in processes for in situ generation of cyclodextrins.
  • Amino Acids for use in processes for the manufacture of cyclodextrins, in processes for the manufacture of linear oligosaccharides, and in processes for in situ generation of cyclodextrins.
  • a CGTase variant of this invention is a CGTase variant or mutated CGTase, having an amino acid sequence not found in nature.
  • a CGTase variant or mutated CGTase of this invention is a functional derivative of a precursor CGTase enzyme (i.e. the native, parental, or wild-type enzyme), and may be obtained by alteration of a DNA nudeotide sequence of a precursor gene or its derivatives, encoding the precursor enzyme.
  • the CGTase variant or mutated CGTase may be expressed and produced when the DNA nudeotide sequence encoding the CGTase variant is inserted into a suitable vector in a suitable host organism.
  • the host organism is not necessarily identical to the organism from which the precursor gene originated.
  • Amino acid residues which represent insertions in relation to the amino acid sequence of the CGTase from Bacillus circulans Strain 251 are numbered by the addition of letters in alphabetical order to the preceding CGTase number, such as e.g. position 91 aF for the "insert" Phe between Thr at position 91 and Gly at position 92 of the amino acid sequence of the CGTase from Thermoanaerobacter sp. ATCC 53627, cf. Table 1 (j).
  • P149* Deletion of a proline at position 149 is indicated as P149*, and an insertion between position 147 and 148 where no amino acid residue is present, is indicated as *147aD for insertion of an aspartic acid in position 147a.
  • slash marks e.g. S145A/D147L, representing mutations in positions 145 and 147 substituting serine with alanine and aspartic acid with leucine, respectively.
  • Bacillus circulans 251 a Bacillus circulans 251 ; b Bacillus sp. 1 -1 ; c Bacillus sp. 38-2; d Bacillus sp. 1011 ; e Bacillus licheniformis; f Bacillus macerans; g Bacillus ohbensis; h Bacillus stearothermophilus; i Klebsiella pneumoniae; j Thermoanaerobacter ATCC 53627.
  • Fig. 1 shows a model of the structure of the active site cleft (domains A and B) of a CGTase from Bacillus circulans Strain 251 , which has been complexed with a linear starch molecule, and residues involved in the enzyme-substrate interactions;
  • Fig. 2 shows the formation (% cyclodextrin) of ⁇ - ( ⁇ ), ⁇ - ( ⁇ ), and ⁇ - cyclodextrin ( ⁇ ) from 10% PaselliTM WA4 (pre-gelatinized drum-dried starch) during a 50 hour incubation at 50oC catalyzed by (A) wild-type enzyme (Bacillus circulans Strain 251 CGTase), (B) the Y89D CGTase variant, (C) the S146P CGTase variant, and (D) the Y89D/S146P CGTase variant;
  • A wild-type enzyme
  • B Bacillus circulans Strain 251 CGTase
  • B the Y89D CGTase variant
  • C the S146P CGTase variant
  • D the Y89D/S146P CGTase variant
  • FIG. 3 shows the construction of plasmid pDP66K, subcloning steps are indicated adjacent to the arrows;
  • Fig. 4 shows the results of starch binding experiments (% of protein bound to raw starch) at starch concentrations of from 0 to 8 % raw starch, (•) without ⁇ - cyclodextrin, and (O) with 0.1 mM ⁇ -cyclodextrin; (a) wild-type enzyme (Bacillus circulans Strain 251 CGTase), (b) the W616A/W662A variant, and (c) the Y633A variant;
  • Fig. 5 shows the results of reaction kinetic experiments (activity, U/mg) on
  • PaselliTM SA2 i.e. partially hydrolysed potato starch
  • Fig. 6 shows the results of reaction kinetic experiments (activity, U/mg) on raw starch at starch concentration of from 0 to 60 % raw starch, ( ⁇ ) wild-type enzyme (Bacillus circulans Strain 251 CGTase), ( ⁇ ) the W616A/W662A variant, and ( ⁇ ) the Y633A variant; the dotted line indicates the modelled curve resulting from the supposed interaction between MBS2 on the E domain and MBS3 on the C domain;
  • Fig. 7 shows the product formation (O ⁇ -cyclodextrin formation; D ⁇ - cyclodextrin formation, and ⁇ -cyclodextrin formation) of two CGTase variants of the invention (N193G, Fig. 7B, and Y89G, Fig. 7C) compared to the wild-type enzyme (from Bacillus circulans Strain 251 , Fig. 7A) during incubation for 0 to 45 hours;
  • Fig. 8 shows the product formation (O ⁇ -cyclodextrin formation; D ⁇ - cyclodextrin formation, and ⁇ -cyclodextrin formation) of two CGTase variants of the invention (*145al, Fig. 8B, and D371G, Fig. 8C) compared to the wild-type enzyme (from Bacillus circulans Strain 251 , Fig. 8A) during incubation for 0 to 45 hours;
  • Fig. 9 shows the product formation (O ⁇ -cyclodextrin formation; ⁇ ⁇ - cyclodextrin formation, and ⁇ -cyclodextrin formation) of two CGTase variants of the invention (N193G, Fig. 9B, and Y89G, Fig. 9C) compared to the wild-type enzyme (from Bacillus circulans Strain 251 , Fig. 9A) during incubation for 0 to 10 hours; and
  • Fig 10 shows the product formation (O ⁇ -cyclodextrin formation; ⁇ ⁇ - cyclodextrin formation, and ⁇ -cyclodextrin formation) of two CGTase variants of the invention (145al, Fig. 10B, and D371G, Fig. 10C) compared to the wild-type enzyme (from Bacillus circulans Strain 251 , Fig. 10A) during incubation for 0 to 10 hours.
  • the present invention provides a method of modifying the substrate binding and/or increasing the product selectivity of a CGTase enzyme, thereby obtaining a CGTase variant having a modified substrate binding capability and/or an increased product selectivity, as compared to the precursor enzyme.
  • a CGTase variant of modified substrate binding capability is meant to describe a CGTase variant that is able to more efficiently act on its substrate, and/or a CGTase variant that is less affected by product inhibition.
  • product inhibition is meant to describe the phenomenon that increasing amounts of product reduce or even inhibit the substrate conversion. It is desirable to obtain CGTase variants that are less affected by product inhibition (i.e. variants of reduced product inhibition).
  • a CGTase variant of increased product selectivity is meant to describe a CGTase variant that is able to more selectively produce any of the various cyclodextrins thereby increasing the ratio of the desired product, as compared to the precursor enzyme.
  • the present invention is based on the concept of removing and/or introducing "obstacles" in the subsites of the active site cleft, the substrate binding cleft, or the groove leading to these clefts, thereby facilitating introduction of the substrate and its disposition in such a way that products of a predetermined size are obtained, and in such a way that substrate binding is not inhibited by the product.
  • CGTase enzyme By modifying the substrate binding of a CGTase enzyme, its product selectivity can be modified in order that the CGTase variant is able to more selectively produce any of the various cyclodextrins, ⁇ -, ⁇ - and ⁇ -cyclodextrins. Even CGTases capable of producing ⁇ -, ⁇ -, and ⁇ -cyclodextrins with 9, 10 and 11 glucose units, respectively, may be obtained. Modification of the substrate binding of a CGTase may also reduce the tendency of product inhibition, thereby increasing the cyclodextrin yield of the CGTase variant.
  • the concept of the invention may be expressed differently as the modification of enzyme-substrate side chain intermolecular interactions.
  • the intermolecular interactions between substrate and CGTase can be changed in order to direct the substrate to a specific location in the active site cleft, thereby obtaining a cyclic or linear product of predefined size, preferably ⁇ -, a ⁇ - or a ⁇ -cyclodextrin, or ⁇ -, ⁇ -, and ⁇ -cyclodextrins, or a linear oligosaccharide of similar size, preferably of 2-12 glucose units, more preferred 2-9 glucose units.
  • the introduction of more intermolecular interactions in the region around glucose units C to I, preferably C to H, of Fig. 1 , will lock the substrate in a position 6 glucose units from the catalytic site (between glucose units B and C of Fig. 1), and lead to increased product selectivity for ⁇ -cyclodextrins (6 glucose units).
  • the formation of larger cyclodextrins and/or larger linear oligosaccharides may simultaneously be reduced by reducing potential intermolecular interactions of glucose unit I to J of Fig. 1.
  • the introduction of more intermolecular interactions in the region around glucose units F to J, preferably H and I, of Fig. 1 , will lock the substrate in a position 7 glucose units from the catalytic site (between glucose units B and C of Fig. 1), and lead to increased product selectivity for ⁇ -cyclodextrins (7 glucose units).
  • the formation of e.g. ⁇ -cyclodextrins and/or small linear oligosaccharides may simultaneously be reduced by reducing potential intermolecular interactions of glucose unit C to G of Fig. 1.
  • the introduction of more intermolecular interactions in the region around glucose units H to K, preferably I and J, of Fig. 1 , will lock the substrate in a position 8 glucose units from the catalytic site (between glucose units B and C of Fig. 1), and lead to increased product selectivity for ⁇ -cyclodextrins (8 glucose units).
  • the formation of smaller cyclodextrins and/or linear oligosaccharides may simultaneously be reduced by reducing potential intermolecular interactions of glucose unit C to H of Fig. 1.
  • the introduction of more intermolecular interactions in the region around glucose units J to M, preferably K and L, of Fig. 1 , will lock the substrate in a position 9 glucose units from the catalytic site (between glucose units B and C of Fig. 1), and lead to increased product selectivity for ⁇ -cyclodextrins (9 glucose units).
  • the formation of smaller cyclodextrins and/or linear oligosaccharides may simultaneously be reduced by reducing potential intermolecular interactions of glucose unit C to H of Fig. 1.
  • the introduction of more intermolecular interactions in the region around glucose units K to N, preferably L and M, of Fig. 1 , will lock the substrate in a position 10 glucose units from the catalytic site (between glucose units B and C of Fig. 1), and lead to increased product selectivity for ⁇ -cyclodextrins (10 glucose units).
  • the formation of smaller cyclodextrins and/or linear oligosaccharides may simultaneously be reduced by reducing potential intermolecular interactions of glucose unit C to H of Fig. 1.
  • the introduction of more intermolecular interactions in the region around glucose units L to O, preferably M and N, of Fig. 1 , will lock the substrate in a position 11 glucose units from the catalytic site (between glucose units B and C of Fig. 1 ), and lead to increased product selectivity for ⁇ -cyclodextrins (11 glucose units).
  • the formation of smaller cyclodextrins and/or linear oligosaccharides may simultaneously be reduced by reducing potential intermolecular interactions of glucose unit C to H of Fig. 1.
  • the formation of linear oligosaccharides of desired length may be increased by combining the above conditions with substitution at the cyclization axis, corresponding to position 195, CGTase numbering.
  • the CGTase enzyme subjected to the method of the invention may be any one of
  • the CGTase preferably is a microbial enzyme, preferably a bacterial enzyme, and preferably the CGTase is derived from a strain of Bacillus, a strain of Brevibacterium, a strain of Clostridium, a strain of Corynebacterium, a strain of Klebsiella, a strain of Micrococcus, a strain of Thermoanaerobium, a strain of Thermoanaerobacter, a strain of Thermoanaerobacterium, or a strain of Thermoactinomyces.
  • the CGTase is derived from a strain of Bacillus autolyticus, a strain of Bacillus cereus, a strain of Bacillus circulans, a strain of Bacillus circulans var. alkalophilus, a strain of Bacillus coagulans, a strain of Bacillus firmus, a strain of Bacillus halophilus, a strain of Bacillus macerans, a strain of Bacillus megaterium, a strain of Bacillus ohbensis, a strain of Bacillus stearothermophilus, a strain of Bacillus subtilis, a strain of Klebsiella pneumonia, a strain of Thermoanaerobacter ethanolicus, a strain of Thermoanaerobacter finnii, a strain of Clostridium thermoamylolyticum, a strain of Clostridium thermosaccharolyticum, or a strain of Thermoanaerobacterium thermos
  • the CGTase is derived from the strain
  • Bacillus sp. Strain 1011 the strain Bacillus sp. Strain 38-2, the strain Bacillus sp.
  • strain 17-1 the strain Bacillus sp. 1-1 , the strain Bacillus sp. Strain B1018, the strain Bacillus circulans Strain 8, the strain Thermoanaerobacter sp. ATCC 53627, or the strain Bacillus circulans Strain 251, or a mutant or a variant thereof.
  • the strain Thermoanaerobacter sp. ATCC 53627 was deposited according to the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure at the American Type Culture Collection (ATCC), 12301 Parklawn Drive, Rockville, Maryland 20852, USA, on 3 June 1987.
  • the strain Bacillus circulans Strain 251 has been deposited in the open collection at Rijksinstituut voor Herbstzondheid (RIV), Bilthoven, The Netherlands, and allotted the accession number RIV 11115, and thus is publicly available.
  • the method of the invention comprises substitution, insertion and/or deletion of one or more amino acid residue(s) of the enzyme, which residue(s) hold a position close to the substrate, when the substrate has bound to the CGTase enzyme at its substrate binding sites.
  • the method of the invention comprises substitution, insertion and/or deletion of two or more amino acid residue(s), preferably of three or more amino acid residue(s).
  • a CGTase amino acid residue holding a position close to the substrate indicates an amino acid residue located within the enzyme in a way that it is within a potential intermolecular (i.e. enzyme-substrate) interactive distance from a glucose unit of the substrate (i.e. a polysaccharide).
  • potential intermolecular interactions include, but are not limited to hydrogen bonding, salt bridge formation, polar interactions, hydrophobic interactions, and aromatic interactions.
  • an amino acid position close to the substrate indicates a distance less than 8 A (angstrom), preferably less than 5 ⁇ , more preferred less than 3 A, from the substrate.
  • these distances are calculated using the CGTase from Bacillus circulans Strain 251 [cf. Lawson C L, van Montfort R, Strokopytov B, Rozeboom H J, Kalk K H, de Vries G E, Penninga D, Dijkhuizen L, and Dijkstra B W, J. Mol. Biol. 1994 236 590-600], complexed with a derivative of maltonanose, the coordinates of which have been deposited with the Protein Data Bank, Biology Department, Bldg. 463, Brookhaven National Laboratory, P.O. Box 5000, Upton, NY 11973-5000, USA, under the entry code 1 DU.
  • Knowledge of this structure makes it possible to identify similar positions in other CGTases, having a known primary structure, which positions corresponds to the positions stated in e.g. Table 2, cf. also Table 1.
  • CGTases have substrate binding regions located at the A domain, at the
  • the method of the invention comprises substituting one or more amino acid residue(s) of the CGTase enzyme, which residue(s) are located in one or more of the A, B, C and/or E domains, cf. Table 1.
  • sequence alignment and molecular modelling of a CGTase enzyme found in nature amino acid residues located close to the substrate can be identified.
  • sequence alignment the tertiary structure of any homologous CGTase can be modelled based on known three-dimensional CGTase structures.
  • Table 2 presents a list of CGTase amino acid positions located within 8 A from the substrate, and therefore to be considered in the context of this invention.
  • the amino acid residues are identified by CGTase numbering, which allows identification of the corresponding amino acid positions in any CGTase enzyme.
  • the method of the invention comprises substitution, insertion and/or deletion at one or more amino acid residue(s) identified in Table 2, below.
  • the method of the invention comprises substitution, insertion and/or deletion at one or more amino acid residue(s) identified in Tables 3-5, below.
  • the method of the invention comprises substitution, insertion and/or deletion at one or more amino acid residue(s) identified in Tables 6-8, below.
  • the substrate binding and product selectivity of a CGTase variant of the invention can be designed by removing existing and/or introducing potential intermolecular interactions between the CGTase variant and its substrate.
  • intermolecular interactions include, but are not limited to hydrogen bonding, salt bridge formation, polar interactions, hydrophobic interactions, and aromatic interactions.
  • Amino acid residues having side chains with hydrogen bonding potentials are generally the following:
  • amino acids do not in general possess the potential ability to form side chain hydrogen bonds (i.e. no H-bonding capability):
  • Amino acid residues having side chains with salt bridge formation potentials are generally the following:
  • Amino acid residues having side chains with polar interaction potentials are generally the following:
  • Amino acid residues having side chains with hydrophobic interaction potentials are generally the following:
  • Amino acid residues having side chains with aromatic interaction potentials are generally the following:
  • the present invention provides novel CGTase variants, having an amino acid sequence not found in nature.
  • the CGTase variant of the invention is regarded a derivative of a precursor CGTase enzyme (i.e. the native, parental, or wild-type enzyme).
  • the substrate binding and/or product selectivity has been modified, as compared to the precursor CGTase enzyme, by replacement, insertion and/or deletion of one or more amino acid residue(s) holding a position close to the substrate.
  • the CGTase variant of the invention may be derived from any CGTase enzyme found in nature.
  • the CGTase variant of the invention preferably is derived from a microbial enzyme, preferably a bacterial enzyme, and preferably the CGTase variant is derived from a strain of Bacillus, a strain of Brevibacterium, a strain of Clostridium, a strain of Corynebacterium, a strain of Klebsiella, a strain of Micrococcus, a strain of Thermoanaerobium, a strain of Thermoanaerobacter, a strain of Thermoanaerobacterium, or a strain of Thermoactinomyces.
  • the CGTase variant of the invention is derived from a strain of Bacillus autolyticus, a strain of Bacillus cereus, a strain of Bacillus circulans, a strain of Bacillus circulans var. alkalophilus, a strain of Bacillus coagulans, a strain of Bacillus firmus, a strain of Bacillus halophilus, a strain of Bacillus macerans, a strain of Bacillus megaterium, a strain of Bacillus ohbensis, a strain of Bacillus stearothermophilus, a strain of Bacillus subtilis, a strain of Klebsiella pneumonia, a strain of Thermoanaerobacter ethanolicus, a strain of Thermoanaerobacter fmnii, a strain of Clostridium thermoamylolytic ⁇ m, a strain of Clostridium thermosaccharolyticum, or a strain of Thermoan
  • the CGTase variant of the invention is derived from the strain Bacillus sp. Strain 1011 , the strain Bacillus sp. Strain 38-2, the strain Bacillus sp. Strain 17-1 , the strain Bacillus sp. 1-1 , the strain Bacillus sp. Strain B1018, the strain Bacillus circulans Strain 8, the strain Bacillus circulans Strain 251 , or the strain Thermoanaerobacter sp. ATCC 53627, or a mutant or a variant thereof.
  • an amino acid residue holding a position close to the substrate indicates an amino acid residue located within the enzyme in such a way that it is within a potential intermolecular (i.e. enzyme-substrate) interactive distance from a glucose unit of the substrate (i.e. a polysaccharide).
  • a potential intermolecular i.e. enzyme-substrate
  • a glucose unit of the substrate i.e. a polysaccharide
  • an amino acid position close to the substrate indicates a distance less than 8 A (angstrom), preferably less than 5 A, more preferred less than 3 A, from the substrate.
  • CGTases have substrate binding regions located at the A domain, at the B domain, at the C domain and at the E domain. Consequently, in a preferred embodiment, the invention provides a CGTase variant, in which variant a substitution, an insertion and/or a deletion have been introduced at one or more of the amino acid residue(s) located in one or more of the A, B, C and E domains.
  • the invention provides a CGTase variant, in which variant a substitution, an insertion and/or a deletion have been introduced at one or more of the amino acid positions corresponding to the positions stated in Table 2.
  • CGTase numbering a substitutions at positions 195 and 198 (CGTase numbering) have been accomplished, the CGTase is not contemplated a CGTase variant of the invention unless additional substitution, insertion and/or deletion at one or more amino acid residue(s) has been introduced.
  • a CGTase comprising any of the following specific mutations: H140R, H140N, F183L, H233R, H233N, W258V, F259L, F259I, F259Y, F283L, H327R, H327N, T598F and/or W636F, is not contemplated a CGTase variant of the invention, unless additional substitution, insertion and/or deletion of amino acid residue(s) at one or more positions not stated here has been introduced.
  • CGTase comprising any of the following specific mutations: F195Y/F259Y, W258V/F259I, T598F/W636F, and F183L/F259L, is not contemplated a CGTase variant of the invention, unless additional substitution, insertion and/or deletion of amino acid residue(s) at one or more positions has been introduced. Therefore such CGTase variants are disclaimed according to the present invention.
  • the CGTase variant of the invention is a CGTase variant derived from an enzyme obtainable from a strain of Bacillus, which enzyme has been modified by substitution, insertion and/or deletion at one or more amino acid positions corresponding to the positions stated in Tables 3-5.
  • the CGTase variant is derived from a strain of Bacillus autolyticus, a strain of Bacillus cereus, a strain of Bacillus circulans, a strain of Bacillus circulans vac alkalophilus, a strain of Bacillus coagulans, a strain of Bacillus firmus, a strain of Bacillus halophilus, a strain of Bacillus macerans, a strain of Bacillus megaterium, a strain of Bacillus ohbensis, a strain of Bacillus stearothermophilus, or a strain of Bacillus subtilis.
  • the CGTase variant is derived from the strain Bacillus sp.
  • Strain 1011 the strain Bacillus sp. Strain 38-2, the strain Bacillus sp. Strain 17-1 , the strain Bacillus sp. 1 -1 , the strain Bacillus sp. Strain B1018, the strain Bacillus circulans Strain 8, or the strain Bacillus circulans Strain 251 , or a mutant or a variant thereof.
  • the CGTase variant of the invention is a CGTase variant derived from an enzyme obtainable from a strain of Thermoanaerobacter, which enzyme has been modified by substitution, insertion and/or deletion at one or more of the amino acid positions corresponding to the positions stated in Tables 6-8.
  • the CGTase variant is derived from the strain Thermoanaerobacter sp. ATCC 53627, or a mutant or a variant thereof.
  • intermolecular enzyme/substrate interactions have been modified, as compared to the precursor enzyme.
  • potential intermolecular interactions include, but are not limited to hydrogen bonding, salt bridge formation, polar interactions, hydrophobic interactions, and aromatic interactions. Such modifications may be accomplished by substitution, insertion and/or deletion at one or more of the above described positions, according to the following guidance.
  • Amino acid residues having side chains with hydrogen bonding potentials are generally the following:
  • amino acids do not in general possess the potential ability to form side chain hydrogen bonds (i.e. no H-bonding capability):
  • Amino acid residues having side chains with salt bridge formation potentials are generally the following:
  • Amino acid residues having side chains with polar interaction potentials are generally the following: Asp (D), Asn (N), Glu (E), Gln (Q), Lys (K), Arg (R), His (H), Tyr (Y), Trp (W), and Cys (C).
  • Amino acid residues having side chains with hydrophobic interaction potentials are generally the following:
  • Amino acid residues having side chains with aromatic interaction potentials are generally the following:
  • variants are obtained, which possess an altered number of hydrogen bonds or other interactions in the subsites of the active cleft or in the groove leading to this cleft or on the maltose binding sites.
  • altering subsites in the binding cleft it is possible to manipulate the number of sugars which are able to bind and thus alter the ratios of ⁇ -, ⁇ -, ⁇ -cyclodextrins, etc., produced by the enzyme.
  • interactions on or before subsites C-l of the substrate should be increased, and interactions on subsites I and higher should be decreased.
  • sterical hindrance could be applied to prevent binding on subsites I and higher.
  • Mutations which increase hydrogen bonding relative to the substrate are e.g.:
  • N94Q or N94K or N94R or N94W or N94F (subsite E), D371 N or D371 G (subsite E+F), Y89D (subsite E), A144K or A144R or A144D (subsite H), N193D or N193E
  • Mutations which decrease hydrogen bonding relative to the substrate are e.g.:
  • a mutation which increases the hydrogen bonding relative to subsite H is e.g. A144R.
  • a mutation which increases hydrogen bonding relative to the substrate is e.g. N88K.
  • S145W or S145Y or S145F, and S146W or S146I or S146R or S146P prevent binding on subsite I of the substrate.
  • L600W or L600F or L600Y (of maltose binding site 2, cf. below).
  • a ⁇ -cyclodextrin forming CGTase variant of the invention may be a variant, which at positions 87-94 comprises the partial amino acid sequence IKYSGVNN, and/or at positions 143-151 comprises the partial amino acid sequence GRAGTNPGF, or at positions 143-145 comprises the partial amino acid sequence GRW.
  • Mutations which alter the conformation of the substrate binding cleft close to the active site and thus create space for larger cyclodextrins are e.g.:
  • N88P Y89* (a deletion), 91 aY (an insertion), V92* or N92*. and N94*.
  • a mutation which increases hydrogen bonding relative to the substrate is e.g. S146E.
  • Mutations which decrease hydrogen bonding relative to the substrate are e.g.
  • Mutations which remove hydrogen bonds from subsites D, E, F, H, I and J of the substrate are e.g.:
  • a mutation which introduce sterical hindrance between subsites I and J of the substrate, designed to shift the product ratio towards the production of smaller cyclodextrins is e.g. D147W.
  • a ⁇ -cyclodextrin forming CGTase variant of the invention may be a variant, which at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAETWPAF.
  • a ⁇ -cyclodextrin forming CGTase variant of the invention may be a variant, which at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAETWPAF, and which variant at position 195 holds a leucine residue (X195L).
  • a CGTase variant of the invention capable of forming linear oligosaccharides may be a variant, which at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAETWPAF, and which variant at position 195 holds a glycine residue (X195G).
  • Mutations which alter the conformation of the substrate binding cleft close to the active site and thus create space for larger cyclodextrins are e.g.:
  • N88P Y89* (a deletion), 91 aY (an insertion), V92* or N92*. and N94*.
  • a mutation which increases hydrogen bonding relative to the substrate is e.g. S146E.
  • Mutations which decrease hydrogen bonding relative to the substrate are e.g.
  • Mutations which remove hydrogen bonds from subsites D, E, F and H of the substrate are e.g.:
  • Mutations which change the binding properties at subsites I and J of the substrate are e.g.:
  • X145al or *145al via insertion
  • S145A, and Q148E in particular S145A/X145al or A145AT145al, and X145al/Q148E or *145al/Q148E.
  • Mutations which reduce the coupling activity at subsites A, D and E are e.g.:
  • Mutations reducing the coupling activity by changing specific binding of cyclodextrins is e.g. R47Q.
  • V21 F or V21Y Less coupling and disproportionating activity is achieved by removing interactions between the enzyme and the donor/acceptor, i.e. between the CGTase and subsites A, B, C and D. Mutations which remove hydrogen bonds are e.g.:
  • a ⁇ -cyclodextrin forming CGTase variant of the invention may be a variant, which at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAEADPNF.
  • a ⁇ -cyclodextrin forming CGTase variant of the invention may be a variant, which at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAEADPNF, and which variant at position 195 holds a leucine residue (X195W).
  • the variants of the invention may be combined with a substitution at the central amino acid residue forming the cyclization axis, corresponding to position 195, CGTase numbering.
  • a substitution at the central amino acid residue forming the cyclization axis corresponding to position 195, CGTase numbering.
  • tyrosine and phenylalanine are predominant in wild-type CGTases (cf. Table 1 ).
  • glycine is introduced at this position (X195G).
  • a CGTase variant of the invention is an enzyme which has been modified by substitution, insertion and/or deletion at one or more of the amino acid positions corresponding to the positions stated in Table 9, below. As indicated in this table, the introduction of one or more of these substitutions/insertions/deletions lead to CGTase variants of increased product selectivity in respect of ⁇ -, ⁇ - or ⁇ -cyclodextrins, respectively.
  • the E domain of the Bacillus circulans Strain 251 CGTase has now been identified as a raw starch binding domain.
  • MBS maltose binding sites
  • a CGTase variant of the invention is an enzyme which has been modified by substitution, insertion and/or deletion at one or more of the amino acid positions corresponding to the positions stated in Table 10, below. Such modifications lead to CGTase variants of reduced product inhibition.
  • Mutations which reduces non-competitive product inhibition are e.g.:
  • Y633A (takes place on MBS2, this mutation completely removes non- competitive product inhibition), 599aP or 599aR or 599aH, and L600R.
  • Residues 595-605 form a loop next to MBS2. Insertion enlarges the loop, thereby preventing binding of a cyclodextrin to MBS2 by sterical hindrance, while the role of MBS2 in guidance of the substrate chain is preserved. Mutations at position 600 and adjacent residues could reduce the binding of cyclic products to MBS2, while the binding of linear substrates remains unaffected. Substitution of leucine at position 600 with aspartate, alanine or glycine has minor effects on product inhibition. Substitution with arginine, due to its large size and charged nature, affect binding of cyclodextrins, thereby reducing product inhibition.
  • Mutations that decrease electrostatic interactions around MBS1 , leading to decreased product affinity are e.g. W616A and/or W662A.
  • Mutations that decrease electrostatic interactions around MBS2, leading to decreased product affinity are e.g. L600A or L600S, and/or Y663A.
  • a mutations that decreases electrostatic interactions around MBS3, leading to decreased product affinity is e.g. W413A.
  • Second (malto-oligosaccharide) substrate is contemplated caused by coupling reactions. Reduction of this coupling reaction may be achieved by reducing the binding of the first (cyclodextrin) and second (malto-oligosaccharide) substrate.
  • Mutations reducing competitive product inhibition by reducing cyclodextrin binding are e.g.:
  • R47A or R47Q or R47L Y89G, D196A or D196L, D371G or D371 N or
  • D371A or D371L and R375G or R375Q or R375N or R375A or R375L.
  • Mutations reducing competitive product inhibition by reducing binding of the second substrate are e.g.: K232Q or K232N or K232A or K232L, E264A or E264N or E264L, T186A, and E268A.
  • the CGTase variant of the invention is a CGTase variant derived from an enzyme obtainable from a strain of Bacillus, which enzyme has been modified by substitution, insertion and/or deletion at one or more of the amino acid positions corresponding to the positions stated in Table 11 , below. Such modifications lead to CGTase variants of increased product selectivity, as indicated in the table.
  • the CGTase variant is derived from a strain of a strain of Bacillus autolyticus, a strain of Bacillus cereus, a strain of Bacillus circulans, a strain of Bacillus circulans vac alkalophilus, a strain of Bacillus coagulans, a strain of Bacillus firmus, a strain of Bacillus halophilus, a strain of Bacillus macerans, a strain of Bacillus megaterium, a strain of Bacillus ohbensis, a strain of Bacillus stearothermophilus, or a strain of Bacillus subtilis.
  • the CGTase variant is derived from the strain Bacillus sp. Strain 1011 , the strain Bacillus sp. Strain 38-2, the strain Bacillus sp. Strain 17-1 , the strain Bacillus sp. 1-1 , the strain Bacillus sp. Strain B1018, the strain Bacillus circulans Strain 8, or the strain Bacillus circulans Strain 251 , or a mutant or a variant thereof.
  • the CGTase variant of the invention is a CGTase variant derived from an enzyme obtainable from a strain of Bacillus, which enzyme has been modified by substitution, insertion and/or deletion at one or more of the amino acid positions corresponding to the positions stated in Table 12, below. Such modifications lead to CGTase variants of reduced product inhibition.
  • a CGTase variant which variant at position 47 holds a glutamine residue (R47Q), or an alanine residue (R47A), or a leucine residue (R47L), or a histidine residue (R47H).
  • N88P a lysine residue
  • N88K a lysine residue
  • a CGTase variant which variant at position 89 holds an aspartic acid residue (Y89D), or an alanine residue (Y89A), or a glycine residue
  • a CGTase variant which variant at position 91a (via insertion) holds an alanine residue (*91aA), or a tyrosine residue (*91aY).
  • a CGTase variant which variant at position 94 holds a glutamine residue (N94Q), or a lysine residue (N94K), or an arginine residue (N94R), or a tryptophan residue (N94W), or a phenylalanine residue (N94F), or in which variant position 94 has been deleted (N94*).
  • a CGTase variant which variant at position 135 holds a leucine residue
  • a CGTase variant which variant at position 143 holds a natural amino acid residue different from that of the wild-type enzyme (P143X).
  • a CGTase variant which variant at position 143 holds an alanine residue
  • a CGTase variant which variant at position 144 holds a natural amino acid residue different from that of the wild-type enzyme (A144X).
  • a CGTase variant which variant at position 144 holds an arginine residue (A144R), or a lysine residue (A144K), or an aspartic acid residue
  • a CGTase variant which variant at position 145 holds a natural amino acid residue different from that of the wild-type enzyme (S145X).
  • a CGTase variant which variant at position 145 holds an alanine residue
  • S145A or a glutamic acid (S145E), or a tryptophan residue (S145W), or a glycine residue (S145G), or a phenylalanine residue (S145F), or a tyrosine residue (S145Y), or a leucine residue (S145L).
  • a CGTase variant which variant at position 145a (via insertion) holds a natural amino acid residue (*145aX).
  • a CGTase variant which variant at position 145a (via insertion) holds an isoleucine residue (*145al).
  • a CGTase variant which variant at position 146 holds a natural amino acid residue different from that of the wild-type enzyme (S146X).
  • a CGTase variant which variant at position 146 holds a proline residue
  • S146P or an isoleucine residue (S146I), or a glutamine residue (S146Q), or a tryptophan residue (S146W), or an arginine residue
  • a CGTase variant, which variant at position 147 holds a natural amino acid residue different from that of the wild-type enzyme (D147X).
  • a CGTase variant, which variant at position 147 holds an isoleucine residue (D147I), or a leucine residue (D147L), or an alanine residue
  • D147A or a serine residue (D147S), or a tryptophan residue (D147W).
  • a CGTase variant which variant at position 147a (via insertion) holds an alanine residue (*147aA).
  • a CGTase variant which variant at position 147a (via insertion) holds a natural amino acid residue (*147aX).
  • a CGTase variant which variant at position 148 holds a natural amino acid residue different from that of the wild-type enzyme (Q148X).
  • a CGTase variant which variant at position 148 holds an alanine residue (Q148A), or a glycine residue (Q148G), or a glutamic acid residue
  • a CGTase variant, which variant at position 149 holds a natural amino acid residue different from that of the wild-type enzyme (P149X).
  • a CGTase variant which variant at position 179 holds a serine residue
  • G179S an asparagine residue (G179N), or an aspartic acid residue (G179D).
  • a CGTase variant which variant at position 180 holds a serine residue
  • a CGTase variant which variant at position 185 holds an arginine residue (T185R), or a glutamic acid residue (T185E), or an aspartic acid residue (T185D).
  • a CGTase variant which variant at position 186 holds an alanine residue
  • T186A A CGTase variant, which variant at position 193 holds a natural amino acid residue different from that of the wild-type enzyme (N193X).
  • N193G or an alanine residue (N193A), or an aspartic acid residue (N193D), or a glutamic acid residue (N193E).
  • a CGTase variant, which variant at position 196 holds a natural amino acid residue different from that of the wild-type enzyme (D196X).
  • a CGTase variant, which variant at position 196 holds an alanine residue
  • D196A a serine residue (D196S), or a leucine residue (D196L).
  • a CGTase variant which variant at position 197 holds an aspartic acid residue (L197D), or a glutamic acid residue (L197E).
  • a CGTase variant which variant at position 232 holds a glutamine residue (K232Q), or an asparagine residue (K232N), or an alanine residue (K232A), or a leucine residue (K232L).
  • a CGTase variant which variant at position 264 holds a glutamine residue (E264Q), or an alanine residue (E264A), or an asparagine residue (E264N), or a leucine residue (E264L).
  • a CGTase variant which variant at position 268 holds an alanine residue
  • a CGTase variant which variant at position 371 holds a natural amino acid residue different from that of the wild-type enzyme (D371X).
  • a CGTase variant which variant at position 371 holds a glycine residue
  • a CGTase variant which variant at position 375 holds a natural amino acid residue different from that of the wild-type enzyme (R375X).
  • R375P or a glycine residue (R375G), or a glutamine residue (R375Q), or an asparagine residue (R375N), or an alanine residue (R375A), or a leucine residue (R375L).
  • a CGTase variant which variant at position 599a (via insertion) holds a proline residue (*599aP), or an arginine residue (*599aR), or a histidine residue (*599aH).
  • a CGTase variant which variant position 600 has been substituted for a different naturally occurring amino acid residue, in particular a tryptophan residue (L600W), a phenylalanine residue (L600F), a tyrosine residue (L600Y), an arginine residue (L600R), a proline residue (L600P), or an asparagine residue (L600N).
  • a tryptophan residue L600W
  • a phenylalanine residue L600F
  • a tyrosine residue L600Y
  • an arginine residue L600R
  • L600P proline residue
  • asparagine residue L600N
  • a CGTase variant which variant at position 616 holds an alanine residue
  • a CGTase variant which variant at position 633 holds an alanine residue
  • a CGTase variant which variant at position 662 holds an alanine residue
  • a CGTase variant which variant at position 47 holds a histidine residue, and at position 135 holds a leucine residue (R47H/D135L).
  • a CGTase variant which variant at position 88 holds a proline residue, and at position 143 holds a glycine residue (N88P/P143G).
  • a CGTase variant, in which variant positions 92 and 94 have been deleted (V92VN94*).
  • a CGTase variant, which variant at position 143 holds an alanine residue, and at position 144 holds an arginine residue (P143A/A144R).
  • a CGTase variant, which variant at position 143 holds a glycine residue, and at position 144 holds an arginine residue, and at position 145 holds a tryptophan residue (P143G/A144R/S145W).
  • a CGTase variant which variant at position 143 holds a glycine residue, and at position 144 holds an arginine residue, and at position 145 holds a tryptophan residue (P143G/A144R/S145W), and which variant at position 179 holds a serine residue (G179S), an asparagine residue (G179N), or an aspartic acid residue (G179D).
  • a CGTase variant which variant at positions 143-148 comprises the partial amino acid sequence GRA**A, the partial amino acid sequence
  • GRAAAA the partial amino acid sequence GRAPAA, or the partial amino acid sequence GRGPAA.
  • a CGTase variant which variant at position 144 holds an arginine residue, at position 145 holds an alanine residue, and at position 146 holds a proline residue (A144R/S145A/S146P).
  • a CGTase variant which variant at position 145 holds an alanine residue, and at position 145a (via insertion) holds an isoleucine residue
  • a CGTase variant which variant at position 145 holds an alanine residue, and at position 146 holds a glycine residue (S145A/S146G).
  • a CGTase variant which variant at position 145 holds a tryptophan residue, and in position 146 holds a tryptophan residue, or an isoleucine residue, or an arginine residue (S145W/S146W or S145W/S146I or S145W/S146R).
  • a CGTase variant which variant at position 145 holds an alanine residue, at position 145a (via insertion) holds an isoleucine residue, and at position 148 holds a glutamic acid residue (S145A/*145al/Q148E).
  • a CGTase variant which variant at position 145a (via insertion) holds an isoleucine residue, and at position 148 holds a glutamic acid residue (*145al/Q148E).
  • a CGTase variant which variant at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAETWPAF.
  • a CGTase variant which variant at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAETWPAF, and which variant at position 195 holds a leucine residue (Y195L).
  • the above CGTase variants are derived from a strain of
  • Bacillus autolyticus a strain of Bacillus cereus, a strain of Bacillus circulans, a strain of Bacillus circulans var. alkalophilus, a strain of Bacillus coagulans, a strain of Bacillus firmus, a strain of Bacillus halophilus, a strain of Bacillus macerans, a strain of Bacillus megaterium, a strain of Bacillus ohbensis, a strain of Bacillus stearothermophilus, or a strain of Bacillus subtilis.
  • the above CGTase variants are derived from the strain Bacillus sp. Strain 1011 , the strain Bacillus sp. Strain 38-2, the strain Bacillus sp. Strain 17-1 , the strain Bacillus sp. 1 -1 , the strain Bacillus sp. Strain B1018, the strain Bacillus circulans Strain 8, or the strain Bacillus circulans Strain 251 , or a mutant or a variant thereof.
  • the CGTase variant of the invention is a CGTase variant derived from an enzyme obtainable from a strain of Thermoanaerobacter, which enzyme has been modified by substitution, insertion and/or deletion at one or more of the amino acid positions corresponding to the positions stated in Table 13, below. Such modification lead to CGTase variants of increased product selectivity, as indicated in the table.
  • the CGTase variant is derived from a strain of
  • the CGTase variant of the invention is a CGTase variant derived from an enzyme obtainable from a strain of Thermoanaerobacter, which enzyme has been modified by substitution, insertion and/or deletion at one or more of the amino acid residues corresponding to the positions stated in Table 14, below. Such modifications lead to CGTase variants of reduced product inhibition.
  • the CGTase variant is derived from a strain of Thermoanaerobacter sp. ATCC 53627, or a mutant or a variant thereof.
  • CGTase variants derived from a strain of Thermoanaerobacter sp., preferably the strain of Thermoanaerobacter ATCC 53627, or a mutant or a variant thereof:
  • a CGTase variant which variant at position 21 holds a phenylalanine residue (V21 F) or a tyrosine residue (V21Y).
  • K47Q or an alanine residue (K47A), or a leucine residue (K47L), or a histidine residue (K47H), or an arginine residue (K47R).
  • a CGTase variant which variant at position 88 holds a lysine residue (P88K).
  • a CGTase variant which variant at position 91 a holds an alanine residue (F91aA) or a tyrosine residue (F91aY), or in which variant position 91a has been deleted (F91a*).
  • a CGTase variant which variant at position 94 holds a glutamine residue (S94Q), or a lysine residue (S94K), or an arginine residue (S94R), or a tryptophan residue (S94W), or a phenylalanine residue (S94F), or in which variant position 94 has been deleted (S94*).
  • a CGTase variant which variant at position 135 holds a leucine residue
  • a CGTase variant which variant at position 143 holds an alanine residue
  • a CGTase variant which variant at position 144 holds a natural amino acid residue different from that of the wild-type enzyme (A145X).
  • a CGTase variant which variant at position 144 holds an arginine residue (A144R), or a lysine residue (A144K), or an aspartic acid residue
  • a CGTase variant which variant at position 145 holds a natural amino acid residue different from that of the wild-type enzyme (S145X).
  • a CGTase variant which variant at position 145 holds an alanine residue
  • S145A or a glutamic acid (S145E), or a tryptophan residue (S145W), or a glycine residue (S145G), or a phenylalanine residue (S145F), or a tyrosine residue (S145Y), or a leucine residue (S145L).
  • a CGTase variant which variant at position 145a (via insertion) holds a natural amino acid residue (*145aX).
  • a CGTase variant which variant at position 145a (via insertion) holds an isoleucine residue (*145al).
  • a CGTase variant which variant at position 146 holds a natural amino acid residue different from that of the wild-type enzyme (E145X).
  • a CGTase variant which variant at position 146 holds a proline residue
  • E146P or a serine residue (E146S), or an isoleucine residue (E146I), or a glutamine residue (E146Q), or a tryptophan residue (E146W), or an arginine residue (E146R).
  • a CGTase variant which variant at position 147 holds an isoleucine residue (T147I), or a leucine residue (T147L), or an alanine residue (T147A), or a serine residue (T147S), or a tryptophan residue (T147W).
  • a CGTase variant, which variant at position 148 holds a natural amino acid residue different from that of the wild-type enzyme (D148X).
  • a CGTase variant, which variant at position 148 holds an alanine residue
  • D148A or a glycine residue (D148G), or a glutamic acid residue
  • a CGTase variant, which variant at position 149 holds a natural amino acid residue different from that of the wild-type enzyme (P149X).
  • a CGTase variant, which variant at position 149 holds an isoleucine residue (P149I).
  • a CGTase variant which variant at position 179 holds a serine residue (G179S), an asparagine residue (G179N), or an aspartic acid residue
  • a CGTase variant which variant at position 180 holds a serine residue
  • a CGTase variant which variant at position 185 holds an arginine residue (S185R), or a glutamic acid residue (S185E), or an aspartic acid residue (S185D).
  • a CGTase variant which variant at position 186 holds an alanine residue
  • N193G or an alanine residue (N193A), or an aspartic acid residue
  • N193D a glutamic acid residue
  • N193E a glutamic acid residue
  • a CGTase variant, which variant at position 196 holds a natural amino acid residue different from that of the wild-type enzyme (D196X).
  • a CGTase variant, which variant at position 196 holds an alanine residue
  • D196A a serine residue (D196S), or a leucine residue (D196L).
  • a CGTase variant which variant at position 197 holds an aspartic acid residue (L197D), or a glutamic acid residue (L197E).
  • a CGTase variant which variant at position 232 holds a glutamine residue (K232Q), or an asparagine residue (K232N), or an alanine residue (K232A), or a leucine residue (K232L).
  • a CGTase variant which variant at position 259 holds a phenylalanine residue (Y259F).
  • a CGTase variant which variant at position 264 holds a glutamine residue (E264Q), or an alanine residue (E264A), or an asparagine residue (E264N), or a leucine residue (E264L).
  • a CGTase variant which variant at position 268 holds an alanine residue
  • a CGTase variant which variant at position 371 holds a natural amino acid residue different from that of the wild-type enzyme (D371X).
  • a CGTase variant which variant at position 371 holds a glycine residue (D371G), or an asparagine residue (D371 N), or an alanine residue
  • D371A or a leucine residue (D371L), or a glutamic acid residue
  • a CGTase variant, which variant at position 375 holds a natural amino acid residue different from that of the wild-type enzyme (R375X).
  • a CGTase variant, which variant at position 375 holds a proline residue
  • R375P or a glycine residue (R375G), or a glutamine residue (R375Q), or an asparagine residue (R375N), or an alanine residue (R375A), or a leucine residue (R375L).
  • a CGTase variant which variant at position 599a (via insertion) holds a proline residue (*599aP), or an arginine residue (*599aR), or a histidine residue (*599aH).
  • a CGTase variant which variant position 600 has been substituted for a different amino acid residue, in particular a phenylalanine residue (W600F), a tyrosine residue (W600Y), an arginine residue (W600R), a proline residue (W600P), a leucine residue (W600L), or an asparagine residue (W600N).
  • W600F phenylalanine residue
  • W600Y tyrosine residue
  • W600R arginine residue
  • W600P proline residue
  • W600L leucine residue
  • W600N asparagine residue
  • a CGTase variant which variant at position 616 holds an alanine residue (W616A).
  • a CGTase variant which variant at position 633 holds an alanine residue
  • a CGTase variant which variant at position 662 holds an alanine residue
  • a CGTase variant which variant at position 47 holds a histidine residue or an arginine residue, and/or at position 135 holds a leucine residue (K47H/D135L or K47R/D135L).
  • a CGTase variant which variant at positions 87-94 comprises the partial amino acid sequence IKYSGVNN, or the partial amino acid sequence INDSGVNN, and/or at positions 143-151 comprises the partial amino acid sequence GRAGTNPGF, or at positions 143-145 comprises the partial amino acid sequence GRW, and/or at position 195 holds a tyrosine residue (F195Y).
  • a CGTase variant which variant at positions 87-94 comprises the partial amino acid sequence INDSGVNN, and/or at positions 146-150 comprises the partial amino acid sequence SDQPS.
  • a CGTase variant which variant at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAETWPAF.
  • a CGTase variant which variant at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAETWPAF, and which variant at position 195 holds a leucine residue (F195L).
  • a CGTase variant which variant at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAEADPNF.
  • a CGTase variant which variant at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAEADPNF, and which variant at position 195 holds a leucine residue (F195W).
  • a CGTase variant in which variant positions 92 and 94 have been deleted (G92*/S94*).
  • a CGTase variant, which variant at position 143 holds an alanine residue, and at position 144 holds an arginine residue (P143A/A144R).
  • a CGTase variant, which variant at position 143 holds a glycine residue, and at position 144 holds an arginine residue, and at position 145 holds a tryptophan residue (P143G/A144R/S145W).
  • a CGTase variant which variant at position 143 holds a glycine residue, and at position 144 holds an arginine residue, and at position 145 holds a tryptophan residue (P143G/A144R/S145W), and which variant at position 179 holds a serine residue (G179S), an asparagine residue (G179N), or an aspartic acid residue (G179D), and/or at position 180 holds an asparagine residue (G180N), or an aspartic acid residue
  • a CGTase variant which variant at positions 143-148 comprises the partial amino acid sequence GRA**A, the partial amino acid sequence GRAAAA, the partial amino acid sequence GRPAAA, the partial amino acid sequence GRAPAA, or the partial amino acid sequence GRGPAA.
  • a CGTase variant which variant at positions 143-151 comprises the partial amino acid sequence GRAGTNPG.
  • a CGTase variant which variant at positions 143-151 comprises the partial amino acid sequence GRAGTNPG, and at position 195 holds a tyrosine residue (F195Y).
  • a CGTase variant which variant at position 144 holds an arginine residue, at position 145 holds an alanine residue, and at position 146 holds a proline residue (A144R/S145A/E146P).
  • a CGTase variant which variant at position 145 holds an alanine residue, and at position 146 holds a glycine residue (S145A/E146G).
  • a CGTase variant which variant at position 145 holds a tryptophan residue, and in position 146 holds a tryptophan residue, or an isoleucine residue, or an arginine residue (S145W/E146W or S145W/E146I or S145W/E146R).
  • a CGTase variant which variant at position 145 holds an alanine residue, at position 145a (via insertion) holds an isoleucine residue, and at position 148 holds a glutamic acid residue (S145A/*145al/D148E).
  • a CGTase variant which variant at position 145a (via insertion) holds an isoleucine residue, and at position 148 holds a glutamic acid residue (*145al/D148E).
  • a CGTase variant which variant at position 616 holds an alanine residue, and at position 662 holds an alanine residue (W616A/W662A).
  • CGTase variants of the invention follows the general principles of recombinant DNA technology, e.g. as described by Sambrook et al. [Sambrook J, Fritsch E F, Maniatis T; Molecular Cloning: A Laboratory Manual,
  • the invention provides a DNA construct encoding a CGTase variant of the invention.
  • DNA construct is intended to indicate any nucleic acid molecule of cDNA, genomic DNA, synthetic DNA or RNA origin.
  • construct is intended to indicate a nucleic acid segment which may be single- or double-stranded, and which may be based on a complete or partial naturally occurring nudeotide sequence encoding the CGTase variant of interest.
  • the construct may optionally contain other nucleic add segments.
  • the DNA construct of the invention may be prepared by suitably modifying a DNA sequence encoding the precursor CGTase, which modification may bring about:
  • the modification of the DNA sequence may be performed by site- directed mutagenesis or by random mutagenesis, or by a combination of these techniques in accordance with well-known procedures, e.g. as described by Sambrook et al., op cit.
  • the DNA construct of the invention comprises one or more of the partial oligonucleotide sequences (primers) described in the examples below. These partial oligonucleotide sequences are in particular
  • primers A1-A24, primers B1-B15, and C1-C9 of Examples 5, 6 and 7.
  • the CGTase variant may be obtained by combining the DNA construct encoding the CGTase variant of the invention with an appropriate expression signal in an appropriate expression vector.
  • the expression vector of the invention may be any expression vector that is conveniently subjected to recombinant DNA procedures, and the choice of vector will often depend on the host cell into which it is to be introduced.
  • the vector may be an autonomously replicating vector, i.e. a vector which exists as an extra- chromosomal entity, the replication of which is independent of chromosomal replication, e.g. a plasmid.
  • the vector may be one which, when introduced into a host cell, is integrated into the host cell genome and replicated together with the chromosome(s) into which it has been integrated.
  • the DNA sequence encoding the CGTase variant preferably is operably linked to additional segments required for transcription of the DNA.
  • the expression vector is derived from plasmid or viral DNA, or may contain elements of both.
  • operably linked indicates that the segments are arranged so that they function in concert for their intended purposes, e.g. transcription initiates in a promoter and proceeds through the DNA sequence coding for the CGTase variant.
  • the DNA sequence encoding the CGTase variant preferably should be operably connected to a suitable promoter and terminator sequence.
  • the promoter may be any DNA sequence which shows transcriptional activity in the host cell of choice and may be derived from genes encoding proteins either homologous or heterologous to the host cell.
  • the procedures used to ligate the DNA sequences coding for the CGTase variant, the promoter and the terminator, respectively, and to insert them into suitable vectors are well known to persons skilled in the art (cf., for instance, Sambrook et al., op cif)
  • the promoter may be any DNA sequence which shows transcriptional activity in the host cell of choice and may be derived from genes encoding proteins either homologous or heterologous to the host cell.
  • suitable promoters for directing the transcription of the DNA encoding the CGTase variant of the invention in bacterial host cells indude the promoter of the Bacillus stearothermophilus maltogenic amylase gene, the Bacillus licheniformis alpha-amylase gene, the Bacillus amyloliquefaciens BAN amylase gene, the Bacillus subtilis alkaline protease gen, or the Bacillus pumilus xylanase or xylosidase gene, or by the phage Lambda P R or P L promoters or the E. coli lac, trp or tac promoters.
  • promoters for use in yeast host cells include promoters from yeast glycolytic genes [Hitzeman et al., J. Biol. Chem. 1980 255 12073 - 12080; Alberand Kawasaki, J. Mol. APPI. Gen. 1982 1 419 - 434] or alcohol dehydrogenase genes [Young et al., in Genetic Engineering of Microorganisms for Chemicals (Hollaender et al. Eds.), Plenum Press, New York, 1982], or the TPl 1 [US 4.599,311] or ADH2-4c [Russell et al., Nature 1983 304 652 - 654] promoters.
  • suitable promoters for use in filamentous fungus host cells are, for instance, the ADH3 promoter [McKnight et al., EMBO J. 198542093 - 2099] or the tpiA promoter.
  • suitable promoters are those derived from the gene encoding A. oryzae TAKA amylase, Rhizomucor miehei aspartic proteinase, A. niger neutral ⁇ -amylase, A. niger acid stable ⁇ -amylase, A. niger or A. awamori glucoamylase (gluA), Rhizomucor miehei lipase, A. oryzae alkaline protease, A. oryzae triose phosphate isomerase or A. nidulans acetamidase.
  • Preferred are the TAKA-amylase and gluA promoters.
  • the expression vector of the invention may further comprise a DNA sequence enabling the vector to replicate in the host cell in question.
  • the expression vector may also comprise a selectable marker, e.g. a gene the product of which complements a defect in the host cell, such as the gene coding for dihydrofolate reductase (DHFR) or the Schizosaccharomyces pombe TPI gene [Russell PR; Gene 1985 40 125-130], or one which confers resistance to a drug, e.g. ampicillin, kanamycin, tetracydin, chloramphenicol, neomycin, hygromycin ormethotrexate.
  • selectable markers include amdS. pyrG. argB. niaD and sC.
  • a secretory signal sequence (also known as a leader sequence, prepro sequence or pre sequence) may be provided in the expression vector.
  • the secretory signal sequence is joined to the DNA sequence encoding the CGTase in the correct reading frame.
  • Secretory signal sequences are commonly positioned 5' to the DNA sequence encoding the CGTase variant.
  • the secretory signal sequence may be that normally associated with the CGTase or may be from a gene encoding another secreted protein.
  • the expression vector of the invention may comprise a secretory signal sequence substantially identical to the secretory signal encoding sequence of the Bacillus licheniformis ⁇ -amylase gene, e.g. as described in WO 86/05812.
  • measures for amplification of the expression may be taken, e.g. by tandem amplification techniques, involving single or double crossing-over, or by multicopy techniques, e.g. as described in US 4,959,316 or WO 91/09129.
  • the expression vector may include a temperature sensitive origin of replication, e.g. as described in EP 283,075.
  • the invention provides a host cell comprising the DNA construct of the invention and/or the recombinant expression vector of the invention.
  • the host cell of the invention into which the DNA construct or the recombinant expression vector of the invention is to be introduced, may be any cell, preferably a non-pathogenic cell, which is capable of producing the CGTase variant and includes bacteria, yeast, fungi and higher eukaryotic cells.
  • bacterial host cells which, on cultivation, are capable of producing the CGTase variant of the invention are grampositive bacteria such as strains of Bacillus, in particular a strain of B. subtilis, B. licheniformis, B. lentus, B. brevis, B. stearothermophilus, B. alkalophilus, B. amyloliquefaciens, B. coagulans, B. circulans, B. laut ⁇ s, B.
  • the transformation of the bacteria may be effected by protoplast transformation or by using competent cells in a manner known per se (cf. Sambrook et al., op cit).
  • CGTase may be retained in the cytoplasm, typically as insoluble granules (known as inclusion bodies), or may be directed to the periplasmic space by a bacterial secretion sequence.
  • the cells are lysed and the granules are recovered and denatured after which the CGTase is refolded by diluting the denaturing agent.
  • the CGTase may be recovered from the periplasmic space by disrupting the cells, e.g. by sonication or osmotic shock, to release the contents of the periplasmic space and recovering the CGTase variant.
  • yeasts cells include cells of Saccharomyces spp. or Schizosaccharomyces spp., in particular strains of Saccharomyces cerevisiae or Saccharomyces kluyveri. Methods for transforming yeast cells with heterologous DNA and producing heterologous polypeptides therefrom are described, e.g. in US 4,599,311 , US 4,931,373, US 4,870,008, 5,037,743, and US 4,845,075, all of which are hereby incorporated by reference. Transformed cells are selected by a phenotype determined by a selectable marker, commonly drug resistance or the ability to grow in the absence of a particular nutrient, e.g. leucine.
  • a selectable marker commonly drug resistance or the ability to grow in the absence of a particular nutrient, e.g. leucine.
  • a preferred vector for use in yeast is the POT1 vector disclosed in US 4,931 ,373.
  • the DNA sequence encoding the CGTase variant of the invention may be preceded by a signal sequence and optionally a leader sequence , e.g. as described above.
  • suitable yeast cells are strains of Kluyveromyces, such as K. lactis, Hansen ⁇ la, e.g. H. polymorpha, or Pichia, e.g. P. pastoris [Gleeson et al., J. Gen. Microbiol. 1986 132 3459-3465; US 4,882,279].
  • Examples of other fungal cells are cells of filamentous fungi, e.g. Aspergill ⁇ s spp., Neurospora spp., Fusarium spp. or Trichoderma spp., in particular strains of A. oryzae, A. nidulans or A. niger.
  • Aspergillus spp. for the expression of proteins have been described in e.g., EP 272,277 and EP 230,023.
  • the transformation of F. oxysporum may, for instance, be carried out as described by Malardier et al., Gene 1989 78 147-156.
  • the transformed or transfected host cell described above is then cultured in a suitable nutrient medium under conditions permitting the expression of the CGTase, after which the resulting CGTase variant is recovered from the culture.
  • the medium used to culture the cells may be any conventional medium suitable for growing the host cells, such as minimal or complex media containing appropriate supplements. Suitable media are available from commercial suppliers or may be prepared according to published recipes (e.g. in catalogues of the American Type Culture Collection).
  • the CGTase variant produced by the cells may then be recovered from the culture medium by conventional procedures including separating the host cells from the medium by centrifugation or filtration, precipitating the proteinaceous components of the supernatant or filtrate by means of a salt, e.g. ammonium sulphate, purification by a variety of chromatographic procedures, e.g. ion exchange chromatography, gelfiltration chromatography, affinity chromatography, or the like, dependent on the type of CGTase in question.
  • a salt e.g. ammonium sulphate
  • the present invention provides a method of producing the CGTase variant of the invention, wherein a suitable host cell, which has been transformed with a DNA sequence encoding the CGTase, is cultured under conditions permitting the production of the enzyme, and the resulting enzyme is recovered from the culture.
  • the medium used to culture the transformed host cells may be any conventional medium suitable for growing the host cells in question.
  • the expressed CGTase may conveniently be secreted into the culture medium and may be recovered therefrom by well-known procedures including separating the cells from the medium by centrifugation or filtration, precipitating proteinaceous components of the medium by means of a salt such as ammonium sulphate, followed by chromatographic procedures such as ion exchange chromatography, affinity chromatography, or the like.
  • the CGTase variant of the invention find application in processes for the manufacture of cyclodextrins for various industrial applications, particularly in the food, cosmetic, chemical, agrochemical and pharmaceutical industries.
  • the invention provides CGTase variants for use in a process for the manufacture of cyclodextrins, in particular ⁇ -, ⁇ -, ⁇ -, ⁇ -, and/or ⁇ -cyclodextrins.
  • the invention provides CGTase variants for use in a process for the manufacture of ⁇ -, ⁇ - and ⁇ - cydodextrins, or mixtures hereof.
  • the invention provides CGTase variants for use in a process for the manufacture of ⁇ -, ⁇ -, and ⁇ - cydodextrins, or mixtures hereof.
  • the CGTase variants of the invention may also be used in a process for the manufacture of linear oligosaccharides, in particular linear oligosaccharides of 2 to 12 glucose units, preferably linear oligosaccharides of 2 to 9 glucose units.
  • the CGTase variants of the invention may be used for in situ generation of cyclodextrins.
  • the CGTase variants of the invention may be added to a substrate containing medium in which the enzyme variants are capable of forming the desired cyclodextrins.
  • This application is particularly well suited for being implemented in methods of producing baked products, in methods for stabilizing chemical products during their manufacture, and in detergent compositions.
  • CGTase variants of the invention therefore also may be used for implementation into bread-improving additives, e.g. dough compositions, dough additives, dough conditioners, pre-mixes, and similar preparations conventionally used for adding to the flour and/or the dough during processes for making bread or other baked products.
  • bread-improving additives e.g. dough compositions, dough additives, dough conditioners, pre-mixes, and similar preparations conventionally used for adding to the flour and/or the dough during processes for making bread or other baked products.
  • Cyclodextrins have an inclusion ability useful for stabilization, solubilization, etc.
  • cyclodextrins can make oxidizing and photolytic substances stable, volatile substances non-volatile, poorly-soluble substances soluble, and odoriferous substances odorless, etc. and thus are useful to encapsulate perfumes, vitamins, dyes, pharmaceuticals, pesticides and fungicides.
  • Cyclodextrins are also capable of binding lipophilic substances such as cholesterol, to remove them from egg yolk, butter, etc.
  • Cyclodextrins also find utilization in products and processes relating to plastics and rubber, where they have been used for different purposes in plastic laminates, films, membranes, etc. Also cyclodextrins have been used for the manufacture of biodegradable plastics.
  • the CGTase from Bacillus circulans Strain 251 [cf. Lawson C L, van Montfort R, Strokopytov B, Rozeboom H J, Kalk K H, de Vries G E, Penninga D, Dijkhuizen L, and Dijkstra B W, J. Mol. Biol. 1994 236 590-600] was soaked in a buffer solution containing the non-hydrolyzable tetrasaccharide acarbose, and an X- ray structure of the CGTase including the pseudo-tetrasaccharide located in the catalytic site was obtained, cf. Strokopytov et al.
  • a nonasaccharide (A-l) was formed in an enzyme-substrate-complex structure. Coordinates of this structure have been deposited with the Protein Data Bank, Biology Department, Bldg. 463, Brookhaven National Laboratory, P.O. Box 5000, Upton, NY 11973-5000, USA, under the entry code 1 DIJ.
  • J-L trisaccharide
  • Fig. 1 The residues listed in Fig. 1 are referring to Bacillus circulans Strain 251 CGTase and comprise only the closest contacts between the substrate and the enzyme. By changing the number of hydrogen-bonds and other interactions between the enzyme and the substrate, the product selectivity can be altered. Normally, cleavage of the starch takes place between glucose unit B and C in the model.
  • the structure of a Thermoanaerobacter CGTase was modelled based on the known structure of Bacillus circulans CGTase. Again the computer program InsightTM from Biosym was employed, using the homology module, according to the manufacturers instructions. The substrate found in Bacillus circulanswas docked into the Thermoanaerobacter model, and the positions stated in Tables 5-7 identified.
  • This example describes the construction of three ⁇ -cyclodextrin producing CGTase variants, in which site-directed mutagenesis have lead to an altered number of hydrogen bonds in the subsites of the active site deft.
  • the variants are derived from a Bacillus circulans Strain 251 CGTase (i.e. the wild-type enzyme), obtained as described by Lawson et al. [Lawson C L, van Montfort R, Strokopytov B, Rozeboom H J, Kalk K H, de Vries G E, Penninga D, Dijkhuizen L, and Dijkstra B W, J. Mol. Biol. 1994 236 590-600].
  • oligonucleotides were used to produce the mutations: Y89G: 5'-GCA TCA TCA ATG GAT CCG GCG TAA AC-3' (Bam HI); and
  • Mutant proteins were produced by the use of an amylase and protease negative Bacillus subtilis strain, and purified using affinity chromatography.
  • CGTase activity was determined by incubating appropriately diluted enzyme solutions with substrate in 10 mM sodium citrate, pH 6.0, for 5-10 minutes at 50oC.
  • Cyclodextrin forming activity was determined using 5% PaselliTM SA2 (i.e. partially hydrolysed potato starch with an average degree of polymerization of 50, available from AVEBE, Foxhol, The Netherlands) as substrate.
  • the ⁇ -cyclodextrin formed was determined with phenolphthalein.
  • One unit of activity is defined as the amount of enzyme able to produce 1 ⁇ mol of ⁇ - cyclodextrin per minute, ⁇ - and ⁇ -cyclodextrin formation was subsequently determined by use of HPLC (cf. below).
  • Cyclodextrin formation was also determined under industrial production process conditions. For this purpose 0.1 U/ml CGTase was incubated with 10% PaselliTM WA4 (i.e. jet-cooked, pre-gelatinized drum-dried starch) in a 10 mM sodium citrate buffer (pH 6.0) at 50oC for 45 hours. Samples were collected at regular intervals of time, boiled for 5 minutes, and the products formed analyzed by HPLC using a 25 cm Econosil-NH 2 10 micron column (Alltech Associates Inc., USA) eluted with acetonitril/water (60/40% v/v) at a flow rate of 1 ml per minute.
  • PaselliTM WA4 i.e. jet-cooked, pre-gelatinized drum-dried starch
  • Variants were designed in order to increase ⁇ -cyclodextrin formation.
  • a tyrosine residue at position 89 was changed into an aspartic acid residue (Y89D), which introduces an additional hydrogen bond with subsite F of the substrate, cf. Fig. 1.
  • This gives rise to stronger binding of the amylose chain in the active site cleft, with the formation of smaller cyclodextrins.
  • an increase in ⁇ -cyclodextrin forming activities was detected, with a simultaneous decrease in the ⁇ -cyclodextrin forming activity, as seen from the ratio of cyclodextrins produced from PaselliTM WA4, cf.
  • This example describes the construction of two CGTase variants, holding mutations in the E domain cleft.
  • the variants are derived from a Bacillus circulans Strain 251 CGTase (i.e. the wild-type enzyme), obtained as described by Lawson et al. [Lawson C L, van Montfort R, Strokopytov B, Rozeboom H J, Kalk K H, de Vries
  • MBS maltose binding sites
  • Mutations were introduced by a method based on two PCR reactions using VENT-DNA polymerase. For each mutation specific oligonucleotides were developed. The mutations were confirmed by restriction analysis and sequencing. Variants were obtained from an amylase and protease negative Bacillus subtilis strain and were purified using affinity chromatography.
  • Escherichia coli MC 1061 [Meissner P S, Sisk WP, Berman M L; Proc. Natl. Acad. Sci. USA 1987 84 4171-4175] was used for recombinant DNA manipulations and site-directed mutagenesis.
  • E coli DH5 ⁇ [Hanahan D; J. Mol. Biol. 1983 166 557] was used for the production of monomeric supercoiled plasmid DNA for sequencing.
  • CGTases variants were produced with the ⁇ -amylase and protease negative Bacillus subtilis Strain DB104A [Smith H, de Jong A, Bron S, Venema G; Gene 1988 70 351-361].
  • the fragment containing the kanamycin-resistance marker was ligated with the largest fragment from plasmid pDP66S [Penninga D, Strokopytov B, Rozeboom H J, Lawson C L, Dijkstra B W, Bergsma J, Dijkhuizen L; Biochemistry 1995 34 3368-3376] containing the Bacillus circulans CGTase gene, digested with Hlndlll and Xbal (made blunt with Klenow polymerase).
  • the resulting CGTase protein expression shuttle vector pDP66K with the CGTase gene under control of the erthromycin-inducible p32 promotor [van der Vossen J M B M, Kodde J, Haandrikman A J, Venema G, Kok J; APPI. Environ. Microbiol. 1992 58 3142-3149], was transformed to E. coli MC1061 under seledion for erythromycin and kanamycin resistance, d. Fig. 3.
  • CGTase Variants As only relatively low stability with plasmid pDP66S (8.5 kb) [Saenger W, Anoew. Chem. 1980 19 344-362] was found, pDP66K (7.7 kb) was constructed, cf. Fig. 3, with the CGTase gene under the control of the strong p32 promotor [van der Vossen J MB M, Kodde J, Haandrikman A J, Venema G, Kok J; APPI. Environ. Microbiol. 1992 58 3142-3149]. Plasmid pDP66K containing the additional antibiotic resistance marker for kanamycin appeared to be considerably more stable in E. coli as well as in B.
  • subtilis cells than plasmid pDP66S containing the streptomycin/spectinomycin resistance cassette.
  • a shuttle vector Using this shuttle vector, a high extracellular production of wild-type enzyme and CGTase variants was obtained reproducibly in batch fermentations with the ⁇ - amylase and protease negative B. subtilis Strain DB104A.
  • a single 5 I erlenmeyer flask with 1 I B. subtilis Strain DB104A culture allowed purification to homogeneity of up to 25 mg of the CGTase variants. Mutations were constructed via site-directed (PCR) mutagenesis. Using specific oligonucleotide primers a mutation frequency close to 70% was observed. All mutations were confirmed by restriction analysis and DNA sequencing.
  • Plasmid carrying bacterial strains were grown on LB medium in presence of the antibiotics erythromycin and kanamycin, at concentrations of 100 and 5 ⁇ g/ml for E coli and Bacillus subtilis, respectively [Sambrook et al., op cit]. When appropriate, agar plates contained 1 % starch to screen for halo formation. Bacillus subtilis Strain DB 104A was grown in a 5 I flask, containing 1 I medium with 2% tryptone, 0.5% yeast extract, 1% sodium chloride and 1% casamino adds (pH 7.0) with 10 ⁇ g/ml erythromycin and 5 ⁇ g/ml kanamydn.
  • Y633A 5'-G GTC GTT TAC CAG GCG CCG AAC TGG-3'
  • W616A 5'-GC GAG CTC GGG AAC GCG GAC CCG-3'
  • W662A 5'-CC GTC ACC GCG GAA GGC GGC-3'
  • Successful mutagenesis resulted in the appearance of the underlined restriction sites, allowing rapid screening of potential mutations.
  • this restriction site was Narl, for W616A Sad, and for W662A Sacll.
  • Plasmid pDP66K carrying the right restriction site was transformed to E. coli DH5 ⁇ cells. DNA sequence determination was performed on supercoiled plasmid DNA using the dideoxy-chain termination method [Sanger F,
  • Plasmid pDP66K carrying positively characterized mutant CGtase genes, was transformed to Bacillus subtilis Strain DB104A. The organism was grown to an optical density of 4.5 determined at 600 nm in a 5 I flask (for approx. 36 hours). Under these conditions high extracellular CGTase levels were produced. The culture was centrifuged (x 10,000 g) at 4oC for 30 minutes. The (mutant) CGTases were further purified to homogeneity by affinity chromatography using a 30 ML ⁇ -cyclodextrin-Sepharose- 6FF column (Pharmada, Sweden) [Sundberg L, Porath J; J. Chromatoor.
  • ⁇ -cyclodextrin Forming Activity ⁇ -cydodextrin forming activity was determined using 5% PaselliTM SA2 (i.e. partially hydrolysed potato starch with an average degree of polymerization of 50, available from AVEBE, Foxhol, The Netherlands) as substrate and after incubation for 3 minutes at 50oC. 0.1-0.1 units of activity were used. The ⁇ -cyclodextrin formed was determined based on its ability to form a stable colorless inclusion complex with phenolphthalein. One unit of activity is defined as the amount of enzyme able to form 1 ⁇ mol of ⁇ -cyclodextrin per minute.
  • Raw Starch Binding Properties were studied by incubating 6 ⁇ g/ml of enzyme with increasing amounts (0-10%) of granular potato starch (PaselliTM SA2, available from AVEBE, Foxhol, The Netherlands) for 1 hour at 4°C, with and without 0.1 mM of ⁇ -cyclodextrin (equilibrium was reached within 10 minutes). After incubation, protein bound to the starch granules was spun down for 1 minute at 4°C and at 10,000xg, and the remaining ⁇ -cyclodextrin forming activity of the supernatant was determined as described above.
  • PaselliTM SA2 available from AVEBE, Foxhol, The Netherlands
  • maltose binding site 1 (MBS1) includes two tryptophan residues
  • the double mutation W616A/W662A was constructed. In this way we created comparable changes in the two binding sites, which were designed to completely remove the hydrophobic interactions of the aromatic residues with the glucose units of the substrate.
  • the two separate CGTase variants, W616A and W662A gave intermediate results compared to the double mutant, W616A/W662A.
  • ⁇ -cyclodextrin on raw starch binding indicates that it can inhibit the binding by competition with a starch chain for the binding sites of the enzyme. This effect is more pronounced for the variants produced as compared to the wild-type, indicating that when one MBS is deleted, competition of ⁇ -cyclodextrin with raw starch for the remaining site is stronger. This also indicates a form of cooperativity between MBS's.
  • the Y633A variant has the same "n” value as the wild-type enzyme. This suggests that sites other than MBS2 cooperate with MBS1 in binding.
  • This example describes the construction of several ⁇ -and ⁇ -cyclodextrin producing CGTase variants, in which site directed mutagenesis has lead to an altered number of hydrogen bonds in the active site cleft.
  • the variants are derived from a Bacillus circulans Strain 251 CGTase (i.e. the wild-type enzyme), obtained as described by Lawson et al. [Lawson C L, van MOntfort R, Strokopytov B, Rozeboom H J, Kalk K H, de Vries G E, Penninga D, Dijkhuizen L and Dijkstra B W, J. Mol. Biol. 1994 236 590-600].
  • Mutations were introduced with a PCR method using VENT-DNA polymerase (New-England Biolabs, Beverly, MA, USA).
  • a first PCR reaction was carried out with a mutagenesis primer for the coding strand, plus a primer downstream on the template strand.
  • the reaction product was subsequently used as primer in a second PCR reaction together with a primer upstream on the coding strand.
  • the produd of the last reaction was cut with PvuU and Sa/I and exchanged with the corresponding fragment (1200 bp) from the vector pDP66K (cf. Fig. 3).
  • the resulting (mutant) plasmid was transformed to E coli MC1061 cells [Meissner P S, Sisk W P, Berman M L; Proc. Natl. Acad. Sci. USA 1987 84 4171-4175].
  • N193G 5'-GC ATC TAC AAG GGC CTG TACGAT CTC G-3' (Dra II);
  • Y89G 5'-GCA TCA TCA ATG GAT CCG GCG TAA AC-3' (Bam HI);
  • D371G 5'-CG GGC GGG ACC GGT CCG GAC AAC CG-3' (Pin Al);
  • D371N 5'-G TCG GGC GGT ACC AAT CCG GAC AAC C-3' (Kpn I);
  • N326Q 5'-CG TTC ATC GAT CAG CAT GAC ATG G-3' (Cla I).
  • Plasmid pDP66K carrying the right restriction site was transformed to E. coli DH5 ⁇ cells [Hanahan D; J. Mol. Biol. 1983 166 557]. DNA sequence determination was performed on supercoiled plasmid DNA using the dideoxy-chain termination method [Sanger F, Coulson A R; J. Mol. Biol. 1975 94441-448] and the T7-sequencing kit from Pharmacia-LKB Biotechnology, Sweden. Plasmid pDP66K, carrying positively characterized mutant cgt genes, was transformed to B. subtilis strain DB104A [Smith H, de Jong A, Bron S, Venema G;
  • the culture was centrifuged at 4oC for 30 minutes at 10,000 xg.
  • the CGTases variant in the culture supematants were further purified to homogeneity by affinity chromatography, using a 30 ml ⁇ -cyclodextrin-Sepharose-6FF column (Pharmada, Sweden) [Sundberg L, Porath J; J. Chromatoor. 1974 90 87-98] with a maximal capacity of 3.5 mg protein per ml. After washing with 10 mM sodium acetate buffer (pH 5.5), bound CGTase was eluted with the same buffer containing 10 mg/ml ⁇ -cyclodextrin.
  • ⁇ -cyclodextrin forming activity was determined by incubating an appropriately diluted enzyme sample (0.1-0.2 units of adivity) for 3 minutes at 50°C. PaselliTM SA2 (5% solution), partially hydrolysed potato starch with an average degree of polymerization of 50 (AVEBE, Foxhol, The Netherlands), was used as a substrate.
  • the ⁇ -cyclodextrin formed was determined based on its ability to form a stable colorless inclusion complex with phenolphthalein.
  • One unit of activity is defined as the amount of enzyme able to produce 1 ⁇ mol of ⁇ -cydodextrin per minute.
  • Cyclodextrin forming activity was also measured under production process conditions.
  • 0.1 U/ml CGTase was incubated with 10 % PaselliTM WA4 (i.e. jet-cooked, pregelatinized drum-dried starch) in a 10 mM sodium dtrate buffer (pH 6.0) at 50oC for 45 hours.
  • Samples were collected at regular time intervals, diluted 10 times, boiled for 8 min. and the products formed analyzed by HPLC using a 25 cm Econosphere-NH 2 5 micron column (Alltech Associates Inc., USA) eluted with acetonitrile/water (60/40 v/v) at 1 ml per min.
  • the variants of this example were designed in order to increase ⁇ -and ⁇ -cyclodextrin formation.
  • CGTase variants were all designed with the intention to decrease the interactions between the amylose chain and the first part of the active site cleft (Subsites C-G). As a result, the amylose chain would be able to move further into the active site cleft, thereby changing the ratio of cyclodextrins towards the ⁇ -and ⁇ -cydodextrins.
  • the N193G CGTase variant demonstrates a rapid increase in ⁇ -cyclodextrin (Figs. 7 and 9).
  • the ratio is changed already dramatically after 5 hours of incubation (Table 20) towards ⁇ -and ⁇ -cyclodextrin.
  • Table 21 the ratio has changed towards ⁇ -cyclodextrin formation only.
  • This mutation seems particulariy well suited for combination with other mutations, e.g. D371G or D371N.
  • the Y89G CGTase variant results in a small change towards ⁇ -cyclodextrin after 45 hours of incubation at the expense of ⁇ -cyclodextrin (cf. Fig. 7 and Table 21 ).
  • the D371 N and D371 G CGTase variants both show a shift towards formation of the larger cyclodextrins (cf. Fig. 8 and Table 21). Both ⁇ -and ⁇ -cyclodextrin increased at the expense of ⁇ -cyclodextrin. This shift is more pronounced at early incubation times (cf. Table 20 and Fig. 10).
  • the Y89G/N193G CGTase double mutant resulted in a shift from ⁇ -cyclodextrin to both ⁇ -and ⁇ -cyclodextrin (cf. Table 21).
  • this mutation could give rise to a single shift to ⁇ -cyclodextrin.
  • the *145al CGTase variant was constructed on the basis of alignment studies. This insertion mutation seems especially advantageous for obtaining ⁇ -cyclodextrin producing CGTase variants. Both short incubation times (cf. Fig. 10 and Table 20) and long incubation times (cf. Fig. 8 and Table 21) gave a shift from ⁇ -cyclodextrin to both ⁇ -and ⁇ -cyclodextrin. Also, in order to obtain a single shift to ⁇ -cyclodextrin, this mutation seems particulariy well suited for combination with other mutations, e.g. D371G or D371 N.
  • the N326Q CGTase variant was constructed and shown to cause a shift from ⁇ -cydodextrin to ⁇ - and ⁇ -cyclodextrin formation (cf. Table 21 ).
  • This example describes the construction of 24 ⁇ -cyclodextrin producing CGTase variants (A1-A24), in which site-directed mutagenesis either has lead to an altered number of hydrogen bonds in the subsites of the active cleft or, alternatively, to sterical hindrance in parts of the substrate binding left.
  • the variants are derived from a Thermoanaerobacter sp. CGTase obtained according to WO 89/03421 , and having the nudeotide and amino add sequences presented as SEQ ID NOS: 1-2 (i.e. the wild-type enzyme).
  • Mutations were introduced by a method based on PCR by the use of PWO polymerase. For each mutation, specific oligonudeotides (primers) were developed. The mutations were confirmed by restriction analysis whenever possible, and by sequencing. Mutant proteins were expressed in either Escherichia coli MC1061 [Meissner P S, Sisk W P, Berman M L; Proc. Natl. Acad. Sci. USA 1987 84 4171- 4175], or in the ⁇ -amylase and protease negative Bacillus subtilis Strain DB104A [Smith H, de Jong A, Bron S, Venema G; Gene 1988 70 351-361]. Proteins were purified from the media using affinity chromatography (AfC) and/or anion-exchange chromatography (AEC). Enzyme Assays
  • Phadebas amylase test Phadebas tablets (PhadebasTM Amylase Test, Pharmacia) are used as substrate.
  • This substrate is a cross-linked insoluble blue- colored starch polymer, which is mixed with bovine serum albumin and a buffer substance. After suspension in water, starch is hydrolyzed by the enzyme, thereby yielding blue fragments. The determination is carried out after incubation at 60oC, pH 6.2, in 0.15 nM calcium for 15 minutes. The absorbance of the resulting blue solution, determined at 620 nm, corresponds the enzymatic activity.
  • the enzyme activity is compared to that of an enzyme standard, and the activity is expressed in the same unit as that of the enzyme standard.
  • the enzyme standard was TermamylTM (Novo Nordisk A/D, Denmark), the amylolytic activity of which has been be determined using potato starch as substrate. This method is based on the break-down of modified potato starch by the enzyme, and the reaction is followed by mixing samples of the starch/enzyme solution with an iodine solution. Initially, a blackish-blue color is formed, but during the break-down of the starch the blue color gets weaker and gradually turns into a reddish-brown, which is compared to a colored glass standard.
  • KNU One Kilo Novo alfa Amylase Unit
  • CGTase activity was determined by incubating diluted enzyme with substrate in 10 mM sodium citrate, pH 6.0 for 4-10 minutes at 60oC.
  • Cyclodextrin forming activity was determined using 5% PaselliTM SA2 (i.e. partially hydrolysed potato starch with an average degree of polymerization of 50, available from AVEBE, Foxhol, The Netherlands) as substrate.
  • the ⁇ -cyclodextrin formed was determined with Methyl-orange, the ⁇ -cyclodextrin formed was determined with phenolphthalein, and the ⁇ -cyclodextrin formed was determined with bromo cresol green.
  • the activity is expressed in units per mg (U/mg).
  • One unit of enzyme activity is defined as the amount of enzyme able to produce one ⁇ mol of the specific cyclodextrin per minute. Cyclodextrin formation was also determined under conventional industrial production process conditions. A precooked 10% amylopectin solution in 0.5 mM
  • oligonudeotides were synthesized in order to initiate the site- directed mutagenesis (the numbers indicate positions according to the CGTase numbering):
  • 5'-TTACCGTAATTTATATGACTTAGCAG-3' was used to introduce the F195Y mutation and using this variant as starting point, the 87-94(1 KY S G - V N N) mutations was introduced using the A1 primer;
  • the Spe I - Bst X I fragment of A2 was ligated into the CGTase gene holding the F195Y mutation.
  • the F195Y was introduced by the use of the A3 primer; A5: P143G-A144R-S145W;
  • the 146-150(S D Q P S) mutations were introduced using the primer 5'-CTCCTGCATC- ATCTGATCAACCGTCCTTTGGGGAAAATGG-3'; A8: 143-148(G R G P A A);
  • the G180N mutation was introduced using the primer 5'-CCATCATTACGGAAACACTA- AT T T TCATC-3';
  • the G180N mutation was introduced using the primer 5'-CCATCATTACGGAGACACTAA- T T T TCATC-3';
  • the G180N mutation was introduced using the primer 5'-CCATCATTATAATGGAACTAA- T T T TCATC-3';
  • A23 G179S + P143G-A144R-S145W; Using the A5 variant (P143G-A144R-S145W) as starting point, the G180N mutation was introduced using the primer 5'-CCATCATTATAGTGGAACTAA- T T T T T CATC-3'; and
  • the G180N mutation was introduced using the primer 5'-CCATCATTATGATGGAACTAA- T T T T T CATC-3'.
  • experiment A1 the loop at positions 143 to 151 was replaced by (G R A G T N P G) in order to increase the interactions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J (cf. Fig. 1 ).
  • the initial rate of both ⁇ -CD formation and of ⁇ -CD formation has decreased.
  • the ratio of ⁇ -CD has increased, whereas the ⁇ -CD ratio has decreased.
  • experiment A5 the region at positions 143 to 145 was replaced by (G R W) in order to increase the interactions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J by making a sterical hindrance (cf. Fig. 1 ).
  • the initial rate of ⁇ -CD formation has increased, whereas the initial rate of both ⁇ -CD formation and of ⁇ -CD formation has decreased.
  • the ratio of ⁇ -CD has increased whereas the ⁇ -CD ratio has decreased.
  • experiment A10 the loop at positions 143 to 148 was replaced by (G R A * * A) in order to increase the interactions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J (cf. Fig. 1 ).
  • experiment A11 the region at positions 143 to 148 was replaced by (G R W) in order to increase the interactions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J (cf. Fig. 1).
  • the initial rate of both ⁇ -CD formation and of ⁇ -CD formation has decreased more significantly than the initial rate of ⁇ -CD formation, which results in an increased ration between ⁇ -cd formation and ⁇ -CD formation.
  • G180 was replaced by 180N in order to increase the interactions between the enzyme and glucose unit H (cf. Fig. 1).
  • the region at positions 143 to 145 was replaced by (G R W) in order to increase the interadions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J by making a sterical hindrance (cf. Fig. 1).
  • G180 was replaced by 180D in order to increase the interactions between the enzyme and glucose unit H (cf. Fig. 1).
  • the region at positions 143 to 145 was replaced by (G R W) in order to increase the interactions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J by making a sterical hindrance (cf. Fig. 1 ).
  • G179 was replaced by 179N in order to increase the interactions between the enzyme and glucose unit H (cf. Fig. 1 ).
  • the region at positions 143 to 145 was replaced by (G R W) in order to increase the interactions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J by making a sterical hindrance (cf. Fig. 1).
  • G179 was replaced by 179S in order to increase the interadions between the enzyme and glucose unit H (cf. Fig. 1).
  • the region at positions 143 to 145 was replaced by (G R W) in order to increase the interactions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J by making a sterical hindrance (cf. Fig. 1).
  • G179 was replaced by 179D in order to increase the interactions between the enzyme and glucose unit H (cf. Fig. 1).
  • the region at positions 143 to 145 was replaced by (G R W) in order to increase the interactions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J by making a sterical hindrance (cf. Fig. 1).
  • This example describes the construction of 15 ⁇ -cyclodextrin producing CGTase variants (B1-B9), in which site-directed mutagenesis either has lead to an altered number of hydrogen bonds in the subsites of the active cleft or, alternatively, to sterical hindrance in parts of the substrate binding left.
  • the variants are derived from a Thermoanaerobacter sp. CGTase obtained according to WO 89/03421 , and having the nudeotide and amino acid sequences presented as SEQ ID NOS: 1-2 (i.e. the wild-type enzyme).
  • Mutations were introduced by a method based on PCR by the use of PWO polymerase. For each mutation, specific oligonudeotides (primers) were developed. The mutations were confirmed by restriction analysis whenever possible, and by sequencing. Mutant proteins were expressed in either Escherichia coli MC1061 [Meissner P S, Sisk W P, Berman M L; Proc. Natl. Acad. Sci. USA 1987 84 4171- 4175], or in the ⁇ -amylase and protease negative Bacillus subtilis Strain DB104A [Smith H, de Jong A, Bron S, Venema G; Gene 1988 70 351-361]. Proteins were purified from the media using affinity chromatography (AfC) and/or anion-exchange chromatography (AEC). Enzyme Assays
  • Phadebas amylase test Phadebas tablets (PhadebasTM Amylase Test, Pharmacia) are used as substrate.
  • This substrate is a cross-linked insoluble blue- colored starch polymer, which is mixed with bovine serum albumin and a buffer substance. After suspension in water, starch is hydrolyzed by the enzyme, thereby yielding blue fragments. The determination is carried out after incubation at 60°C, pH 6.2, in 0.15 nM calcium for 15 minutes. The absorbance of the resulting blue solution, determined at 620 nm, corresponds the enzymatic activity.
  • the enzyme activity is compared to that of an enzyme standard, and the activity is expressed in the same unit as that of the enzyme standard.
  • the enzyme standard was TermamylTM (Novo Nordisk A/D, Denmark), the amylolytic activity of which has been be determined using potato starch as substrate. This method is based on the break-down of modified potato starch by the enzyme, and the reaction is followed by mixing samples of the starch/enzyme solution with an iodine solution. Initially, a blackish-blue color is formed, but during the break-down of the starch the blue color gets weaker and gradually turns into a reddish-brown, which is compared to a colored glass standard.
  • KNU One Kilo Novo alfa Amylase Unit
  • CGTase activity was determined by incubating diluted enzyme with substrate in 10 mM sodium citrate, pH 6.0 for 4-10 minutes at 85oC.
  • Cyclodextrin forming activity was determined using 5% PaselliTM SA2 (i.e. partially hydrolysed potato starch with an average degree of polymerization of 50, available from AVEBE, Foxhol, The Netherlands) as substrate.
  • the ⁇ -cyclodextrin formed was determined with Methyl-orange, the ⁇ -cyclodextrin formed was determined with phenolphthalein, and the ⁇ -cyclodextrin formed was determined with bromo cresol green.
  • the activity is expressed in units per mg (U/mg).
  • One unit of enzyme activity is defined as the amount of enzyme able to produce one ⁇ mol of the specific cyclodextrin per minute. Cyclodextrin formation was also determined under conventional industrial production process conditions. A precooked 10% amylopectin solution in 0.5 mM
  • oligonudeotides were synthesized in order to initiate the site- directed mutagenesis (the numbers indicate positions according to the CGTase numbering):
  • 5'-TTACCGTAATTTATATGACTTAGCAG-3' was used to introduce the F195Y mutation.
  • the 87-94(1KYSG-VNN) mutations was introduced using primer B9. Simultaneously, the F195 was replaced by 195Y in order to decrease the contact between enzyme and substrate;
  • experiment B1 S145 was replaced by 145A in order to decrease the interactions between the enzyme and glucose unit J (cf. Fig.1).
  • the initial rate of both ⁇ -CD formation and of ⁇ -CD formation has increased.
  • the ratio of ⁇ -CD has decreased whereas the ⁇ -CD ratio has increased.
  • T147 was replaced by 147A in order to decrease the interactions between the enzyme and glucose unit J (cf. Fig. 1 ).
  • the ratio of ⁇ -CD has decreased, whereas the ⁇ -CD ratio has increased.
  • experiment B4 T147 was replaced by 147L in order to decrease the interactions between the enzyme and glucose unit J (cf. Fig. 1).
  • the ratio of ⁇ -CD has decreased, whereas the ⁇ -CD ratio has increased.
  • experiment B10 5'-TTACCGTAATTTATATGACTTAGCAG-3' was used to introduce the F195Y mutation.
  • the 87-94(1 K Y S G - V N N) mutations was introduced using primer B9.
  • the F195 was replaced by 195Y in order to decrease the contact between enzyme and substrate.
  • D196 was replaced by 196S in order to decrease the interactions between the enzyme and glucose unit E and glucose unit F.
  • This example describes the construction of 9 ⁇ -cyclodextrin producing CGTase variants (C1-C9), in which site-directed mutagenesis either has lead to an altered number of hydrogen bonds in the subsites of the active cleft or, alternatively, to sterical hindrance in parts of the substrate binding left.
  • the variants are derived from a Thermoanaerobacter sp. CGTase obtained according to WO 89/03421 , and having the nudeotide and amino acid sequences presented as SEQ ID NOS: 1-2 (i.e. the wild-type enzyme).
  • Variants were introduced by a method based on Unique Site Elimination (USE), following the protocol from the supplier (Stratagene®).
  • the unique restriction site BsaMI at the plasmid opposite to the CGTase gene was removed by the use of the 5'P-CACTGTTCCTTCGAACGCGTAACCTTAAATACC-3, oligonucleotide.
  • "P” indicates a 5' phosphorylation necessary for the procedure.
  • For each mutation specific oligonudeotides were developed. The mutations were confirmed by restriction analysis whenever possible, and by sequencing. Mutant proteins were expressed in either Escherichia coli MC1061 [Meissner P S, Sisk W P, Berman M L; Proc. Natl. Acad. Sci. USA 1987 84 4171-4175]. Proteins were purified from the media using affinity chromatography (AfC).
  • Phadebas amylase test Phadebas tablets (PhadebasTM Amylase Test, Pharmacia) are used as substrate.
  • This substrate is a cross-linked insoluble blue- colored starch polymer, which is mixed with bovine serum albumin and a buffer substance. After suspension in water, starch is hydrolyzed by the enzyme, thereby yielding blue fragments. The determination is carried out after incubation at 60oC, pH 6.2, in 0.15 nM calcium for 15 minutes. The absorbance of the resulting blue solution, determined at 620 nm, corresponds the enzymatic activity.
  • the enzyme activity is compared to that of an enzyme standard, and the activity is expressed in the same unit as that of the enzyme standard.
  • the enzyme standard was TermamylTM (Novo Nordisk A/D, Denmark), the amylolytic activity of which has been be determined using potato starch as substrate. This method is based on the break-down of modified potato starch by the enzyme, and the reaction is followed by mixing samples of the starch/enzyme solution with an iodine solution. Initially, a blackish-blue color is formed, but during the break-down of the starch the blue color gets weaker and gradually turns into a reddish-brown, which is compared to a colored glass standard.
  • KNU One Kilo Novo alfa Amylase Unit
  • CGTase activity was determined by incubating diluted enzyme with substrate in 10 mM sodium citrate, pH 6.0 for 4-10 minutes at 85oC.
  • Cyclodextrin forming activity was determined using 5% PaselliTM SA2 (i.e. partially hydrolysed potato starch with an average degree of polymerization of 50, available from AVEBE, Foxhol, The Netherlands) as substrate.
  • the ⁇ -cyclodextrin formed was determined with Methyl-orange, the ⁇ -cyclodextrin formed was determined with phenolphthalein and the ⁇ -cyclodextrin formed was determined with bromo cresol green.
  • the activity is expressed in units per mg (U/mg). One unit of enzyme activity is defined as the amount of enzyme able to produce one ⁇ mol of the specific cyclodextrin per minute.
  • Cyclodextrin formation was also determined under conventional industrial production process conditions.
  • a precooked 10% amylopectin solution in 0.5 mM CaCI 2 at pH 5.5 was incubated with 50 NU of CGTase per gram of substrate, at 60oC and for 24 hours. Samples are regularly withdrawn and boiled for 10 minutes at a pH of 2.5-3 prior to analysis by HPLC.
  • oligonudeotides were synthesized in order to initiate the site- directed mutagenesis (the numbers indicate positions according to the CGTase numbering):
  • experiment C1 N193 were replaced by 193A in order to decrease the interactions between the enzyme and glucose unit H.
  • the ratio of ⁇ -CD has decreased, and the ratio of ⁇ -CD has increased.
  • experiment C2 the region at positions 146-150 was replaced by (S D Q P S) in order to decrease the interactions between the enzyme and glucose unit J, and in order to increase the interactions between the enzyme and glucose unit I.
  • experiment C3 the region at positions 145-148 was replaced by (A E L A) in order to decrease the interactions between the enzyme and glucose unit J, and in order to increase the interadions between the enzyme and glucose unit I.
  • experiment C4 the region at positions 145-148 was replaced by (A E W A) in order to decrease the interactions between the enzyme and glucose unit J, and in order to increase the interactions between the enzyme and glucose unit I.
  • experiment C7 the region at positions 145-148 was replaced by (L E T N) in order to decrease the interactions between the enzyme and glucose unit J, and in order to increase the interactions between the enzyme and glucose unit I.

Landscapes

  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Genetics & Genomics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Biotechnology (AREA)
  • Biomedical Technology (AREA)
  • Molecular Biology (AREA)
  • Medicinal Chemistry (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Chemical & Material Sciences (AREA)
  • Enzymes And Modification Thereof (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Preparation Of Compounds By Using Micro-Organisms (AREA)

Abstract

The present invention relates to variants of cyclomaltodextrin glucanotransferase. More specifically, the invention relates to a maethod of modifying the substrate binding and/or product selectivity of a precursor CGTase enzyme, and CGTase variants derived from a precursor CGTase enzyme by substitution, insertion and/or deletion of one or more amino acid residue(s), which amino acid residue(s) holds a position close to the substrate. Moreover, the invention relates to DNA constructs encoding the CGTase variants, expression vectors, host cells and methods of producing the CGTase variants of the invention.

Description

CYCLOMALTODEXTRIN GLUCANOTRANSFERASE VARIANTS
TECHNICAL FIELD
The present invention relates to variants of cyclomaltodextrin glucanotransferase. More specifically the invention relates to a method of modifying the substrate binding and/or product selectivity of a precursor CGTase enzyme, and CGTase variants derived from a precursor CGTase enzyme by substitution, insertion and/or deletion of one or more amino acid residue(s), which amino acid residue(s) holds a position close to the substrate. Moreover, the invention relates to DNA constructs encoding the CGTase variants, expression vectors, host cells and methods of producing the CGTase variants of the invention.
BACKGROUND ART
Cyclomaltodextrin glucanotransferase (E.C. 2.4.1.19), also designated cyclodextrin glucanotransferase or cyclodextrin glycosyltransferase, in the following termed CGTase, catalyses the conversion of starch and similar substrates into cydomaltodextrins via an intramolecular transglycosylation reaction, thereby forming cydomaltodextrins, in the following termed cyclodexthns (or CD), of various sizes. Commercially most important are cyclodexthns of 6, 7 and 8 glucose units, which are termed α-, β- and γ-cyclodextrins, respectively. Commercially less important are cyclodexthns of 9, 10, and 11 glucose units, which are termed δ-, ε-, and ζ- cyclodexthns, respectively.
Cyclodexthns are thus cyclic glucose oligomers with a hydrophobic internal cavity. They are able to form inclusion complexes with many small hydrophobic molecules in aqueous solutions, resulting in changes in physical properties, e.g. increased solubility and stability and decreased chemical reactivity and volatility. Cyclodexthns find applications particularly in the food, cosmetic, chemical and pharmaceutical industries.
Most CGTases have both starch-degrading activity and transglycosylation activity. Although some CGTases produce mainly α-cyclodextrins and some CGTases produce mainly β-cyclodextrins, CGTases usually form a mixture of α-, β- and γ-cyclodextrins. Selective precipitation steps with organic solvents may be used for the isolation of separate α-, β- and γ-cydodexthns. To avoid expensive and environmentally harmful procedures, the availability of CGTases capable of producing an increased ratio of one particular type of cyclodextrin is desirable.
CGTases from different bacterial sources, including CGTases obtained from Bacillus, Brevibacterium, Clostridiυm, Corynebactehum, Klebsiella, Micrococcus, Thermoanaerobacter and Thermoanaerobacterium have been described in the literature.
Thus Kimura et al. [Kimura K, Kataoka S, Ishii Y, Takano T and Yamane K; J. Bacteriol. 1987 1694399-4402] describe a Bacillus sp. 1011 CGTase, Kaneko et al. [Kaneko T, Hamamoto T and Horikoshi K; J. Gen. Microbiol. 1988 134 97-105] deschbe a Bacillus sp. Strain 38-2 CGTase, Kaneko et al. [Kaneko T, Song KB, Hamamoto T, Kudo T and Horikoshi K; J. Gen. Microbiol. 1989 135 3447-3457] describe a Bacillus sp. Strain 17-1 CGTase, Itkor et al. [Itkor P, Tsukagoshi N and Udaka S; Biochem. Biophvs. Res. Commun. 1990 166630-636] describe a Bacillus sp. B1018 CGTase, Schmid et al. [Schmid G, Englbrecht A, SchmidD; Proceedings of the Fourth International Symposium on Cyclodexthns (Huber O, Szejtli J, Eds.), 198871-76] describe a Bacillus sp. 1-1 CGTase, Kitamoto etal. [Kitamoto N, Kimura T, Kito Y, Ohmiya K; J. Ferment. Bioenα. 1992 74 345-351] describe a Bacillus sp. KC201 CGTase, Sakai et al. [Sakai S, Kυbota M, Nakada T, Torigoe K, Ando O and Sugimoto T; J. Jpn. Soc. Starch. Sci. 1987 34 140-147] deschbe a Bacillus stearothermophilus CGTase and a Bacillus macerans CGTase, Takano et al. [Takano T, Fυkuda M, Monma M, Kobayashi S, Kainuma K and Yamane K; S, Bacteriol. 1986 166 (3) 1118-1122] deschbe a Bacillus macerans CGTase, Sin et al. [Sin K A, Nakamυra A, Kobayashi K, Masaki H and Uozumi T ; Appl. Microbiol. Biotechnol. 1991 35 600-605] describe a Bacillus ohbensis CGTase, Nitschke et al. [Nitschke L, Heeger K, Bender H and Schultz G; APPI. Microbiol. Biotechnol. 1990 33 542-546] describe a Bacillus circulans CGTase, Hill et al. [Hill D E, Aldape R and Rozzell J D\ Nucleic Acids Res. 1990 18 199] describe a Bacillus licheniformis CGTase, Tomita et al. [Tomita K, Kaneda M, Kawamura K and Nakanishi K; J. Ferm. Bioeng. 1993 75 (2) 89-92] deschbe a Bacillus autolyticus CGTase, Jamuna et al. [Jamuna R, Saswathi N, Sheela R and Ramakrishna S V; APPI. Biochem. Biotechnol. 1993 43 163-176] describe a Bacillus cereus CGTase, Akimaru et al. [Akimaru K, Yagi T and Yamamoto S: J. ferm. Bioeng. 1991 71 (5) 322-328] describe a Bacillus coagulans CGTase, Schmid G [Schmid G; New Trends in Cvdodextrins and Derivatives (Duchene D, Ed.), Editions de Sante, Paris, 1991 , 25- 54] describes a Bacillus firmus CGTase, Abelian et al. [Abelian V A, Adamian M O, Abelian L A A, Balayan A M and Afrikian E K; Biochememistrv (Moscow) 1995 60 (6) 665-669] describe a Bacillus halophilus CGTase, and Kato et al. [Kato T and Horikoshi K; J. Jpn. Soc. Starch Sci. 1986 33 (2) 137-143] describe a Bacillus subtilis CGTase.
EP 614971 describes a Brevibacterium CGTase, Haeckel & Bahl [Haeckel K, Bahl H; FEMS Microbiol. Lett. 1989 60 333-338] describe Clostridium thermosυlfurogenes CGTase, Podkovyrov & Zeikυs [Podkovyrov S M, Zeikus J G; J. Bacteriol. 1992 174 5400-5405] describe a Clostridium thermohydrosulfuricum CGTase, JP 7000183 describes a Corynebacterium CGTase, Binder et al. [Binder F, Huber O and Bόck A; Gene 1986 47 269-277] describe a Klebsiella pneumoniae CGTase, US 4,317,881 describes a Micrococcus CGTase, and Wind et al. [Wind R D, Liebl W, Bυitelaar R M, Penninga D, Spreinat A, Dijkhuizen L, Bahl H; AppI. Environ. Microbiol. 1995 61 (4) 1257-1265] describe Thermoanaerobacterium thermosulfurigenes CGTase.
A CGTase produced by Thermoanaerobacter sp. has been reported by Norman & Jørgensen [Norman B E, Jørgensen S T; Denpun Kagaku 1992 39 99- 106, and WO 89/03421], however, its amino acid sequence has never been disclosed. Here we report the nucleotide sequence encoding the Thermoanaerobacter sp. CGTase (presented as SEQ ID:NO 1), as well as its amino acid sequence (presented as SEQ ID.NO 2).
Also, CGTases from thermophilic Actinomycetes have been reported [Abelian V A, Afyan K B, Avakian Z G, Melkumyan A G and Afrikian E G; Biochemistry (Moscow) 1995 60 (10) 1223-1229].
Recently protein engineering has been employed in order to modify certain CGTases to selectively produce more or less of a specific cyclodextrin. The Structure of CGTases
CGTases are functionally related to α-amylases. CGTases and α- amylases both degrade starch by hydrolysis of the α-(1 ,4)-glycosidic bonds, but produce virtually exclusively cyclic and linear products, respectively.
Members of the CGTase family possess a high overall amino acid sequence identity, more than 60 %. CGTases and α-amylases share about 30% amino acid sequence identity. However, the active site clefts of CGTases and α- amylases, located between the A and B domain (Asp229, Glu257 and Asp328), are rather similar.
Recently, the tertiary structures of CGTases were determined. Thus,
Hofman et al. [Hofman B E, Bender H, Schultz G E; J. Mol. Biol. 1989 209 793-800] and Klein & Schulz [Klein C, Schulz G E; J. Mol. Biol. 1991 217 737-750] report the tertiary structure of a CGTase derived from Bacillus circulans Strain 8, Kubota et al. [Kubota M, Matsuura Y, Sakai S and Katsυbe Y; Denoun Kagaku 1991 38 141-146] report the tertiary structure of a CGTase derived from Bacillus stearothermophilus TC-91 , Lawson et al. [Lawson C L, van Montfort R, Strokopytov B, Rozeboom H J, Kalk K H, de Vries G E, Penninga D, Dijkhuizen L, and Dijkstra B W, J. Mol. Biol. 1994 236 590-600] report the tertiary structure of a CGTase derived from Bacillus circulans Strain 251 , Strokopytov et al. [Strokopytov B, Penninga D, Rozeboom H J; Kalk K H, Dijkhuizen L and Dijkstra B W, Biochemistry 1995 342234-2240] report the tertiary structure of a CGTase derived from Bacillus circulans Strain 251 , which CGTase has been complexed with acarbose, an effective CGTase inhibitor, and Knegtel et al. [Knegtel R M A, Wind R D, Rozeboom H J, Kalk K H, Buitelaar R M, Dijkhuizen L and Dijkstra B W, J. Mol. Biol. 1996 256 611-622] report the tertiary structure of a CGTase derived from Thermoanaerobacterium thermosulfurigenes.
These and other studies reveal that Bacillus circulans CGTases are composed of five domains. The three-dimensional structures also reveal that the N- terminal domains of CGTases have structural similarities to those of α-amylases, whereas the C-terminal domains were found to be unique to CGTases.
The catalytic site of CGTases is located in the A domain, and has three catalytic residues (in Bacillus circulans strain 251 these are Asp229, Glu257 and Asp328, respectively, cf. Strokopytov et al. 1995, op cit.). A central amino acid residue is located in the B domain, around which residue the cyclodextrins are formed, i.e. the cyclization axis. Substitution of this central residue, e.g. tyrosine at residue 188 in Bacillus ohbensis (corresponding to position 195, CGTase numbering) in order to increase the relative production of γ-cyclodextrin to β-cydodextrin has been the object of the study described by Sin et al. [Sin K, Nakamura A, Masaki H, Matsuura Y and Uozumi T; Journal of Biotechnology 1994 32 283-288] and JP-A- 5219948.
Nakamura et al. [Nakamura A, Haga K and Yamane K; Biochemistry 1994 33 9929-9936] describe the effects on substrate binding and cyclization characteristics by replacements carried out at four residues in the active center of a Bacillus sp. Strain 1011 CGTase. In these CGTase variants, a phenylalanine at position 183 has been replaced by leucine, a tyrosine at position 195 has been replaced by alanine, phenylalanine, leucine, threonine, valine, and tryptophan, respectively, a phenylalanine at position 259 has been replaced by leucine, and a phenylalanine at position 283 has been replaced by leucine.
Penninga et al. [Penninga D, Strokopytov B, Rozeboom H J, Lawson
C L, Dijkstra B W, Bergsma J and Dijkhuizen L; Biochemistry 1995 34 3368-3376] describe the effect on activity and product selectivity of site-directed mutations in tyrosine at position 195 of a Bacillus circulans Strain 251 CGTase. In this publication four CGTase variants have been produced, in which variants the tyrosine at position 195 have been replaced by phenylalanine, tryptophan, leucine and glycine, respectively.
Fujiware et al. [Fυjiwara S, Kakihara H, Sakaguchi K and Imanaka T; J. Bacteriol. 1992 174 (22) 7478-7481] describe CGTase variants derived from Bacillus stearothermophilus, in which a tyrosine residue at position 191 (corresponding to position 195 CGTase numbering) has been replaced by phenylalanine, a tryptophan residue at position 254 (corresponding to position 258, CGTase numbering) has been replaced by valine, a phenylalanine at position 255 (corresponding to position 259, CGTase numbering) has been replaced by phenylalanine and isoleucine, respectively, a threonine residue at position 591 (corresponding to position 598, CGTase numbering) has been replaced by phenylalanine, and a tryptophan residue at position 629 (corresponding to position 636, CGTase numbering) has been replaced by phenylalanine. JP-A-7023781 describes CGTase variants derived from Bacillus sp. 1011 , in which a tyrosine residue at position 195 has been replaced by leucine, valine, phenylalanine and isoleucine, respectively.
JP-A-5244945 describes CGTase variants derived from Bacillus stearothermophilus TC-91 , in which tyrosine residues at positions 222 and 286
(corresponding to positions 195 and 259, CGTase numbering) have been replaced by phenylalanine in order to increase the relative production of α-cyclodextrin to β- cyclodextrin.
JP-A-5041985 describes CGTase variants derived from Bacillus sp. #1011 , in which histidine at residue 140 in region A, histidine at residue 233 in region B, and histidine at residue 327 in region C, respectively, have been replaced by arginine and asparagine residues, respectively.
EP 630,967 describes CGTase variants in which a tyrosine residue at position 211 of a Bacillus sp.290-3 CGTase (corresponding to position 195, CGTase numbering), at position 217 of a Bacillus sp. 1-1 CGTase (corresponding to position 195, CGTase numbering), and at position 229 of a Bacillus circulans CGTase (corresponding to position 195, CGTase numbering), have been substituted for tryptophan and serine.
Up to now, all efforts in making CGTase variants have lead to substitutions in the region around the active site, in particular at the central cyclization residue, corresponding to position 195, CGTase numbering. Only few CGTase variants holding substitutions at more distant regions have been suggested, and the manufacture of these variants have not been based on any particular concept. SUMMARY OF THE INVENTION
It is an object of the present invention to provide novel variants of CGTases, which variants, when compared to the precursor enzyme, show increased product selectivity and/or reduced product inhibition.
Accordingly, in its first aspect, the invention provides a method of modifying the substrate binding and/or product selectivity of a precursor CGTase enzyme, which method comprises substitution, insertion and/or deletion of one or more amino acid residue(s) of the precursor enzyme, which amino acid residue(s) holds a position close to the substrate.
In another aspect, the invention provides a CGTase variant derived from a precursor CGTase enzyme by substitution, insertion and/or deletion of one or more amino acid residue(s), which amino acid residue(s) holds a position close to the substrate.
In a third aspect, the invention provides a DNA construct encoding a CGTase variant of the invention.
In a fourth aspect, the invention provides a recombinant expression vector comprising the DNA construct of the invention.
In a fifth aspect, the invention provides a host cell comprising the DNA construct of the invention, or the recombinant expression vector of the invention.
In a sixth aspect, the invention provides a method of producing a CGTase variant of the invention, which method comprises culturing the host cell of the invention under conditions permitting the production of the CGTase variant, and recovering the enzyme from the culture.
In further aspects, the invention provides CGTase variants for use in processes for the manufacture of cyclodextrins, in processes for the manufacture of linear oligosaccharides, and in processes for in situ generation of cyclodextrins. Amino Acids
In the context of this invention the following symbols and abbreviations for amino acids and amino acid residues are used:
Figure imgf000009_0001
Figure imgf000010_0001
CGTase Variants
A CGTase variant of this invention is a CGTase variant or mutated CGTase, having an amino acid sequence not found in nature.
A CGTase variant or mutated CGTase of this invention is a functional derivative of a precursor CGTase enzyme (i.e. the native, parental, or wild-type enzyme), and may be obtained by alteration of a DNA nudeotide sequence of a precursor gene or its derivatives, encoding the precursor enzyme. The CGTase variant or mutated CGTase may be expressed and produced when the DNA nudeotide sequence encoding the CGTase variant is inserted into a suitable vector in a suitable host organism. The host organism is not necessarily identical to the organism from which the precursor gene originated.
In the literature, enzyme variants have also been referred to as mutants or muteins. CGTase Numbering
In the context of this invention a specific numbering of amino acid residue positions in CGTase enzymes is employed. By alignment of the amino acid sequences of various known CGTases it is possible to unambiguously allot a
CGTase amino acid position number to any amino acid residue position in any CGTase enzyme, which amino acid sequence is known.
Using the numbering system originating from the amino acid sequence of the CGTase obtained from Bacillus circulans Strain 251 , which sequence is shown in Table 1 (a), aligned with the amino acid sequence of a number of other known CGTases, it is possible to indicate the position of an amino acid residue in a CGTase enzyme unambiguously.
In describing the various CGTase variants produced or contemplated according to the invention, the following nomenclatures are adapted for ease of reference:
[Original amino acid; Position; Substituted amino acid] Accordingly, the substitution of serine with alanine in position 145 is designated as S145A.
Amino acid residues which represent insertions in relation to the amino acid sequence of the CGTase from Bacillus circulans Strain 251 , are numbered by the addition of letters in alphabetical order to the preceding CGTase number, such as e.g. position 91 aF for the "insert" Phe between Thr at position 91 and Gly at position 92 of the amino acid sequence of the CGTase from Thermoanaerobacter sp. ATCC 53627, cf. Table 1 (j).
Deletion of a proline at position 149 is indicated as P149*, and an insertion between position 147 and 148 where no amino acid residue is present, is indicated as *147aD for insertion of an aspartic acid in position 147a.
Multiple mutations are separated by slash marks ("/"), e.g. S145A/D147L, representing mutations in positions 145 and 147 substituting serine with alanine and aspartic acid with leucine, respectively.
If a substitution is made by mutation in e.g. a CGTase derived from a strain of Bacillus circulans, the product is designated e.g. "B. circulans^ 45 A".
All positions referred to in this application by CGTase numbering refer to the CGTase numbers described above. Table 1
Amino Acid Sequence Alignment, CGTase Numbering and Domains
of Selected CGTases of Different Bacterial Origin a Bacillus circulans 251 ; b Bacillus sp. 1 -1 ; c Bacillus sp. 38-2; d Bacillus sp. 1011 ; e Bacillus licheniformis; f Bacillus macerans; g Bacillus ohbensis; h Bacillus stearothermophilus; i Klebsiella pneumoniae; j Thermoanaerobacter ATCC 53627.
Figure imgf000012_0001
Figure imgf000013_0001
Figure imgf000014_0001
Figure imgf000015_0001
Figure imgf000016_0001
Figure imgf000017_0001
Figure imgf000018_0001
Figure imgf000019_0001
Figure imgf000020_0001
Figure imgf000021_0001
Figure imgf000022_0001
Figure imgf000023_0001
Figure imgf000024_0001
Figure imgf000025_0001
Figure imgf000026_0001
Figure imgf000027_0001
Figure imgf000028_0001
Figure imgf000029_0001
Figure imgf000030_0001
Figure imgf000031_0001
Figure imgf000032_0001
Figure imgf000033_0001
* Amino acid residue absent in this position
BRIEF DESCRIPTION OF THE DRAWINGS The present invention is further illustrated by reference to the accompanying drawings, in which:
Fig. 1 shows a model of the structure of the active site cleft (domains A and B) of a CGTase from Bacillus circulans Strain 251 , which has been complexed with a linear starch molecule, and residues involved in the enzyme-substrate interactions;
Fig. 2 shows the formation (% cyclodextrin) of α- (●), β- (■), and γ- cyclodextrin (Δ) from 10% Paselli™ WA4 (pre-gelatinized drum-dried starch) during a 50 hour incubation at 50ºC catalyzed by (A) wild-type enzyme (Bacillus circulans Strain 251 CGTase), (B) the Y89D CGTase variant, (C) the S146P CGTase variant, and (D) the Y89D/S146P CGTase variant;
Fig. 3 shows the construction of plasmid pDP66K, subcloning steps are indicated adjacent to the arrows;
Fig. 4 shows the results of starch binding experiments (% of protein bound to raw starch) at starch concentrations of from 0 to 8 % raw starch, (•) without β- cyclodextrin, and (O) with 0.1 mM β-cyclodextrin; (a) wild-type enzyme (Bacillus circulans Strain 251 CGTase), (b) the W616A/W662A variant, and (c) the Y633A variant;
Fig. 5 shows the results of reaction kinetic experiments (activity, U/mg) on
Paselli™ SA2 (i.e. partially hydrolysed potato starch) at concentrations of from 0 to
5 % Paselli™, (●) without β-cyclodextrin, (O) with 0.1 mM β-cyclodextrin, and (♦) with 0.2 mM β-cyclodextrin; (a) wild-type enzyme (Bacillus circulans Strain 251 CGTase),
(b) the W616A/W662A variant, and (c) the Y633A variant;
Fig. 6 shows the results of reaction kinetic experiments (activity, U/mg) on raw starch at starch concentration of from 0 to 60 % raw starch, (●) wild-type enzyme (Bacillus circulans Strain 251 CGTase), (♤) the W616A/W662A variant, and (■) the Y633A variant; the dotted line indicates the modelled curve resulting from the supposed interaction between MBS2 on the E domain and MBS3 on the C domain;
Fig. 7 shows the product formation (O α-cyclodextrin formation; D β- cyclodextrin formation, and Δγ-cyclodextrin formation) of two CGTase variants of the invention (N193G, Fig. 7B, and Y89G, Fig. 7C) compared to the wild-type enzyme (from Bacillus circulans Strain 251 , Fig. 7A) during incubation for 0 to 45 hours;
Fig. 8 shows the product formation (O α-cyclodextrin formation; D β- cyclodextrin formation, and Δγ-cyclodextrin formation) of two CGTase variants of the invention (*145al, Fig. 8B, and D371G, Fig. 8C) compared to the wild-type enzyme (from Bacillus circulans Strain 251 , Fig. 8A) during incubation for 0 to 45 hours;
Fig. 9 shows the product formation (O α-cyclodextrin formation; ♤ β- cyclodextrin formation, and Δγ-cyclodextrin formation) of two CGTase variants of the invention (N193G, Fig. 9B, and Y89G, Fig. 9C) compared to the wild-type enzyme (from Bacillus circulans Strain 251 , Fig. 9A) during incubation for 0 to 10 hours; and
Fig 10 shows the product formation (O α-cyclodextrin formation; ♤ β- cyclodextrin formation, and Δγ-cyclodextrin formation) of two CGTase variants of the invention (145al, Fig. 10B, and D371G, Fig. 10C) compared to the wild-type enzyme (from Bacillus circulans Strain 251 , Fig. 10A) during incubation for 0 to 10 hours. DETAILED DISCLOSURE OF THE INVENTION
Methods of Making CGTase Variants
In its first aspect, the present invention provides a method of modifying the substrate binding and/or increasing the product selectivity of a CGTase enzyme, thereby obtaining a CGTase variant having a modified substrate binding capability and/or an increased product selectivity, as compared to the precursor enzyme.
In the context of this invention, a CGTase variant of modified substrate binding capability is meant to describe a CGTase variant that is able to more efficiently act on its substrate, and/or a CGTase variant that is less affected by product inhibition. In the context of this invention, product inhibition is meant to describe the phenomenon that increasing amounts of product reduce or even inhibit the substrate conversion. It is desirable to obtain CGTase variants that are less affected by product inhibition (i.e. variants of reduced product inhibition).
Moreover, in the context of this invention, a CGTase variant of increased product selectivity is meant to describe a CGTase variant that is able to more selectively produce any of the various cyclodextrins thereby increasing the ratio of the desired product, as compared to the precursor enzyme.
The present invention is based on the concept of removing and/or introducing "obstacles" in the subsites of the active site cleft, the substrate binding cleft, or the groove leading to these clefts, thereby facilitating introduction of the substrate and its disposition in such a way that products of a predetermined size are obtained, and in such a way that substrate binding is not inhibited by the product.
By modifying the substrate binding of a CGTase enzyme, its product selectivity can be modified in order that the CGTase variant is able to more selectively produce any of the various cyclodextrins, α-, β- and γ-cyclodextrins. Even CGTases capable of producing δ-, ε-, and ζ-cyclodextrins with 9, 10 and 11 glucose units, respectively, may be obtained. Modification of the substrate binding of a CGTase may also reduce the tendency of product inhibition, thereby increasing the cyclodextrin yield of the CGTase variant.
The concept of the invention may be expressed differently as the modification of enzyme-substrate side chain intermolecular interactions. By introducing specific mutations according to the invention, the intermolecular interactions between substrate and CGTase can be changed in order to direct the substrate to a specific location in the active site cleft, thereby obtaining a cyclic or linear product of predefined size, preferably α-, a β- or a γ-cyclodextrin, or δ-, ε-, and ζ-cyclodextrins, or a linear oligosaccharide of similar size, preferably of 2-12 glucose units, more preferred 2-9 glucose units.
In a preferred embodiment of the invention, the introduction of more intermolecular interactions (e.g. more hydrogen bonding potential) in the region around glucose units C to I, preferably C to H, of Fig. 1 , will lock the substrate in a position 6 glucose units from the catalytic site (between glucose units B and C of Fig. 1), and lead to increased product selectivity for α-cyclodextrins (6 glucose units). Moreover, the formation of larger cyclodextrins and/or larger linear oligosaccharides may simultaneously be reduced by reducing potential intermolecular interactions of glucose unit I to J of Fig. 1.
In another preferred embodiment of the invention, the introduction of more intermolecular interactions (e.g. more hydrogen bonding potential) in the region around glucose units F to J, preferably H and I, of Fig. 1 , will lock the substrate in a position 7 glucose units from the catalytic site (between glucose units B and C of Fig. 1), and lead to increased product selectivity for β-cyclodextrins (7 glucose units). Moreover, the formation of e.g. α-cyclodextrins and/or small linear oligosaccharides may simultaneously be reduced by reducing potential intermolecular interactions of glucose unit C to G of Fig. 1.
In a third preferred embodiment of the invention, the introduction of more intermolecular interactions (e.g. more hydrogen bonding potential) in the region around glucose units H to K, preferably I and J, of Fig. 1 , will lock the substrate in a position 8 glucose units from the catalytic site (between glucose units B and C of Fig. 1), and lead to increased product selectivity for γ-cyclodextrins (8 glucose units). Moreover, the formation of smaller cyclodextrins and/or linear oligosaccharides may simultaneously be reduced by reducing potential intermolecular interactions of glucose unit C to H of Fig. 1.
In a fourth preferred embodiment of the invention, the introduction of more intermolecular interactions (e.g. more hydrogen bonding potential) in the region around glucose units J to M, preferably K and L, of Fig. 1 , will lock the substrate in a position 9 glucose units from the catalytic site (between glucose units B and C of Fig. 1), and lead to increased product selectivity for δ-cyclodextrins (9 glucose units). Moreover, the formation of smaller cyclodextrins and/or linear oligosaccharides may simultaneously be reduced by reducing potential intermolecular interactions of glucose unit C to H of Fig. 1.
In a fifth preferred embodiment of the invention, the introduction of more intermolecular interactions (e.g. more hydrogen bonding potential) in the region around glucose units K to N, preferably L and M, of Fig. 1 , will lock the substrate in a position 10 glucose units from the catalytic site (between glucose units B and C of Fig. 1), and lead to increased product selectivity for ε-cyclodextrins (10 glucose units). Moreover, the formation of smaller cyclodextrins and/or linear oligosaccharides may simultaneously be reduced by reducing potential intermolecular interactions of glucose unit C to H of Fig. 1.
In a sixth preferred embodiment of the invention, the introduction of more intermolecular interactions (e.g. more hydrogen bonding potential) in the region around glucose units L to O, preferably M and N, of Fig. 1 , will lock the substrate in a position 11 glucose units from the catalytic site (between glucose units B and C of Fig. 1 ), and lead to increased product selectivity for ζ-cyclodextrins (11 glucose units). Moreover, the formation of smaller cyclodextrins and/or linear oligosaccharides may simultaneously be reduced by reducing potential intermolecular interactions of glucose unit C to H of Fig. 1.
In a seventh preferred embodiment of the invention, the formation of linear oligosaccharides of desired length may be increased by combining the above conditions with substitution at the cyclization axis, corresponding to position 195, CGTase numbering.
The CGTase enzyme subjected to the method of the invention may be any
CGTase found in nature. However, the CGTase preferably is a microbial enzyme, preferably a bacterial enzyme, and preferably the CGTase is derived from a strain of Bacillus, a strain of Brevibacterium, a strain of Clostridium, a strain of Corynebacterium, a strain of Klebsiella, a strain of Micrococcus, a strain of Thermoanaerobium, a strain of Thermoanaerobacter, a strain of Thermoanaerobacterium, or a strain of Thermoactinomyces.
In more preferred embodiments, the CGTase is derived from a strain of Bacillus autolyticus, a strain of Bacillus cereus, a strain of Bacillus circulans, a strain of Bacillus circulans var. alkalophilus, a strain of Bacillus coagulans, a strain of Bacillus firmus, a strain of Bacillus halophilus, a strain of Bacillus macerans, a strain of Bacillus megaterium, a strain of Bacillus ohbensis, a strain of Bacillus stearothermophilus, a strain of Bacillus subtilis, a strain of Klebsiella pneumonia, a strain of Thermoanaerobacter ethanolicus, a strain of Thermoanaerobacter finnii, a strain of Clostridium thermoamylolyticum, a strain of Clostridium thermosaccharolyticum, or a strain of Thermoanaerobacterium thermosulfurigenes.
In most preferred embodiments, the CGTase is derived from the strain
Bacillus sp. Strain 1011 , the strain Bacillus sp. Strain 38-2, the strain Bacillus sp.
Strain 17-1 , the strain Bacillus sp. 1-1 , the strain Bacillus sp. Strain B1018, the strain Bacillus circulans Strain 8, the strain Thermoanaerobacter sp. ATCC 53627, or the strain Bacillus circulans Strain 251, or a mutant or a variant thereof.
The strain Thermoanaerobacter sp. ATCC 53627 was deposited according to the Budapest Treaty on the International Recognition of the Deposit of Microorganisms for the Purposes of Patent Procedure at the American Type Culture Collection (ATCC), 12301 Parklawn Drive, Rockville, Maryland 20852, USA, on 3 June 1987. The strain Bacillus circulans Strain 251 has been deposited in the open collection at Rijksinstituut voor Volksgezondheid (RIV), Bilthoven, The Netherlands, and allotted the accession number RIV 11115, and thus is publicly available.
The method of the invention comprises substitution, insertion and/or deletion of one or more amino acid residue(s) of the enzyme, which residue(s) hold a position close to the substrate, when the substrate has bound to the CGTase enzyme at its substrate binding sites. In more specific aspects, the method of the invention comprises substitution, insertion and/or deletion of two or more amino acid residue(s), preferably of three or more amino acid residue(s).
In the context of this invention, a CGTase amino acid residue holding a position close to the substrate indicates an amino acid residue located within the enzyme in a way that it is within a potential intermolecular (i.e. enzyme-substrate) interactive distance from a glucose unit of the substrate (i.e. a polysaccharide). Examples of potential intermolecular interactions include, but are not limited to hydrogen bonding, salt bridge formation, polar interactions, hydrophobic interactions, and aromatic interactions.
In a preferred embodiment of this invention, an amino acid position close to the substrate indicates a distance less than 8 A (angstrom), preferably less than 5 Å, more preferred less than 3 A, from the substrate.
In a more preferred embodiment of this invention, these distances are calculated using the CGTase from Bacillus circulans Strain 251 [cf. Lawson C L, van Montfort R, Strokopytov B, Rozeboom H J, Kalk K H, de Vries G E, Penninga D, Dijkhuizen L, and Dijkstra B W, J. Mol. Biol. 1994 236 590-600], complexed with a derivative of maltonanose, the coordinates of which have been deposited with the Protein Data Bank, Biology Department, Bldg. 463, Brookhaven National Laboratory, P.O. Box 5000, Upton, NY 11973-5000, USA, under the entry code 1 DU. Knowledge of this structure makes it possible to identify similar positions in other CGTases, having a known primary structure, which positions corresponds to the positions stated in e.g. Table 2, cf. also Table 1.
CGTases have substrate binding regions located at the A domain, at the
B domain, at the C domain and at the E domain of the enzyme. Consequently, in a preferred embodiment, the method of the invention comprises substituting one or more amino acid residue(s) of the CGTase enzyme, which residue(s) are located in one or more of the A, B, C and/or E domains, cf. Table 1.
By sequence alignment and molecular modelling of a CGTase enzyme found in nature, amino acid residues located close to the substrate can be identified. By using sequence alignment, the tertiary structure of any homologous CGTase can be modelled based on known three-dimensional CGTase structures.
Table 2, below, presents a list of CGTase amino acid positions located within 8 A from the substrate, and therefore to be considered in the context of this invention. The amino acid residues are identified by CGTase numbering, which allows identification of the corresponding amino acid positions in any CGTase enzyme.
Preferably, the method of the invention comprises substitution, insertion and/or deletion at one or more amino acid residue(s) identified in Table 2, below.
Figure imgf000040_0001
By molecular modelling of the CGTase obtained from Bacillus circulans Strain 251 , the amino acid positions presented in Tables 3-5, below, have been identified as positions close to the substrate, i.e. at a distance of 8A, 5A and 3A, respectively.
In a more preferred embodiment, the method of the invention comprises substitution, insertion and/or deletion at one or more amino acid residue(s) identified in Tables 3-5, below.
Figure imgf000042_0001
Figure imgf000043_0001
Figure imgf000043_0002
In a similar manner, molecular modelling of the CGTase obtained from the strain Thermoanaerobacter sp. ATCC 53627, has revealed the amino acid positions presented in Tables 6-8, below, as being positions close to the substrate, i.e. at a distance of 8A, 5A and 3A, respectively. In another preferred embodiment, the method of the invention comprises substitution, insertion and/or deletion at one or more amino acid residue(s) identified in Tables 6-8, below.
Figure imgf000045_0001
Figure imgf000046_0001
Figure imgf000046_0002
As described above, the substrate binding and product selectivity of a CGTase variant of the invention can be designed by removing existing and/or introducing potential intermolecular interactions between the CGTase variant and its substrate. Examples of intermolecular interactions include, but are not limited to hydrogen bonding, salt bridge formation, polar interactions, hydrophobic interactions, and aromatic interactions.
Amino acid residues having side chains with hydrogen bonding potentials (i.e. having H-bonding capability) are generally the following:
Ser (S), Thr (T), Asn (N), Gln (Q), His (H), Asp (D), Tyr (Y), Glu (E), Lys
(K), Arg (R), Trp (W), and Cys (C).
Correspondingly the following amino acids do not in general possess the potential ability to form side chain hydrogen bonds (i.e. no H-bonding capability):
Ala (A), Val (V), Leu (L), lle (I), Phe (F), Gly (G), Met (M), and Pro (P).
Amino acid residues having side chains with salt bridge formation potentials are generally the following:
Asp (D), Glu (E), Lys (K), Arg (R), and His (H).
Amino acid residues having side chains with polar interaction potentials are generally the following:
Asp (D), Asn (N), Glu (E), Gln (Q), Lys (K), Arg (R), His (H), Tyr (Y), Trp (W), and Cys (C).
Amino acid residues having side chains with hydrophobic interaction potentials are generally the following:
Ala (A), Val (V), Leu (L), lle (I), Phe (F), Met (M), Pro (P), and part of the
Arg (R), Glu (E) and Gln (Q) side-chains.
Amino acid residues having side chains with aromatic interaction potentials are generally the following:
His (H), Phe (F), Tyr (Y) and Trp (W). CGTase Variants
In its second aspect, the present invention provides novel CGTase variants, having an amino acid sequence not found in nature. Functionally, the CGTase variant of the invention is regarded a derivative of a precursor CGTase enzyme (i.e. the native, parental, or wild-type enzyme).
In a CGTase variant of the invention, the substrate binding and/or product selectivity has been modified, as compared to the precursor CGTase enzyme, by replacement, insertion and/or deletion of one or more amino acid residue(s) holding a position close to the substrate.
The CGTase variant of the invention may be derived from any CGTase enzyme found in nature. However, the CGTase variant of the invention preferably is derived from a microbial enzyme, preferably a bacterial enzyme, and preferably the CGTase variant is derived from a strain of Bacillus, a strain of Brevibacterium, a strain of Clostridium, a strain of Corynebacterium, a strain of Klebsiella, a strain of Micrococcus, a strain of Thermoanaerobium, a strain of Thermoanaerobacter, a strain of Thermoanaerobacterium, or a strain of Thermoactinomyces.
In more preferred embodiments, the CGTase variant of the invention is derived from a strain of Bacillus autolyticus, a strain of Bacillus cereus, a strain of Bacillus circulans, a strain of Bacillus circulans var. alkalophilus, a strain of Bacillus coagulans, a strain of Bacillus firmus, a strain of Bacillus halophilus, a strain of Bacillus macerans, a strain of Bacillus megaterium, a strain of Bacillus ohbensis, a strain of Bacillus stearothermophilus, a strain of Bacillus subtilis, a strain of Klebsiella pneumonia, a strain of Thermoanaerobacter ethanolicus, a strain of Thermoanaerobacter fmnii, a strain of Clostridium thermoamylolyticυm, a strain of Clostridium thermosaccharolyticum, or a strain of Thermoanaerobacterium thermosulfurigenes.
In most preferred embodiments, the CGTase variant of the invention is derived from the strain Bacillus sp. Strain 1011 , the strain Bacillus sp. Strain 38-2, the strain Bacillus sp. Strain 17-1 , the strain Bacillus sp. 1-1 , the strain Bacillus sp. Strain B1018, the strain Bacillus circulans Strain 8, the strain Bacillus circulans Strain 251 , or the strain Thermoanaerobacter sp. ATCC 53627, or a mutant or a variant thereof.
In the context of this invention, an amino acid residue holding a position close to the substrate indicates an amino acid residue located within the enzyme in such a way that it is within a potential intermolecular (i.e. enzyme-substrate) interactive distance from a glucose unit of the substrate (i.e. a polysaccharide).
Examples of potential intermolecular interactions include, but are not limited to hydrogen bonding, salt bridge formation, polar interactions, hydrophobic interactions, and aromatic interactions. In a preferred embodiment of this invention, an amino acid position close to the substrate indicates a distance less than 8 A (angstrom), preferably less than 5 A, more preferred less than 3 A, from the substrate.
Moreover, CGTases have substrate binding regions located at the A domain, at the B domain, at the C domain and at the E domain. Consequently, in a preferred embodiment, the invention provides a CGTase variant, in which variant a substitution, an insertion and/or a deletion have been introduced at one or more of the amino acid residue(s) located in one or more of the A, B, C and E domains.
In another preferred embodiment, the invention provides a CGTase variant, in which variant a substitution, an insertion and/or a deletion have been introduced at one or more of the amino acid positions corresponding to the positions stated in Table 2.
However, if a substitutions at positions 195 and 198 (CGTase numbering) have been accomplished, the CGTase is not contemplated a CGTase variant of the invention unless additional substitution, insertion and/or deletion at one or more amino acid residue(s) has been introduced. Moreover, a CGTase comprising any of the following specific mutations: H140R, H140N, F183L, H233R, H233N, W258V, F259L, F259I, F259Y, F283L, H327R, H327N, T598F and/or W636F, is not contemplated a CGTase variant of the invention, unless additional substitution, insertion and/or deletion of amino acid residue(s) at one or more positions not stated here has been introduced. Finally, a CGTase comprising any of the following specific mutations: F195Y/F259Y, W258V/F259I, T598F/W636F, and F183L/F259L, is not contemplated a CGTase variant of the invention, unless additional substitution, insertion and/or deletion of amino acid residue(s) at one or more positions has been introduced. Therefore such CGTase variants are disclaimed according to the present invention.
In a more preferred embodiment, the CGTase variant of the invention is a CGTase variant derived from an enzyme obtainable from a strain of Bacillus, which enzyme has been modified by substitution, insertion and/or deletion at one or more amino acid positions corresponding to the positions stated in Tables 3-5. Preferably the CGTase variant is derived from a strain of Bacillus autolyticus, a strain of Bacillus cereus, a strain of Bacillus circulans, a strain of Bacillus circulans vac alkalophilus, a strain of Bacillus coagulans, a strain of Bacillus firmus, a strain of Bacillus halophilus, a strain of Bacillus macerans, a strain of Bacillus megaterium, a strain of Bacillus ohbensis, a strain of Bacillus stearothermophilus, or a strain of Bacillus subtilis. Most preferred, the CGTase variant is derived from the strain Bacillus sp. Strain 1011 , the strain Bacillus sp. Strain 38-2, the strain Bacillus sp. Strain 17-1 , the strain Bacillus sp. 1 -1 , the strain Bacillus sp. Strain B1018, the strain Bacillus circulans Strain 8, or the strain Bacillus circulans Strain 251 , or a mutant or a variant thereof.
In another preferred embodiment, the CGTase variant of the invention is a CGTase variant derived from an enzyme obtainable from a strain of Thermoanaerobacter, which enzyme has been modified by substitution, insertion and/or deletion at one or more of the amino acid positions corresponding to the positions stated in Tables 6-8. Preferably the CGTase variant is derived from the strain Thermoanaerobacter sp. ATCC 53627, or a mutant or a variant thereof.
In a CGTase variant of the invention, the intermolecular enzyme/substrate interactions have been modified, as compared to the precursor enzyme. Examples of potential intermolecular interactions include, but are not limited to hydrogen bonding, salt bridge formation, polar interactions, hydrophobic interactions, and aromatic interactions. Such modifications may be accomplished by substitution, insertion and/or deletion at one or more of the above described positions, according to the following guidance.
Amino acid residues having side chains with hydrogen bonding potentials (i.e. having H-bonding capability) are generally the following:
Ser (S), Thr (T), Asn (N), Gln (Q), His (H), Asp (D), Tyr (Y), Glu (E), Lys
(K), Arg (R), Trp (W), and Cys (C).
Correspondingly the following amino acids do not in general possess the potential ability to form side chain hydrogen bonds (i.e. no H-bonding capability):
Ala (A), Val (V), Leu (L), He (I), Phe (F), Gly (G), Met (M), and Pro (P).
Amino acid residues having side chains with salt bridge formation potentials are generally the following:
Asp (D), Glu (E), Lys (K), Arg (R), and His (H).
Amino acid residues having side chains with polar interaction potentials are generally the following: Asp (D), Asn (N), Glu (E), Gln (Q), Lys (K), Arg (R), His (H), Tyr (Y), Trp (W), and Cys (C).
Amino acid residues having side chains with hydrophobic interaction potentials are generally the following:
Ala (A), Val (V), Leu (L), lle (I), Phe (F), Met (M), Pro (P), and part of the
Arg (R), Glu (E) and Gln (Q) side-chains.
Amino acid residues having side chains with aromatic interaction potentials are generally the following:
His (H), Phe (F), Tyr (Y) and Trp (W).
By the method of the invention variants are obtained, which possess an altered number of hydrogen bonds or other interactions in the subsites of the active cleft or in the groove leading to this cleft or on the maltose binding sites. By altering subsites in the binding cleft it is possible to manipulate the number of sugars which are able to bind and thus alter the ratios of α-, β-, γ-cyclodextrins, etc., produced by the enzyme.
In particular, when construction of α-cyclodextrin forming CGTase variants is contemplated, interactions on or before subsites C-l of the substrate (cf. Fig. 1) should be increased, and interactions on subsites I and higher should be decreased. Alternatively sterical hindrance could be applied to prevent binding on subsites I and higher. For instance, starting from an Bacillus CGTase, the following mutations are contemplated, separately or in combinations.
Less coupling and disproportionating activity is achieved by removing interactions between the enzyme and the donor/acceptor, i.e. between the CGTase and subsites A, B, C and D. Mutations which remove hydrogen bonds are e.g.:
H233Q, D135L, R47L or R47Q.
Mutations which increase hydrogen bonding relative to the substrate are e.g.:
H233Q (relative to subsite B of the substrate), L197D or L197E (subsite D),
N94Q or N94K or N94R or N94W or N94F (subsite E), D371 N or D371 G (subsite E+F), Y89D (subsite E), A144K or A144R or A144D (subsite H), N193D or N193E
(subsite H), Y167F (in order to release the residue at position 193 for H-bonding to subsite H), and T185R or T185E or T185D (on maltose binding site 2, cf. below). Mutations which alter the conformation of the substrate binding cleft, and thus make new enzyme-substrate interactions are e.g.:
N88P, and P143G.
Mutations which decrease hydrogen bonding relative to the substrate are e.g.:
S145E or S145A, and S146P or S146Q or S146G (relative to subsite I of the substrate).
A mutation which increases the hydrogen bonding relative to subsite H is e.g. A144R.
A mutation which increases hydrogen bonding relative to the substrate is e.g. N88K.
Mutations which leads to sterical hindrance are e.g.:
S145W or S145Y or S145F, and S146W or S146I or S146R or S146P (prevent binding on subsite I of the substrate).
Mutations which increase electrostatic interactions (stacking) are e.g.:
L600W or L600F or L600Y (of maltose binding site 2, cf. below).
In a preferred embodiment, a α-cyclodextrin forming CGTase variant of the invention may be a variant, which at positions 87-94 comprises the partial amino acid sequence IKYSGVNN, and/or at positions 143-151 comprises the partial amino acid sequence GRAGTNPGF, or at positions 143-145 comprises the partial amino acid sequence GRW.
In order to produce an enzyme with an improved product selectivity towards β-cyclodextrins it is necessary to circumvent the production of both smaller and larger cyclic products. A rationale might be to prevent the production of α- cyclodextrin by removing hydrogen bonds between the enzyme and substrate, which enable the substrate to move more quickly into the active site. Conversely, introduction of hydrogen bonds at relevant positions slow down the movement of substrate leading to the production of larger cyclodextrins. This approach, coupled with the substitution of amino acid residues which cause sterical hindrance for smaller amino acid residues at positions designed to block the movement of substrate, prevent the formation of cyclodextrins larger than β-cyclodextrin. Therefore, if construction of β-cyclodextrin forming CGTase variants is contemplated, the following mutations are contemplated, separately or in combinations, also starting from an Bacillus CGTase.
Mutations which alter the conformation of the substrate binding cleft close to the active site and thus create space for larger cyclodextrins (β- and γ- cyclodextrins) are e.g.:
N88P, Y89* (a deletion), 91 aY (an insertion), V92* or N92*. and N94*.
A mutation which increases hydrogen bonding relative to the substrate is e.g. S146E.
Mutations which decrease hydrogen bonding relative to the substrate are e.g.
S145L, and Q148N.
Mutations which remove hydrogen bonds from subsites D, E, F, H, I and J of the substrate are e.g.:
R375G, D371G, D371 N, Y89G, N193G, S145A, Q148A, and *145al. A mutation which introduce sterical hindrance between subsites I and J of the substrate, designed to shift the product ratio towards the production of smaller cyclodextrins is e.g. D147W.
In a preferred embodiment, a β-cyclodextrin forming CGTase variant of the invention may be a variant, which at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAETWPAF.
In another preferred embodiment, a β-cyclodextrin forming CGTase variant of the invention may be a variant, which at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAETWPAF, and which variant at position 195 holds a leucine residue (X195L).
In a third preferred embodiment, a CGTase variant of the invention capable of forming linear oligosaccharides may be a variant, which at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAETWPAF, and which variant at position 195 holds a glycine residue (X195G).
Similarly, if construction of γ-cyclodextrin forming CGTase variants is contemplated, the following mutations are contemplated, separately or in combinations, again starting from an Bacillus CGTase.
Mutations which alter the conformation of the substrate binding cleft close to the active site and thus create space for larger cyclodextrins (β- and γ- cyclodextrins) are e.g.:
N88P, Y89* (a deletion), 91 aY (an insertion), V92* or N92*. and N94*. A mutation which increases hydrogen bonding relative to the substrate is e.g. S146E.
Mutations which decrease hydrogen bonding relative to the substrate are e.g.
S145L, and Q148N.
Mutations which remove hydrogen bonds from subsites D, E, F and H of the substrate are e.g.:
N193G, R375G, D371G, and D371 N.
A mutation which remove hydrogen bonds and hydrophobic stacking from subsites D, E, F and H of the substrate e.g. Y89G.
Mutations which change the binding properties at subsites I and J of the substrate are e.g.:
X145al or *145al (via insertion), S145A, and Q148E, in particular S145A/X145al or A145AT145al, and X145al/Q148E or *145al/Q148E.
Mutations which reduce the coupling activity at subsites A, D and E are e.g.:
R375G, D371G, K232Q, and E264Q.
Mutations reducing the coupling activity by changing specific binding of cyclodextrins is e.g. R47Q.
In particular, when considering CGTase variants derived from a strain of Thermoanaerobacter, mutations which lead to less hydrolysis, obtained by removing water molecules close to the active site, are e.g.:
V21 F or V21Y. Less coupling and disproportionating activity is achieved by removing interactions between the enzyme and the donor/acceptor, i.e. between the CGTase and subsites A, B, C and D. Mutations which remove hydrogen bonds are e.g.:
Y259F, H233Q, and D135L.
In a preferred embodiment, a γ-cyclodextrin forming CGTase variant of the invention may be a variant, which at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAEADPNF.
In another preferred embodiment, a γ-cyclodextrin forming CGTase variant of the invention may be a variant, which at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAEADPNF, and which variant at position 195 holds a leucine residue (X195W).
In a third preferred embodiment, in order to obtain linear oligosaccharides of a desired length, the variants of the invention may be combined with a substitution at the central amino acid residue forming the cyclization axis, corresponding to position 195, CGTase numbering. At this position, tyrosine and phenylalanine are predominant in wild-type CGTases (cf. Table 1 ). By changing this residue, the cyclization properties are affected, and cyclization may be prohibited. In a preferred embodiment, glycine is introduced at this position (X195G).
In yet another preferred embodiment, a CGTase variant of the invention is an enzyme which has been modified by substitution, insertion and/or deletion at one or more of the amino acid positions corresponding to the positions stated in Table 9, below. As indicated in this table, the introduction of one or more of these substitutions/insertions/deletions lead to CGTase variants of increased product selectivity in respect of α-, β- or γ-cyclodextrins, respectively.
Figure imgf000056_0001
Figure imgf000057_0001
In respect to product binding and product inhibition, the E domain of the Bacillus circulans Strain 251 CGTase has now been identified as a raw starch binding domain. In the maltose dependent crystal structure, three maltose molecules have been found on each enzyme molecule on contact points between these molecules (maltose binding sites, MBS). Two of these maltoses are bound to specific sites on the E domain (MBS1 and MBS2, near 616 and 662), the third site is located on the C domain (MBS3, near 413). Thus, the binding sites on the E domain are required for the conversion of raw starch into cyclodextrins. Experiments, as conducted below, indicate that the enzyme binds to the raw starch granule via MBS1 , while MBS2 guides a starch chain protruding from the granule to the active site. In another preferred embodiment, a CGTase variant of the invention is an enzyme which has been modified by substitution, insertion and/or deletion at one or more of the amino acid positions corresponding to the positions stated in Table 10, below. Such modifications lead to CGTase variants of reduced product inhibition.
For instance, in the context of this invention, the following mutations, starting from an Bacillus CGTase, are contemplated, separately or in combination, in order to reduce product inhibition.
Mutations which reduces non-competitive product inhibition are e.g.:
Y633A (takes place on MBS2, this mutation completely removes non- competitive product inhibition), 599aP or 599aR or 599aH, and L600R.
Residues 595-605 form a loop next to MBS2. Insertion enlarges the loop, thereby preventing binding of a cyclodextrin to MBS2 by sterical hindrance, while the role of MBS2 in guidance of the substrate chain is preserved. Mutations at position 600 and adjacent residues could reduce the binding of cyclic products to MBS2, while the binding of linear substrates remains unaffected. Substitution of leucine at position 600 with aspartate, alanine or glycine has minor effects on product inhibition. Substitution with arginine, due to its large size and charged nature, affect binding of cyclodextrins, thereby reducing product inhibition.
Mutations that decrease electrostatic interactions around MBS1 , leading to decreased product affinity are e.g. W616A and/or W662A.
Mutations that decrease electrostatic interactions around MBS2, leading to decreased product affinity are e.g. L600A or L600S, and/or Y663A.
A mutations that decreases electrostatic interactions around MBS3, leading to decreased product affinity is e.g. W413A.
Competitive product inhibition is contemplated caused by coupling reactions. Reduction of this coupling reaction may be achieved by reducing the binding of the first (cyclodextrin) and second (malto-oligosaccharide) substrate.
Mutations reducing competitive product inhibition by reducing cyclodextrin binding are e.g.:
R47A or R47Q or R47L, Y89G, D196A or D196L, D371G or D371 N or
D371A or D371L, and R375G or R375Q or R375N or R375A or R375L.
Mutations reducing competitive product inhibition by reducing binding of the second substrate are e.g.: K232Q or K232N or K232A or K232L, E264A or E264N or E264L, T186A, and E268A.
Figure imgf000059_0001
Figure imgf000060_0001
X = any natural amino acid residue
In a preferred embodiment, the CGTase variant of the invention is a CGTase variant derived from an enzyme obtainable from a strain of Bacillus, which enzyme has been modified by substitution, insertion and/or deletion at one or more of the amino acid positions corresponding to the positions stated in Table 11 , below. Such modifications lead to CGTase variants of increased product selectivity, as indicated in the table.
More preferred, the CGTase variant is derived from a strain of a strain of Bacillus autolyticus, a strain of Bacillus cereus, a strain of Bacillus circulans, a strain of Bacillus circulans vac alkalophilus, a strain of Bacillus coagulans, a strain of Bacillus firmus, a strain of Bacillus halophilus, a strain of Bacillus macerans, a strain of Bacillus megaterium, a strain of Bacillus ohbensis, a strain of Bacillus stearothermophilus, or a strain of Bacillus subtilis.
Most preferred, the CGTase variant is derived from the strain Bacillus sp. Strain 1011 , the strain Bacillus sp. Strain 38-2, the strain Bacillus sp. Strain 17-1 , the strain Bacillus sp. 1-1 , the strain Bacillus sp. Strain B1018, the strain Bacillus circulans Strain 8, or the strain Bacillus circulans Strain 251 , or a mutant or a variant thereof.
Figure imgf000060_0002
Figure imgf000061_0001
Figure imgf000062_0002
X = any natural amino acid residue
- conserved residue
* deleted or absent residue
In another preferred embodiment, the CGTase variant of the invention is a CGTase variant derived from an enzyme obtainable from a strain of Bacillus, which enzyme has been modified by substitution, insertion and/or deletion at one or more of the amino acid positions corresponding to the positions stated in Table 12, below. Such modifications lead to CGTase variants of reduced product inhibition.
Figure imgf000062_0001
Figure imgf000063_0001
X = any natural amino acid residue As its most preferred embodiments, the invention provides the following
CGTase variants:
A CGTase variant, which variant at position 21 holds a tyrosine residue
(F21Y).
A CGTase variant, which variant at position 47 holds a glutamine residue (R47Q), or an alanine residue (R47A), or a leucine residue (R47L), or a histidine residue (R47H).
A CGTase variant, which variant at position 88 holds a proline residue
(N88P) or a lysine residue (N88K).
A CGTase variant, which variant at position 89 holds an aspartic acid residue (Y89D), or an alanine residue (Y89A), or a glycine residue
(Y89G). A CGTase variant, which variant at position 91a (via insertion) holds an alanine residue (*91aA), or a tyrosine residue (*91aY).
A CGTase variant, in which variant position 92 has been deleted (V92*).
A CGTase variant, which variant at position 94 holds a glutamine residue (N94Q), or a lysine residue (N94K), or an arginine residue (N94R), or a tryptophan residue (N94W), or a phenylalanine residue (N94F), or in which variant position 94 has been deleted (N94*).
A CGTase variant, which variant at position 135 holds a leucine residue
(D135L).
A CGTase variant, which variant at position 143 holds a natural amino acid residue different from that of the wild-type enzyme (P143X).
A CGTase variant, which variant at position 143 holds an alanine residue
(P143A), or a glycine residue (P143G).
A CGTase variant, which variant at position 144 holds a natural amino acid residue different from that of the wild-type enzyme (A144X).
A CGTase variant, which variant at position 144 holds an arginine residue (A144R), or a lysine residue (A144K), or an aspartic acid residue
(A144D).
A CGTase variant, which variant at position 145 holds a natural amino acid residue different from that of the wild-type enzyme (S145X).
A CGTase variant, which variant at position 145 holds an alanine residue
(S145A), or a glutamic acid (S145E), or a tryptophan residue (S145W), or a glycine residue (S145G), or a phenylalanine residue (S145F), or a tyrosine residue (S145Y), or a leucine residue (S145L).
A CGTase variant, which variant at position 145a (via insertion) holds a natural amino acid residue (*145aX).
A CGTase variant, which variant at position 145a (via insertion) holds an isoleucine residue (*145al).
A CGTase variant, which variant at position 146 holds a natural amino acid residue different from that of the wild-type enzyme (S146X).
A CGTase variant, which variant at position 146 holds a proline residue
(S146P), or an isoleucine residue (S146I), or a glutamine residue (S146Q), or a tryptophan residue (S146W), or an arginine residue
(S146R), or a glutamic acid residue (S146E).
A CGTase variant, which variant at position 147 holds a natural amino acid residue different from that of the wild-type enzyme (D147X). A CGTase variant, which variant at position 147 holds an isoleucine residue (D147I), or a leucine residue (D147L), or an alanine residue
(D147A), or a serine residue (D147S), or a tryptophan residue (D147W).
A CGTase variant, which variant at position 147a (via insertion) holds an alanine residue (*147aA).
A CGTase variant, which variant at position 147a (via insertion) holds a natural amino acid residue (*147aX).
A CGTase variant, which variant at position 148 holds a natural amino acid residue different from that of the wild-type enzyme (Q148X).
A CGTase variant, which variant at position 148 holds an alanine residue (Q148A), or a glycine residue (Q148G), or a glutamic acid residue
(Q148E), or an asparagine residue (Q148N).
A CGTase variant, which variant at position 149 holds a natural amino acid residue different from that of the wild-type enzyme (P149X).
A CGTase variant, which variant at position 149 holds an isoleucine residue (P149I).
A CGTase variant, which variant at position 167 holds a phenylalanine residue (Y167F).
A CGTase variant, which variant at position 179 holds a serine residue
(G179S), an asparagine residue (G179N), or an aspartic acid residue (G179D).
A CGTase variant, which variant at position 180 holds a serine residue
(G180S), an asparagine residue (G180N), or an aspartic acid residue
(G180D).
A CGTase variant, which variant at position 185 holds an arginine residue (T185R), or a glutamic acid residue (T185E), or an aspartic acid residue (T185D).
A CGTase variant, which variant at position 186 holds an alanine residue
(T186A). A CGTase variant, which variant at position 193 holds a natural amino acid residue different from that of the wild-type enzyme (N193X).
A CGTase variant, which variant at position 193 holds a glycine residue
(N193G), or an alanine residue (N193A), or an aspartic acid residue (N193D), or a glutamic acid residue (N193E).
A CGTase variant, which variant at position 195 holds a natural amino acid residue different from that of the wild-type enzyme (Y195X).
A CGTase variant, which variant at position 196 holds a natural amino acid residue different from that of the wild-type enzyme (D196X). A CGTase variant, which variant at position 196 holds an alanine residue
(D196A), a serine residue (D196S), or a leucine residue (D196L).
A CGTase variant, which variant at position 197 holds an aspartic acid residue (L197D), or a glutamic acid residue (L197E).
A CGTase variant, which variant at position 232 holds a glutamine residue (K232Q), or an asparagine residue (K232N), or an alanine residue (K232A), or a leucine residue (K232L).
A CGTase variant, which variant at position 233 holds a glutamine residue (H233Q).
A CGTase variant, which variant at position 264 holds a glutamine residue (E264Q), or an alanine residue (E264A), or an asparagine residue (E264N), or a leucine residue (E264L).
A CGTase variant, which variant at position 268 holds an alanine residue
(E268A).
A CGTase variant, which variant at position 371 holds a natural amino acid residue different from that of the wild-type enzyme (D371X).
A CGTase variant, which variant at position 371 holds a glycine residue
(D371G), or an asparagine residue (D371 N), or an alanine residue
(D371A), or a leucine residue (D371 L).
A CGTase variant, which variant at position 375 holds a natural amino acid residue different from that of the wild-type enzyme (R375X).
A CGTase variant, which variant at position 375 holds a proline residue
(R375P), or a glycine residue (R375G), or a glutamine residue (R375Q), or an asparagine residue (R375N), or an alanine residue (R375A), or a leucine residue (R375L).
A CGTase variant, which variant at position 599a (via insertion) holds a proline residue (*599aP), or an arginine residue (*599aR), or a histidine residue (*599aH).
A CGTase variant, which variant position 600 has been substituted for a different naturally occurring amino acid residue, in particular a tryptophan residue (L600W), a phenylalanine residue (L600F), a tyrosine residue (L600Y), an arginine residue (L600R), a proline residue (L600P), or an asparagine residue (L600N).
A CGTase variant, which variant at position 616 holds an alanine residue
(W616A).
A CGTase variant, which variant at position 633 holds an alanine residue
(Y633A).
A CGTase variant, which variant at position 662 holds an alanine residue
(W662A).
A CGTase variant, which variant at position 47 holds a histidine residue, and at position 135 holds a leucine residue (R47H/D135L).
A CGTase variant, which variant at position 88 holds a proline residue, and at position 143 holds a glycine residue (N88P/P143G).
A CGTase variant, which variant at position 89 holds an aspartic acid residue, and at position 146 holds a proline residue (Y89D/S146P). A CGTase variant, which variant at position 89 holds a glycine residue, and at position 193 holds a glycine residue (Y89G/N193G).
A CGTase variant, in which variant positions 92 and 94 have been deleted (V92VN94*).
A CGTase variant, which variant at position 143 holds an alanine residue, and at position 144 holds an arginine residue (P143A/A144R). A CGTase variant, which variant at position 143 holds a glycine residue, and at position 144 holds an arginine residue, and at position 145 holds a tryptophan residue (P143G/A144R/S145W).
A CGTase variant, which variant at position 143 holds a glycine residue, and at position 144 holds an arginine residue, and at position 145 holds a tryptophan residue (P143G/A144R/S145W), and which variant at position 179 holds a serine residue (G179S), an asparagine residue (G179N), or an aspartic acid residue (G179D).
A CGTase variant, which variant at positions 143-148 comprises the partial amino acid sequence GRA**A, the partial amino acid sequence
GRAAAA, the partial amino acid sequence GRAPAA, or the partial amino acid sequence GRGPAA.
A CGTase variant, which variant at position 144 holds an arginine residue, at position 145 holds an alanine residue, and at position 146 holds a proline residue (A144R/S145A/S146P).
A CGTase variant, which variant at position 145 holds an alanine residue, and at position 145a (via insertion) holds an isoleucine residue
(S145A/*145al).
A CGTase variant, which variant at position 145 holds an alanine residue, and at position 146 holds a glycine residue (S145A/S146G).
A CGTase variant, which variant at position 145 holds a leucine residue, and at position 148 holds an asparagine residue (S145L/Q148N). A CGTase variant, which variant at position 145 holds a glutamic acid residue, and in position 146 holds a proline residue or a glutamine residue (S145E/S146P or S145E/S146Q).
A CGTase variant, which variant at position 145 holds a tryptophan residue, and in position 146 holds a tryptophan residue, or an isoleucine residue, or an arginine residue (S145W/S146W or S145W/S146I or S145W/S146R).
A CGTase variant, which variant at position 145 holds an alanine residue, at position 145a (via insertion) holds an isoleucine residue, and at position 148 holds a glutamic acid residue (S145A/*145al/Q148E). A CGTase variant, which variant at position 145a (via insertion) holds an isoleucine residue, and at position 148 holds a glutamic acid residue (*145al/Q148E).
A CGTase variant, which variant at position 148 holds a glutamic acid residue, and at position 193 holds a glutamine residue. A CGTase variant, which variant at position 616 holds an alanine residue, and at position 662 holds an alanine residue (W616A/W662A). A CGTase variant, which variant at positions 87-94 comprises the partial amino acid sequence IKYSGVNN, and/or at positions 143-151 comprises the partial amino acid sequence GRAGTNPGF, or at positions 143-145 comprises the partial amino acid sequence GRW.
A CGTase variant, which variant at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAETWPAF.
A CGTase variant, which variant at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAETWPAF, and which variant at position 195 holds a leucine residue (Y195L).
A CGTase variant, which variant at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAEADPNF. A CGTase variant, which variant at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAEADPNF, and which variant at position 195 holds a leucine residue (Y195W). Preferably, the above CGTase variants are derived from a strain of
Bacillus autolyticus, a strain of Bacillus cereus, a strain of Bacillus circulans, a strain of Bacillus circulans var. alkalophilus, a strain of Bacillus coagulans, a strain of Bacillus firmus, a strain of Bacillus halophilus, a strain of Bacillus macerans, a strain of Bacillus megaterium, a strain of Bacillus ohbensis, a strain of Bacillus stearothermophilus, or a strain of Bacillus subtilis.
Most preferred, the above CGTase variants are derived from the strain Bacillus sp. Strain 1011 , the strain Bacillus sp. Strain 38-2, the strain Bacillus sp. Strain 17-1 , the strain Bacillus sp. 1 -1 , the strain Bacillus sp. Strain B1018, the strain Bacillus circulans Strain 8, or the strain Bacillus circulans Strain 251 , or a mutant or a variant thereof.
In yet another preferred embodiment, the CGTase variant of the invention is a CGTase variant derived from an enzyme obtainable from a strain of Thermoanaerobacter, which enzyme has been modified by substitution, insertion and/or deletion at one or more of the amino acid positions corresponding to the positions stated in Table 13, below. Such modification lead to CGTase variants of increased product selectivity, as indicated in the table.
Preferably the CGTase variant is derived from a strain of
Thermoanaerobacter sp. ATCC 53627, or a mutant or a variant thereof.
Figure imgf000070_0001
Figure imgf000071_0001
X - any natural amino acid residue
- conserved residue
* deleted I or absent residue In yet another preferred embodiment, the CGTase variant of the invention is a CGTase variant derived from an enzyme obtainable from a strain of Thermoanaerobacter, which enzyme has been modified by substitution, insertion and/or deletion at one or more of the amino acid residues corresponding to the positions stated in Table 14, below. Such modifications lead to CGTase variants of reduced product inhibition.
Preferably the CGTase variant is derived from a strain of Thermoanaerobacter sp. ATCC 53627, or a mutant or a variant thereof.
Figure imgf000072_0001
Figure imgf000073_0001
X = any natural amino acid residue As its most preferred embodiments, the invention provides the following
CGTase variants, derived from a strain of Thermoanaerobacter sp., preferably the strain of Thermoanaerobacter ATCC 53627, or a mutant or a variant thereof:
A CGTase variant, which variant at position 21 holds a phenylalanine residue (V21 F) or a tyrosine residue (V21Y).
A CGTase variant, which variant at position 47 holds a glutamine residue
(K47Q), or an alanine residue (K47A), or a leucine residue (K47L), or a histidine residue (K47H), or an arginine residue (K47R).
A CGTase variant, which variant at position 88 holds a lysine residue (P88K).
A CGTase variant, which variant at position 89 holds an alanine residue
(D89A), or a glycine residue (D89G).
A CGTase variant, which variant at position 91 a holds an alanine residue (F91aA) or a tyrosine residue (F91aY), or in which variant position 91a has been deleted (F91a*).
A CGTase variant, in which variant position 92 has been deleted (G92*).
A CGTase variant, which variant at position 94 holds a glutamine residue (S94Q), or a lysine residue (S94K), or an arginine residue (S94R), or a tryptophan residue (S94W), or a phenylalanine residue (S94F), or in which variant position 94 has been deleted (S94*).
A CGTase variant, which variant at position 135 holds a leucine residue
(D135L). A CGTase variant, which variant at position 143 holds a natural amino acid residue different from that of the wild-type enzyme (p143X).
A CGTase variant, which variant at position 143 holds an alanine residue
(P143A), or holds a glycine residue (P143G).
A CGTase variant, which variant at position 144 holds a natural amino acid residue different from that of the wild-type enzyme (A145X).
A CGTase variant, which variant at position 144 holds an arginine residue (A144R), or a lysine residue (A144K), or an aspartic acid residue
(A144D).
A CGTase variant, which variant at position 145 holds a natural amino acid residue different from that of the wild-type enzyme (S145X).
A CGTase variant, which variant at position 145 holds an alanine residue
(S145A), or a glutamic acid (S145E), or a tryptophan residue (S145W), or a glycine residue (S145G), or a phenylalanine residue (S145F), or a tyrosine residue (S145Y), or a leucine residue (S145L).
A CGTase variant, which variant at position 145a (via insertion) holds a natural amino acid residue (*145aX).
A CGTase variant, which variant at position 145a (via insertion) holds an isoleucine residue (*145al).
A CGTase variant, which variant at position 146 holds a natural amino acid residue different from that of the wild-type enzyme (E145X).
A CGTase variant, which variant at position 146 holds a proline residue
(E146P), or a serine residue (E146S), or an isoleucine residue (E146I), or a glutamine residue (E146Q), or a tryptophan residue (E146W), or an arginine residue (E146R).
A CGTase variant, which variant at position 147 holds a natural amino acid residue different from that of the wild-type enzyme (T147X).
A CGTase variant, which variant at position 147 holds an isoleucine residue (T147I), or a leucine residue (T147L), or an alanine residue (T147A), or a serine residue (T147S), or a tryptophan residue (T147W).
A CGTase variant, which variant at position 147a (via insertion) holds a natural amino acid residue (*147aX). A CGTase variant, which variant at position 147a (via insertion) holds an alanine residue (*147aA).
A CGTase variant, which variant at position 148 holds a natural amino acid residue different from that of the wild-type enzyme (D148X). A CGTase variant, which variant at position 148 holds an alanine residue
(D148A), or a glycine residue (D148G), or a glutamic acid residue
(D148E), or an asparagine residue (D148N).
A CGTase variant, which variant at position 149 holds a natural amino acid residue different from that of the wild-type enzyme (P149X). A CGTase variant, which variant at position 149 holds an isoleucine residue (P149I).
A CGTase variant, which variant at position 167 holds a phenylalanine residue (Y167F).
A CGTase variant, which variant at position 179 holds a serine residue (G179S), an asparagine residue (G179N), or an aspartic acid residue
(G179D).
A CGTase variant, which variant at position 180 holds a serine residue
(G180S), an asparagine residue (G180N), or an aspartic acid residue
(G180D).
A CGTase variant, which variant at position 185 holds an arginine residue (S185R), or a glutamic acid residue (S185E), or an aspartic acid residue (S185D).
A CGTase variant, which variant at position 186 holds an alanine residue
(Y186A).
A CGTase variant, which variant at position 193 holds a natural amino acid residue different from that of the wild-type enzyme (N193X).
A CGTase variant, which variant at position 193 holds a glycine residue
(N193G), or an alanine residue (N193A), or an aspartic acid residue
(N193D), or a glutamic acid residue (N193E).
A CGTase variant, which variant at position 195 holds a natural amino acid residue different from that of the wild-type enzyme (F195X).
A CGTase variant, which variant at position 196 holds a natural amino acid residue different from that of the wild-type enzyme (D196X). A CGTase variant, which variant at position 196 holds an alanine residue
(D196A), a serine residue (D196S), or a leucine residue (D196L).
A CGTase variant, which variant at position 197 holds an aspartic acid residue (L197D), or a glutamic acid residue (L197E).
A CGTase variant, which variant at position 232 holds a glutamine residue (K232Q), or an asparagine residue (K232N), or an alanine residue (K232A), or a leucine residue (K232L).
A CGTase variant, which variant at position 233 holds a glutamine residue (H233Q).
A CGTase variant, which variant at position 259 holds a phenylalanine residue (Y259F).
A CGTase variant, which variant at position 264 holds a glutamine residue (E264Q), or an alanine residue (E264A), or an asparagine residue (E264N), or a leucine residue (E264L).
A CGTase variant, which variant at position 268 holds an alanine residue
(N268A).
A CGTase variant, which variant at position 371 holds a natural amino acid residue different from that of the wild-type enzyme (D371X).
A CGTase variant, which variant at position 371 holds a glycine residue (D371G), or an asparagine residue (D371 N), or an alanine residue
(D371A), or a leucine residue (D371L), or a glutamic acid residue
(D371E).
A CGTase variant, which variant at position 375 holds a natural amino acid residue different from that of the wild-type enzyme (R375X). A CGTase variant, which variant at position 375 holds a proline residue
(R375P), or a glycine residue (R375G), or a glutamine residue (R375Q), or an asparagine residue (R375N), or an alanine residue (R375A), or a leucine residue (R375L).
A CGTase variant, which variant at position 599a (via insertion) holds a proline residue (*599aP), or an arginine residue (*599aR), or a histidine residue (*599aH).
A CGTase variant, which variant position 600 has been substituted for a different amino acid residue, in particular a phenylalanine residue (W600F), a tyrosine residue (W600Y), an arginine residue (W600R), a proline residue (W600P), a leucine residue (W600L), or an asparagine residue (W600N).
A CGTase variant, which variant at position 616 holds an alanine residue (W616A).
A CGTase variant, which variant at position 633 holds an alanine residue
(Y633A).
A CGTase variant, which variant at position 662 holds an alanine residue
(W662A).
A CGTase variant, which variant at position 47 holds a histidine residue or an arginine residue, and/or at position 135 holds a leucine residue (K47H/D135L or K47R/D135L).
A CGTase variant, which variant at positions 87-94 comprises the partial amino acid sequence IKYSGVNN, or the partial amino acid sequence INDSGVNN, and/or at positions 143-151 comprises the partial amino acid sequence GRAGTNPGF, or at positions 143-145 comprises the partial amino acid sequence GRW, and/or at position 195 holds a tyrosine residue (F195Y).
A CGTase variant, which variant at positions 87-94 comprises the partial amino acid sequence INDSGVNN, and/or at positions 146-150 comprises the partial amino acid sequence SDQPS.
A CGTase variant, which variant at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAETWPAF.
A CGTase variant, which variant at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAETWPAF, and which variant at position 195 holds a leucine residue (F195L).
A CGTase variant, which variant at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAEADPNF.
A CGTase variant, which variant at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAEADPNF, and which variant at position 195 holds a leucine residue (F195W).
A CGTase variant, in which variant positions 92 and 94 have been deleted (G92*/S94*).
A CGTase variant, which variant at position 143 holds an alanine residue, and at position 144 holds an arginine residue (P143A/A144R). A CGTase variant, which variant at position 143 holds a glycine residue, and at position 144 holds an arginine residue, and at position 145 holds a tryptophan residue (P143G/A144R/S145W).
A CGTase variant, which variant at position 143 holds a glycine residue, and at position 144 holds an arginine residue, and at position 145 holds a tryptophan residue (P143G/A144R/S145W), and which variant at position 179 holds a serine residue (G179S), an asparagine residue (G179N), or an aspartic acid residue (G179D), and/or at position 180 holds an asparagine residue (G180N), or an aspartic acid residue
(G180D).
A CGTase variant, which variant at positions 143-148 comprises the partial amino acid sequence GRA**A, the partial amino acid sequence GRAAAA, the partial amino acid sequence GRPAAA, the partial amino acid sequence GRAPAA, or the partial amino acid sequence GRGPAA.
A CGTase variant, which variant at positions 143-151 comprises the partial amino acid sequence GRAGTNPG.
A CGTase variant, which variant at positions 143-151 comprises the partial amino acid sequence GRAGTNPG, and at position 195 holds a tyrosine residue (F195Y).
A CGTase variant, which variant at position 144 holds an arginine residue, at position 145 holds an alanine residue, and at position 146 holds a proline residue (A144R/S145A/E146P). A CGTase variant, which variant at position 145 holds an alanine residue, and at position 145a (via insertion) holds an isoleucine residue (S145A/*145al).
A CGTase variant, which variant at position 145 holds an alanine residue, and at position 146 holds a glycine residue (S145A/E146G).
A CGTase variant, which variant at position 145 holds a leucine residue, and at position 148 holds an asparagine residue (S145L/D148N). A CGTase variant, which variant at position 145 holds a glutamic add residue, and in position 146 holds a proline residue or a glutamine residue (S145E/E146P or S145E/E146Q).
A CGTase variant, which variant at position 145 holds a tryptophan residue, and in position 146 holds a tryptophan residue, or an isoleucine residue, or an arginine residue (S145W/E146W or S145W/E146I or S145W/E146R).
A CGTase variant, which variant at position 145 holds an alanine residue, at position 145a (via insertion) holds an isoleucine residue, and at position 148 holds a glutamic acid residue (S145A/*145al/D148E). A CGTase variant, which variant at position 145a (via insertion) holds an isoleucine residue, and at position 148 holds a glutamic acid residue (*145al/D148E).
A CGTase variant, which variant at position 616 holds an alanine residue, and at position 662 holds an alanine residue (W616A/W662A).
Methods of Producing CGTase Variants
The production of the CGTase variants of the invention follows the general principles of recombinant DNA technology, e.g. as described by Sambrook et al. [Sambrook J, Fritsch E F, Maniatis T; Molecular Cloning: A Laboratory Manual,
Cold Spring Harbor Laboratory Press, 1989, New York], and known to the person skilled in the art.
Formally, the production takes rise in the provision of a DNA construct encoding CGTase variant of the invention. DNA Constructs
In another aspect, the invention provides a DNA construct encoding a CGTase variant of the invention. As defined herein, the term "DNA construct" is intended to indicate any nucleic acid molecule of cDNA, genomic DNA, synthetic DNA or RNA origin. The term "construct" is intended to indicate a nucleic acid segment which may be single- or double-stranded, and which may be based on a complete or partial naturally occurring nudeotide sequence encoding the CGTase variant of interest. The construct may optionally contain other nucleic add segments.
The DNA construct of the invention may be prepared by suitably modifying a DNA sequence encoding the precursor CGTase, which modification may bring about:
(i) introduction of one or more amino acid residues at one or more different sites in the amino add sequence; and/or
(ii) substitution of one or more amino add residues at one or more different sites in the amino acid sequence; and/or
(iii) deletion of one or more amino acid residues at one or more sites in the amino acid sequence.
The modification of the DNA sequence may be performed by site- directed mutagenesis or by random mutagenesis, or by a combination of these techniques in accordance with well-known procedures, e.g. as described by Sambrook et al., op cit.
In more preferred embodiments, the DNA construct of the invention comprises one or more of the partial oligonucleotide sequences (primers) described in the examples below. These partial oligonucleotide sequences are in particular
5'-G GTC GTT TAC CAG GCG CCG AAC TGG-3' (Y633A);
5'-GC GAG CTC GGG AAC GCG GAC CCG-3' (W616A:);
5'-CC GTC ACC GCG GAA GGC GGC-3' (W662A);
5'-GC ATC TAC AAG GGC CTG TACGAT CTC G-3' (N193G);
5'-GCA TCA TCA ATG GAT CCG GCG TAA AC-3' (Y89G); 5'-CAT ACG TCG CCC GCT AGC ATT TCC GAC CAG CCT TCC-3'
(145al);
5'-CG GGC GGG ACC GGT CCG GAC AAC CG-3' (D371 G);
5'-G TCG GGC GGT ACC AAT CCG GAC AAC C-3' (D371 N); 5'-CG TTC ATC GAT CAG CAT GAC ATG G-3' (N326Q);
5'-GC ATC ATC AAT GAT TCC GGA GTA AAC AAC ACG GC-3' (Y89D); and
5'-G CCC GCC TCT CCG GAC CAG CCT TC-3' (S146P); and the the partial oligonucleotide sequences (primers) described as primers A1-A24, primers B1-B15, and C1-C9, of Examples 5, 6 and 7.
Expression Vectors
Subsequent to modification, the CGTase variant may be obtained by combining the DNA construct encoding the CGTase variant of the invention with an appropriate expression signal in an appropriate expression vector.
The expression vector of the invention may be any expression vector that is conveniently subjected to recombinant DNA procedures, and the choice of vector will often depend on the host cell into which it is to be introduced. Thus, the vector may be an autonomously replicating vector, i.e. a vector which exists as an extra- chromosomal entity, the replication of which is independent of chromosomal replication, e.g. a plasmid. Alternatively, the vector may be one which, when introduced into a host cell, is integrated into the host cell genome and replicated together with the chromosome(s) into which it has been integrated.
In the expression vector of the invention, the DNA sequence encoding the CGTase variant preferably is operably linked to additional segments required for transcription of the DNA. In general, the expression vector is derived from plasmid or viral DNA, or may contain elements of both. The term, "operably linked" indicates that the segments are arranged so that they function in concert for their intended purposes, e.g. transcription initiates in a promoter and proceeds through the DNA sequence coding for the CGTase variant.
Thus, in the expression vector of the invention, the DNA sequence encoding the CGTase variant preferably should be operably connected to a suitable promoter and terminator sequence. The promoter may be any DNA sequence which shows transcriptional activity in the host cell of choice and may be derived from genes encoding proteins either homologous or heterologous to the host cell. The procedures used to ligate the DNA sequences coding for the CGTase variant, the promoter and the terminator, respectively, and to insert them into suitable vectors are well known to persons skilled in the art (cf., for instance, Sambrook et al., op cif)
The promoter may be any DNA sequence which shows transcriptional activity in the host cell of choice and may be derived from genes encoding proteins either homologous or heterologous to the host cell.
Examples of suitable promoters for directing the transcription of the DNA encoding the CGTase variant of the invention in bacterial host cells indude the promoter of the Bacillus stearothermophilus maltogenic amylase gene, the Bacillus licheniformis alpha-amylase gene, the Bacillus amyloliquefaciens BAN amylase gene, the Bacillus subtilis alkaline protease gen, or the Bacillus pumilus xylanase or xylosidase gene, or by the phage Lambda PR or PL promoters or the E. coli lac, trp or tac promoters.
Examples of suitable promoters for use in yeast host cells include promoters from yeast glycolytic genes [Hitzeman et al., J. Biol. Chem. 1980 255 12073 - 12080; Alberand Kawasaki, J. Mol. APPI. Gen. 1982 1 419 - 434] or alcohol dehydrogenase genes [Young et al., in Genetic Engineering of Microorganisms for Chemicals (Hollaender et al. Eds.), Plenum Press, New York, 1982], or the TPl 1 [US 4.599,311] or ADH2-4c [Russell et al., Nature 1983 304 652 - 654] promoters.
Examples of suitable promoters for use in filamentous fungus host cells are, for instance, the ADH3 promoter [McKnight et al., EMBO J. 198542093 - 2099] or the tpiA promoter. Examples of other useful promoters are those derived from the gene encoding A. oryzae TAKA amylase, Rhizomucor miehei aspartic proteinase, A. niger neutral α-amylase, A. niger acid stable α-amylase, A. niger or A. awamori glucoamylase (gluA), Rhizomucor miehei lipase, A. oryzae alkaline protease, A. oryzae triose phosphate isomerase or A. nidulans acetamidase. Preferred are the TAKA-amylase and gluA promoters.
The expression vector of the invention may further comprise a DNA sequence enabling the vector to replicate in the host cell in question. The expression vector may also comprise a selectable marker, e.g. a gene the product of which complements a defect in the host cell, such as the gene coding for dihydrofolate reductase (DHFR) or the Schizosaccharomyces pombe TPI gene [Russell PR; Gene 1985 40 125-130], or one which confers resistance to a drug, e.g. ampicillin, kanamycin, tetracydin, chloramphenicol, neomycin, hygromycin ormethotrexate. For filamentous fungi, selectable markers include amdS. pyrG. argB. niaD and sC.
To direct the CGTase into the secretory pathway of the host cells, a secretory signal sequence (also known as a leader sequence, prepro sequence or pre sequence) may be provided in the expression vector. The secretory signal sequence is joined to the DNA sequence encoding the CGTase in the correct reading frame. Secretory signal sequences are commonly positioned 5' to the DNA sequence encoding the CGTase variant. The secretory signal sequence may be that normally associated with the CGTase or may be from a gene encoding another secreted protein.
In a preferred embodiment, the expression vector of the invention may comprise a secretory signal sequence substantially identical to the secretory signal encoding sequence of the Bacillus licheniformis α-amylase gene, e.g. as described in WO 86/05812.
Also, measures for amplification of the expression may be taken, e.g. by tandem amplification techniques, involving single or double crossing-over, or by multicopy techniques, e.g. as described in US 4,959,316 or WO 91/09129. Alternatively the expression vector may include a temperature sensitive origin of replication, e.g. as described in EP 283,075.
Procedures for ligating DNA sequences encoding the CGTase variant, the promoter and optionally the terminator and/or secretory signal sequence, respectively, and to insert them into suitable vectors containing the information necessary for replication, are well known to persons skilled in the art (cf., for instance, Sambrook et al., op cit) Host Cells
In yet another aspect the invention provides a host cell comprising the DNA construct of the invention and/or the recombinant expression vector of the invention.
The host cell of the invention, into which the DNA construct or the recombinant expression vector of the invention is to be introduced, may be any cell, preferably a non-pathogenic cell, which is capable of producing the CGTase variant and includes bacteria, yeast, fungi and higher eukaryotic cells. Examples of bacterial host cells which, on cultivation, are capable of producing the CGTase variant of the invention are grampositive bacteria such as strains of Bacillus, in particular a strain of B. subtilis, B. licheniformis, B. lentus, B. brevis, B. stearothermophilus, B. alkalophilus, B. amyloliquefaciens, B. coagulans, B. circulans, B. lautυs, B. megatherium, B. pυmilus, B. thuringiensis or B. agaradherens, or strains of Streptomyces, in particular a strain of S. lividans or S. murinus, or gramnegative bacteria such as Echerichia coli. The transformation of the bacteria may be effected by protoplast transformation or by using competent cells in a manner known per se (cf. Sambrook et al., op cit).
When expressing the CGTase variant in bacteria such as E. coli, the
CGTase may be retained in the cytoplasm, typically as insoluble granules (known as inclusion bodies), or may be directed to the periplasmic space by a bacterial secretion sequence. In the former case, the cells are lysed and the granules are recovered and denatured after which the CGTase is refolded by diluting the denaturing agent. In the latter case, the CGTase may be recovered from the periplasmic space by disrupting the cells, e.g. by sonication or osmotic shock, to release the contents of the periplasmic space and recovering the CGTase variant.
Examples of suitable yeasts cells include cells of Saccharomyces spp. or Schizosaccharomyces spp., in particular strains of Saccharomyces cerevisiae or Saccharomyces kluyveri. Methods for transforming yeast cells with heterologous DNA and producing heterologous polypeptides therefrom are described, e.g. in US 4,599,311 , US 4,931,373, US 4,870,008, 5,037,743, and US 4,845,075, all of which are hereby incorporated by reference. Transformed cells are selected by a phenotype determined by a selectable marker, commonly drug resistance or the ability to grow in the absence of a particular nutrient, e.g. leucine. A preferred vector for use in yeast is the POT1 vector disclosed in US 4,931 ,373. The DNA sequence encoding the CGTase variant of the invention may be preceded by a signal sequence and optionally a leader sequence , e.g. as described above. Further examples of suitable yeast cells are strains of Kluyveromyces, such as K. lactis, Hansenυla, e.g. H. polymorpha, or Pichia, e.g. P. pastoris [Gleeson et al., J. Gen. Microbiol. 1986 132 3459-3465; US 4,882,279].
Examples of other fungal cells are cells of filamentous fungi, e.g. Aspergillυs spp., Neurospora spp., Fusarium spp. or Trichoderma spp., in particular strains of A. oryzae, A. nidulans or A. niger. The use of Aspergillus spp. for the expression of proteins have been described in e.g., EP 272,277 and EP 230,023. The transformation of F. oxysporum may, for instance, be carried out as described by Malardier et al., Gene 1989 78 147-156.
The transformed or transfected host cell described above is then cultured in a suitable nutrient medium under conditions permitting the expression of the CGTase, after which the resulting CGTase variant is recovered from the culture.
The medium used to culture the cells may be any conventional medium suitable for growing the host cells, such as minimal or complex media containing appropriate supplements. Suitable media are available from commercial suppliers or may be prepared according to published recipes (e.g. in catalogues of the American Type Culture Collection). The CGTase variant produced by the cells may then be recovered from the culture medium by conventional procedures including separating the host cells from the medium by centrifugation or filtration, precipitating the proteinaceous components of the supernatant or filtrate by means of a salt, e.g. ammonium sulphate, purification by a variety of chromatographic procedures, e.g. ion exchange chromatography, gelfiltration chromatography, affinity chromatography, or the like, dependent on the type of CGTase in question.
Method of Producing CGTase Variants
In a still further aspect, the present invention provides a method of producing the CGTase variant of the invention, wherein a suitable host cell, which has been transformed with a DNA sequence encoding the CGTase, is cultured under conditions permitting the production of the enzyme, and the resulting enzyme is recovered from the culture.
The medium used to culture the transformed host cells may be any conventional medium suitable for growing the host cells in question. The expressed CGTase may conveniently be secreted into the culture medium and may be recovered therefrom by well-known procedures including separating the cells from the medium by centrifugation or filtration, precipitating proteinaceous components of the medium by means of a salt such as ammonium sulphate, followed by chromatographic procedures such as ion exchange chromatography, affinity chromatography, or the like. Industrial Applications
The CGTase variant of the invention find application in processes for the manufacture of cyclodextrins for various industrial applications, particularly in the food, cosmetic, chemical, agrochemical and pharmaceutical industries.
Therefore, in another aspect, the invention provides CGTase variants for use in a process for the manufacture of cyclodextrins, in particular α-, β-, γ-, δ-, ε-, and/or ζ-cyclodextrins. In a more preferred embodiment, the invention provides CGTase variants for use in a process for the manufacture of α-, β- and γ- cydodextrins, or mixtures hereof. In another preferred embodiment, the invention provides CGTase variants for use in a process for the manufacture of δ-, ε-, and ζ- cydodextrins, or mixtures hereof.
The CGTase variants of the invention may also be used in a process for the manufacture of linear oligosaccharides, in particular linear oligosaccharides of 2 to 12 glucose units, preferably linear oligosaccharides of 2 to 9 glucose units.
In yet another preferred embodiment, the CGTase variants of the invention may be used for in situ generation of cyclodextrins. In this way the CGTase variants of the invention may be added to a substrate containing medium in which the enzyme variants are capable of forming the desired cyclodextrins. This application is particularly well suited for being implemented in methods of producing baked products, in methods for stabilizing chemical products during their manufacture, and in detergent compositions.
Certain cyclodextrins are known to improve the quality of baked products. The CGTase variants of the invention therefore also may be used for implementation into bread-improving additives, e.g. dough compositions, dough additives, dough conditioners, pre-mixes, and similar preparations conventionally used for adding to the flour and/or the dough during processes for making bread or other baked products.
Cyclodextrins have an inclusion ability useful for stabilization, solubilization, etc. Thus cyclodextrins can make oxidizing and photolytic substances stable, volatile substances non-volatile, poorly-soluble substances soluble, and odoriferous substances odorless, etc. and thus are useful to encapsulate perfumes, vitamins, dyes, pharmaceuticals, pesticides and fungicides. Cyclodextrins are also capable of binding lipophilic substances such as cholesterol, to remove them from egg yolk, butter, etc.
Cyclodextrins also find utilization in products and processes relating to plastics and rubber, where they have been used for different purposes in plastic laminates, films, membranes, etc. Also cyclodextrins have been used for the manufacture of biodegradable plastics.
EXAMPLES
The invention is further illustrated with reference to the following examples which are not intended to be in any way limiting to the scope of the invention as claimed.
EXAMPLE 1
Crystal Structure and Molecular Modelling of a CGTase Enzymes
The CGTase from Bacillus circulans Strain 251 [cf. Lawson C L, van Montfort R, Strokopytov B, Rozeboom H J, Kalk K H, de Vries G E, Penninga D, Dijkhuizen L, and Dijkstra B W, J. Mol. Biol. 1994 236 590-600] was soaked in a buffer solution containing the non-hydrolyzable tetrasaccharide acarbose, and an X- ray structure of the CGTase including the pseudo-tetrasaccharide located in the catalytic site was obtained, cf. Strokopytov et al. [Strokopytov B, Penninga D, Rozeboom H J; Kalk K H, Dijkhuizen L and Dijkstra B W, Biochemistry 1995 34 2234-2240]. Coordinates of this structure have been deposited with the Protein Data Bank, Biology Department, Bldg. 463, Brookhaven National Laboratory, P.O. Box 5000, Upton, NY 11973-5000, USA, under the entry code 1 CXG.
By additional soaking in a buffer containing maltoheptaose, a nonasaccharide (A-l) was formed in an enzyme-substrate-complex structure. Coordinates of this structure have been deposited with the Protein Data Bank, Biology Department, Bldg. 463, Brookhaven National Laboratory, P.O. Box 5000, Upton, NY 11973-5000, USA, under the entry code 1 DIJ. By further adding a trisaccharide (J-L) to the non-reducing end of the nonasaccharide by computer modelling, the substrate binding cleft and the residues involved herein in the A and B domain have been located. By aid of a computer program, Insight™ Software Package from Biosym, using subset-zone function, positions within seleded distances could be identified. In this way Tables 1-4 were generated.
The residues listed in Fig. 1 are referring to Bacillus circulans Strain 251 CGTase and comprise only the closest contacts between the substrate and the enzyme. By changing the number of hydrogen-bonds and other interactions between the enzyme and the substrate, the product selectivity can be altered. Normally, cleavage of the starch takes place between glucose unit B and C in the model.
By computer modelling, a trisaccharide has been added to the reducing end of the acarbose (A) and to the non-reducing end of a pentasaccaride located in the E-domain, and hereby linking together the substrate binding sites in the A-B and
E-domains. In total a substrate of 20 glucose-units has been located in the enzyme.
The structure of a Thermoanaerobacter CGTase was modelled based on the known structure of Bacillus circulans CGTase. Again the computer program Insight™ from Biosym was employed, using the homology module, according to the manufacturers instructions. The substrate found in Bacillus circulanswas docked into the Thermoanaerobacter model, and the positions stated in Tables 5-7 identified.
EXAMPLE 2
Construction of α-cyclodextrin Producing CGTase Variants from Bacillus
This example describes the construction of three α-cyclodextrin producing CGTase variants, in which site-directed mutagenesis have lead to an altered number of hydrogen bonds in the subsites of the active site deft. The variants are derived from a Bacillus circulans Strain 251 CGTase (i.e. the wild-type enzyme), obtained as described by Lawson et al. [Lawson C L, van Montfort R, Strokopytov B, Rozeboom H J, Kalk K H, de Vries G E, Penninga D, Dijkhuizen L, and Dijkstra B W, J. Mol. Biol. 1994 236 590-600].
For construction of the variants a method based on PCR for site-directed mutagenesis. The following oligonucleotides (primers) were used to produce the mutations: Y89G: 5'-GCA TCA TCA ATG GAT CCG GCG TAA AC-3' (Bam HI); and
S146P: 5'-G CCC GCC TCT CCG GAC CAG CCT TC-3' (BspE I). Successful mutagenesis resulted in appearance of the underlined restriction sites, allowing rapid screening of potential mutants.
The mutations were confirmed by restriction analysis and sequencing. Mutant proteins were produced by the use of an amylase and protease negative Bacillus subtilis strain, and purified using affinity chromatography.
CGTase activity was determined by incubating appropriately diluted enzyme solutions with substrate in 10 mM sodium citrate, pH 6.0, for 5-10 minutes at 50ºC.
Cyclodextrin forming activity (transglycosylation activity) was determined using 5% Paselli™ SA2 (i.e. partially hydrolysed potato starch with an average degree of polymerization of 50, available from AVEBE, Foxhol, The Netherlands) as substrate. The β-cyclodextrin formed was determined with phenolphthalein. One unit of activity is defined as the amount of enzyme able to produce 1 μmol of β- cyclodextrin per minute, α- and β-cyclodextrin formation was subsequently determined by use of HPLC (cf. below).
Cyclodextrin formation was also determined under industrial production process conditions. For this purpose 0.1 U/ml CGTase was incubated with 10% Paselli™ WA4 (i.e. jet-cooked, pre-gelatinized drum-dried starch) in a 10 mM sodium citrate buffer (pH 6.0) at 50ºC for 45 hours. Samples were collected at regular intervals of time, boiled for 5 minutes, and the products formed analyzed by HPLC using a 25 cm Econosil-NH2 10 micron column (Alltech Associates Inc., USA) eluted with acetonitril/water (60/40% v/v) at a flow rate of 1 ml per minute.
Results
Variants were designed in order to increase α-cyclodextrin formation. In the first experiment, a tyrosine residue at position 89 was changed into an aspartic acid residue (Y89D), which introduces an additional hydrogen bond with subsite F of the substrate, cf. Fig. 1. This gives rise to stronger binding of the amylose chain in the active site cleft, with the formation of smaller cyclodextrins. In result an increase in α-cyclodextrin forming activities was detected, with a simultaneous decrease in the β-cyclodextrin forming activity, as seen from the ratio of cyclodextrins produced from Paselli™ WA4, cf. Table 16, below, and in the cyclodextrin formation profiles, cf. Fig. 2B. In a second experiment, serine at position 146 was changed into a proline residue (S146P). This gives rise to a dramatic change in the hydrogen network at subsite I of the substrate, cf. Fig. 1. As seen from Table 15 below, this mutation has a substantial impact on the cyclodextrin forming activities. The α- cyclodextrin forming activity increased drastically at the expense of the β-cydodextrin forming activity. There was little effect on the γ-cyclodextrin forming activity. This also corresponds with the ratio of cyclodextrins determined and presented in Table 16 and in Fig. 2C.
In a third experiment, a double mutation was accomplished. In this experiment tyrosine at position 89 was changed into an aspartic acid residue, and serine at position 146 was changed into a proline residue (Y89D/S146P). These mutations results in a combination of the effects seen from the two single mutations carried out as described above. This variant possesses the largest α-cyclodextrin forming activity, cf. Table 15, and the largest formation of α-cyclodextrin, cf. Table 16 and Fig. 2D.
Figure imgf000090_0001
Figure imgf000091_0001
EXAMPLE 3
Mutations in the E-domain of a Bacillus CGTase
This example describes the construction of two CGTase variants, holding mutations in the E domain cleft. The variants are derived from a Bacillus circulans Strain 251 CGTase (i.e. the wild-type enzyme), obtained as described by Lawson et al. [Lawson C L, van Montfort R, Strokopytov B, Rozeboom H J, Kalk K H, de Vries
G E, Penninga D, Dijkhuizen L, and Dijkstra B W; J. Mol. Biol. 1994 236 590-600].
Two maltose binding sites (MBS) have been identified in the E domain and in this experiment it is found that these sites are of particular importance for the raw starch binding properties of the enzyme. The first site (MBS1) indudes tryptophan at positions 616 and 662, which bind a maltose unit through van der Waals contacts of their indole groups with the glucose rings of the substrate. In the second site (MBS2), the in most cases conserved tyrosine at position 633, forms van der Waals contacts with a glucose residue of the substrate. Hydrogen bonds with surrounding residues enhance binding at these sites. MBS2 is located near the groove leading to the active site.
Mutations were introduced by a method based on two PCR reactions using VENT-DNA polymerase. For each mutation specific oligonucleotides were developed. The mutations were confirmed by restriction analysis and sequencing. Variants were obtained from an amylase and protease negative Bacillus subtilis strain and were purified using affinity chromatography.
Bacterial Strains and Plasmids: Escherichia coli MC 1061 [Meissner P S, Sisk WP, Berman M L; Proc. Natl. Acad. Sci. USA 1987 84 4171-4175] was used for recombinant DNA manipulations and site-directed mutagenesis. E coli DH5α [Hanahan D; J. Mol. Biol. 1983 166 557] was used for the production of monomeric supercoiled plasmid DNA for sequencing. CGTases variants were produced with the α-amylase and protease negative Bacillus subtilis Strain DB104A [Smith H, de Jong A, Bron S, Venema G; Gene 1988 70 351-361]. The fragment containing the kanamycin-resistance marker was ligated with the largest fragment from plasmid pDP66S [Penninga D, Strokopytov B, Rozeboom H J, Lawson C L, Dijkstra B W, Bergsma J, Dijkhuizen L; Biochemistry 1995 34 3368-3376] containing the Bacillus circulans CGTase gene, digested with Hlndlll and Xbal (made blunt with Klenow polymerase). The resulting CGTase protein expression shuttle vector pDP66K, with the CGTase gene under control of the erthromycin-inducible p32 promotor [van der Vossen J M B M, Kodde J, Haandrikman A J, Venema G, Kok J; APPI. Environ. Microbiol. 1992 58 3142-3149], was transformed to E. coli MC1061 under seledion for erythromycin and kanamycin resistance, d. Fig. 3.
Construction of CGTase Variants: As only relatively low stability with plasmid pDP66S (8.5 kb) [Saenger W, Anoew. Chem. 1980 19 344-362] was found, pDP66K (7.7 kb) was constructed, cf. Fig. 3, with the CGTase gene under the control of the strong p32 promotor [van der Vossen J MB M, Kodde J, Haandrikman A J, Venema G, Kok J; APPI. Environ. Microbiol. 1992 58 3142-3149]. Plasmid pDP66K containing the additional antibiotic resistance marker for kanamycin appeared to be considerably more stable in E. coli as well as in B. subtilis cells than plasmid pDP66S containing the streptomycin/spectinomycin resistance cassette. Using this shuttle vector, a high extracellular production of wild-type enzyme and CGTase variants was obtained reproducibly in batch fermentations with the α- amylase and protease negative B. subtilis Strain DB104A. A single 5 I erlenmeyer flask with 1 I B. subtilis Strain DB104A culture allowed purification to homogeneity of up to 25 mg of the CGTase variants. Mutations were constructed via site-directed (PCR) mutagenesis. Using specific oligonucleotide primers a mutation frequency close to 70% was observed. All mutations were confirmed by restriction analysis and DNA sequencing.
Growth Conditions: Plasmid carrying bacterial strains were grown on LB medium in presence of the antibiotics erythromycin and kanamycin, at concentrations of 100 and 5 μg/ml for E coli and Bacillus subtilis, respectively [Sambrook et al., op cit]. When appropriate, agar plates contained 1 % starch to screen for halo formation. Bacillus subtilis Strain DB 104A was grown in a 5 I flask, containing 1 I medium with 2% tryptone, 0.5% yeast extract, 1% sodium chloride and 1% casamino adds (pH 7.0) with 10 μg/ml erythromycin and 5 μg/ml kanamydn.
DNA Manipulations: Restriction endonucleases and Klenow enzyme were purchased from Pharmacia LKB Biotechnology, Sweden, and used according to the manufacturers instructions. DNA manipulations and calcium chloride transformation of E coli strains were accomplished as described [Sambrook et al., op cit]. Transformation of Bacillus subtilis was performed as described by Bron [Harwood C R and Cutting S M, Eds.; Modern Microbiological Methods for Bacillus. 1990, Wiley & Sons, New York/Chichester; "Plasmids", pp. 146-147].
Site-directed Mutagenesis: To introduce mutations we used a method based on two PCR reactions using VENT-DNA polymerase (New-England Biolabs, Beverly, MA, USA), in which a first PCR was carried out using a mutagenesis primer on the coding strand plus a primer 910-1050 bp downstream on the template strand. The product of this reaction (910-1050 bp) was subsequently used as primer in the second PCR together with a primer 760-900 bp upstream on the coding strand. The product of the last reaction (1800 bp) was cut with Bgll and Hiπdlll and exchanged with the corresponding fragment (600 bp) from the vector pDP66K. The resulting (mutant) plasmid was transformed to E coli MC 1061 cells. The following oligonucleotides (primers) were used to produce the mutations:
Y633A: 5'-G GTC GTT TAC CAG GCG CCG AAC TGG-3'
W616A: 5'-GC GAG CTC GGG AAC GCG GAC CCG-3'
W662A: 5'-CC GTC ACC GCG GAA GGC GGC-3' Successful mutagenesis resulted in the appearance of the underlined restriction sites, allowing rapid screening of potential mutations. For Y633A this restriction site was Narl, for W616A Sad, and for W662A Sacll.
DNA Sequencing: Plasmid pDP66K carrying the right restriction site was transformed to E. coli DH5α cells. DNA sequence determination was performed on supercoiled plasmid DNA using the dideoxy-chain termination method [Sanger F,
Coυlson A R; J. Mol. Biol. 1975 94 441-448] and the T7-sequendng kit from
Pharmada LKB Biotechnology, Sweden.
Production and Purification of CGTase Variants: Plasmid pDP66K, carrying positively characterized mutant CGtase genes, was transformed to Bacillus subtilis Strain DB104A. The organism was grown to an optical density of 4.5 determined at 600 nm in a 5 I flask (for approx. 36 hours). Under these conditions high extracellular CGTase levels were produced. The culture was centrifuged (x 10,000 g) at 4ºC for 30 minutes. The (mutant) CGTases were further purified to homogeneity by affinity chromatography using a 30 ML α-cyclodextrin-Sepharose- 6FF column (Pharmada, Sweden) [Sundberg L, Porath J; J. Chromatoor. 1974 90 87-98] with a maximal capacity of 3.5 mg protein per ml. After washing with 10 mM sodium acetate buffer (pH 5.5), bound CGTase was eluted with the same buffer containing 10 mg/ml α-cyclodextrin. Enzyme Assays
β-cyclodextrin Forming Activity: β-cydodextrin forming activity was determined using 5% Paselli™ SA2 (i.e. partially hydrolysed potato starch with an average degree of polymerization of 50, available from AVEBE, Foxhol, The Netherlands) as substrate and after incubation for 3 minutes at 50ºC. 0.1-0.1 units of activity were used. The β-cyclodextrin formed was determined based on its ability to form a stable colorless inclusion complex with phenolphthalein. One unit of activity is defined as the amount of enzyme able to form 1 μmol of β-cyclodextrin per minute.
Raw Starch Binding Properties: Raw starch binding properties were studied by incubating 6 μg/ml of enzyme with increasing amounts (0-10%) of granular potato starch (Paselli™ SA2, available from AVEBE, Foxhol, The Netherlands) for 1 hour at 4°C, with and without 0.1 mM of β-cyclodextrin (equilibrium was reached within 10 minutes). After incubation, protein bound to the starch granules was spun down for 1 minute at 4°C and at 10,000xg, and the remaining β-cyclodextrin forming activity of the supernatant was determined as described above.
Kinetic Studies: Kinetic studies on Paselli™ SA2 (AVEBE, Foxhol, The
Netherlands) were performed by determination of the β-cydodextrin forming activity of the enzyme on Paselli™ concentrations ranging from 0 to 5%, with and without addition of 0.1 or 0.2 mM of β-cyclodextrin. In these experiments approx. 0.6 μg/ml (0.15-0.18 units) of enzyme was used.
Kinetic Studies: Alternatively, kinetic studies on raw starch were performed by incubating 6 μg/ml of enzyme for 10 minutes with raw starch concentrations in the range of from 0 to 50%. β-cyclodextrin formation was determined as described above.
The data collected from these kinetic and binding studies were fitted using the Hill equation, yielding Ymax and K50 values for the binding studies, and Vmax and K50 values for the kinetic studies. K, values were calculated as follows.
For non-competitive inhibition:
For competitive inhibition:
Figure imgf000095_0001
Results
Since maltose binding site 1 (MBS1) includes two tryptophan residues, the double mutation W616A/W662A was constructed. In this way we created comparable changes in the two binding sites, which were designed to completely remove the hydrophobic interactions of the aromatic residues with the glucose units of the substrate. The two separate CGTase variants, W616A and W662A, gave intermediate results compared to the double mutant, W616A/W662A.
From the results presented in Figs. 4-6, in which the curves are better fitted to a Hill equation than to a Michaelis-Menten equation, indicates that there is a form of cooperativity involved in the reaction and binding kinetics. The results of the raw starch binding experiments are presented in Table 17 and Fig. 4. Determination of raw starch binding revealed a sharp decrease for the W616A/W662A variant, indicating that MBS1 is required and has the highest affinity for substrate binding. The Y633A variant shows only small decreases in affinity and Ymax, which suggests that MBS2 has only little contribution to raw starch binding.
The effect of β-cyclodextrin on raw starch binding indicates that it can inhibit the binding by competition with a starch chain for the binding sites of the enzyme. This effect is more pronounced for the variants produced as compared to the wild-type, indicating that when one MBS is deleted, competition of β-cyclodextrin with raw starch for the remaining site is stronger. This also indicates a form of cooperativity between MBS's.
The Hill factor "n", indicating the degree of cooperativity involved in raw starch binding is strongly decreased in the W616A/W662A variant, showing that MBS1 contributes highly to cooperative binding. The Y633A variant has the same "n" value as the wild-type enzyme. This suggests that sites other than MBS2 cooperate with MBS1 in binding.
The results of the reaction kinetics on hydrolysed potato starch (Paselli™ SA2) are presented in Table 18 and Fig. 5. These results show another role for MBS2 in the wild-type enzyme. The lower affinity for Paselli™ of the Y633A variant suggests that the substrate might be less efficiently guided to the active site in the absence of this binding site. This is also supported by the decrease of factor "n" to approx. 1 , which shows that the cooperativity observed in reaction kinetics has been lost in this variant. The shift from non-competitive to competitive inhibition by β- cydodextrin implies that MBS2 is responsible for the non-competitive produd inhibition. The results with the W616A/W662A variant show that MBS1 is only slightly involved in degradation of Paselli™.
The results of the reaction kinetics on raw starch are presented in Table 19 and Fig. 6. These results show a high decrease in affinity when either of the MBS's are deleted, indicating that for activity on raw starch both MBS's are equally important. At high raw starch concentrations, however, the curve representing the W616A/W662A variant aligns to that of the wild-type enzyme, suggesting that a binding site other than MBS1 takes over its function. This site might be MBS3 on the C domain. From these experiments it is concluded that the E domain with its binding sites is required for the conversion of raw starch into cyclodextrins. The enzyme binds to the raw starch granule via MBS1 , while MBS2 guides the starch chain protruding from the granule to the active site.
Figure imgf000097_0001
Figure imgf000098_0001
Figure imgf000098_0002
EXAMPLE 4
Construction of β-and γ-cyclodextrin Producing CGTase Variants from Bacillus
This example describes the construction of several β-and γ-cyclodextrin producing CGTase variants, in which site directed mutagenesis has lead to an altered number of hydrogen bonds in the active site cleft. The variants are derived from a Bacillus circulans Strain 251 CGTase (i.e. the wild-type enzyme), obtained as described by Lawson et al. [Lawson C L, van MOntfort R, Strokopytov B, Rozeboom H J, Kalk K H, de Vries G E, Penninga D, Dijkhuizen L and Dijkstra B W, J. Mol. Biol. 1994 236 590-600].
Mutations were introduced with a PCR method using VENT-DNA polymerase (New-England Biolabs, Beverly, MA, USA). A first PCR reaction was carried out with a mutagenesis primer for the coding strand, plus a primer downstream on the template strand. The reaction product was subsequently used as primer in a second PCR reaction together with a primer upstream on the coding strand. The produd of the last reaction was cut with PvuU and Sa/I and exchanged with the corresponding fragment (1200 bp) from the vector pDP66K (cf. Fig. 3). The resulting (mutant) plasmid was transformed to E coli MC1061 cells [Meissner P S, Sisk W P, Berman M L; Proc. Natl. Acad. Sci. USA 1987 84 4171-4175].
The following oligonucleotides (primers) were used to produce the mutations:
N193G: 5'-GC ATC TAC AAG GGC CTG TACGAT CTC G-3' (Dra II);
Y89G: 5'-GCA TCA TCA ATG GAT CCG GCG TAA AC-3' (Bam HI);
*145al: 5'-CAT ACG TCG CCC GCT AGC ATT TCC GAC CAG CCT TCC-3'
(Nhe I);
D371G: 5'-CG GGC GGG ACC GGT CCG GAC AAC CG-3' (Pin Al);
D371N: 5'-G TCG GGC GGT ACC AAT CCG GAC AAC C-3' (Kpn I); and
N326Q: 5'-CG TTC ATC GAT CAG CAT GAC ATG G-3' (Cla I).
Successful mutagenesis resulted in appearance of the underlined restriction sites, allowing rapid screening of potential mutants.
Plasmid pDP66K carrying the right restriction site was transformed to E. coli DH5α cells [Hanahan D; J. Mol. Biol. 1983 166 557]. DNA sequence determination was performed on supercoiled plasmid DNA using the dideoxy-chain termination method [Sanger F, Coulson A R; J. Mol. Biol. 1975 94441-448] and the T7-sequencing kit from Pharmacia-LKB Biotechnology, Sweden. Plasmid pDP66K, carrying positively characterized mutant cgt genes, was transformed to B. subtilis strain DB104A [Smith H, de Jong A, Bron S, Venema G;
Gene 1988 70 351-361]. The organism was grown to an optical density at 600 nm of 4.5 in a 5 I flask (for approx. 36 hours). Under these conditions high extracellular CGTase levels were produced.
The culture was centrifuged at 4ºC for 30 minutes at 10,000 xg. The CGTases variant in the culture supematants were further purified to homogeneity by affinity chromatography, using a 30 ml α-cyclodextrin-Sepharose-6FF column (Pharmada, Sweden) [Sundberg L, Porath J; J. Chromatoor. 1974 90 87-98] with a maximal capacity of 3.5 mg protein per ml. After washing with 10 mM sodium acetate buffer (pH 5.5), bound CGTase was eluted with the same buffer containing 10 mg/ml α-cyclodextrin.
β-cyclodextrin forming activity was determined by incubating an appropriately diluted enzyme sample (0.1-0.2 units of adivity) for 3 minutes at 50°C. Paselli™ SA2 (5% solution), partially hydrolysed potato starch with an average degree of polymerization of 50 (AVEBE, Foxhol, The Netherlands), was used as a substrate. The β-cyclodextrin formed was determined based on its ability to form a stable colorless inclusion complex with phenolphthalein. One unit of activity is defined as the amount of enzyme able to produce 1 μmol of β-cydodextrin per minute.
Cyclodextrin forming activity was also measured under production process conditions. For this purpose 0.1 U/ml CGTase was incubated with 10 % Paselli™ WA4 (i.e. jet-cooked, pregelatinized drum-dried starch) in a 10 mM sodium dtrate buffer (pH 6.0) at 50ºC for 45 hours. Samples were collected at regular time intervals, diluted 10 times, boiled for 8 min. and the products formed analyzed by HPLC using a 25 cm Econosphere-NH2 5 micron column (Alltech Associates Inc., USA) eluted with acetonitrile/water (60/40 v/v) at 1 ml per min.
Results
The variants of this example were designed in order to increase β-and γ-cyclodextrin formation. The N193G, Y89G, D371G, D371 N and the Y89G/N193G
CGTase variants were all designed with the intention to decrease the interactions between the amylose chain and the first part of the active site cleft (Subsites C-G). As a result, the amylose chain would be able to move further into the active site cleft, thereby changing the ratio of cyclodextrins towards the β-and γ-cydodextrins.
The N193G CGTase variant demonstrates a rapid increase in β-cyclodextrin (Figs. 7 and 9). As a result, the ratio is changed already dramatically after 5 hours of incubation (Table 20) towards α-and β-cyclodextrin. However, after 45 hours (Table 21) the ratio has changed towards α-cyclodextrin formation only. This mutation seems particulariy well suited for combination with other mutations, e.g. D371G or D371N.
The Y89G CGTase variant results in a small change towards β-cyclodextrin after 45 hours of incubation at the expense of α-cyclodextrin (cf. Fig. 7 and Table 21 ).
The D371 N and D371 G CGTase variants both show a shift towards formation of the larger cyclodextrins (cf. Fig. 8 and Table 21). Both β-and γ-cyclodextrin increased at the expense of α-cyclodextrin. This shift is more pronounced at early incubation times (cf. Table 20 and Fig. 10).
The Y89G/N193G CGTase double mutant resulted in a shift from β-cyclodextrin to both α-and γ-cyclodextrin (cf. Table 21). In combination with other mutations, in particular D371G or D371 N, this mutation could give rise to a single shift to β-cyclodextrin.
The *145al CGTase variant was constructed on the basis of alignment studies. This insertion mutation seems especially advantageous for obtaining β-cyclodextrin producing CGTase variants. Both short incubation times (cf. Fig. 10 and Table 20) and long incubation times (cf. Fig. 8 and Table 21) gave a shift from β-cyclodextrin to both α-and γ-cyclodextrin. Also, in order to obtain a single shift to β-cyclodextrin, this mutation seems particulariy well suited for combination with other mutations, e.g. D371G or D371 N.
The N326Q CGTase variant was constructed and shown to cause a shift from α-cydodextrin to β- and γ-cyclodextrin formation (cf. Table 21 ).
Finally, combinations of the above mutations seems straightforward in order to obtain CGTase variants with increased β- and/or γ-cyclodextrin formation.
Figure imgf000102_0001
Figure imgf000102_0002
Figure imgf000103_0001
EXAMPLE 5
Construction of α-cyclodextrin Producing CGTase Variants from Thermoanaerobacter
This example describes the construction of 24 α-cyclodextrin producing CGTase variants (A1-A24), in which site-directed mutagenesis either has lead to an altered number of hydrogen bonds in the subsites of the active cleft or, alternatively, to sterical hindrance in parts of the substrate binding left.
The variants are derived from a Thermoanaerobacter sp. CGTase obtained according to WO 89/03421 , and having the nudeotide and amino add sequences presented as SEQ ID NOS: 1-2 (i.e. the wild-type enzyme).
Mutations were introduced by a method based on PCR by the use of PWO polymerase. For each mutation, specific oligonudeotides (primers) were developed. The mutations were confirmed by restriction analysis whenever possible, and by sequencing. Mutant proteins were expressed in either Escherichia coli MC1061 [Meissner P S, Sisk W P, Berman M L; Proc. Natl. Acad. Sci. USA 1987 84 4171- 4175], or in the α-amylase and protease negative Bacillus subtilis Strain DB104A [Smith H, de Jong A, Bron S, Venema G; Gene 1988 70 351-361]. Proteins were purified from the media using affinity chromatography (AfC) and/or anion-exchange chromatography (AEC). Enzyme Assays
Enzymatic activity was measured by a slightly modified procedure of the Phadebas amylase test (Pharmacia). Phadebas tablets (Phadebas™ Amylase Test, Pharmacia) are used as substrate. This substrate is a cross-linked insoluble blue- colored starch polymer, which is mixed with bovine serum albumin and a buffer substance. After suspension in water, starch is hydrolyzed by the enzyme, thereby yielding blue fragments. The determination is carried out after incubation at 60ºC, pH 6.2, in 0.15 nM calcium for 15 minutes. The absorbance of the resulting blue solution, determined at 620 nm, corresponds the enzymatic activity.
The enzyme activity is compared to that of an enzyme standard, and the activity is expressed in the same unit as that of the enzyme standard. The enzyme standard was Termamyl™ (Novo Nordisk A/D, Denmark), the amylolytic activity of which has been be determined using potato starch as substrate. This method is based on the break-down of modified potato starch by the enzyme, and the reaction is followed by mixing samples of the starch/enzyme solution with an iodine solution. Initially, a blackish-blue color is formed, but during the break-down of the starch the blue color gets weaker and gradually turns into a reddish-brown, which is compared to a colored glass standard.
One Kilo Novo alfa Amylase Unit (KNU) is defined as the amount of enzyme which, under standard conditions (i.e. at 37ºC +/- 0.05; 0.0003 M Ca2+; and pH 5.6) dextrinizes 5.26 g starch dry substance Merck Amylum solubile. Below the activity is expressed in Novo Units (NU) per ml.
CGTase activity was determined by incubating diluted enzyme with substrate in 10 mM sodium citrate, pH 6.0 for 4-10 minutes at 60ºC.
Cyclodextrin forming activity was determined using 5% Paselli™ SA2 (i.e. partially hydrolysed potato starch with an average degree of polymerization of 50, available from AVEBE, Foxhol, The Netherlands) as substrate. The α-cyclodextrin formed was determined with Methyl-orange, the β-cyclodextrin formed was determined with phenolphthalein, and the γ-cyclodextrin formed was determined with bromo cresol green. The activity is expressed in units per mg (U/mg). One unit of enzyme activity is defined as the amount of enzyme able to produce one μmol of the specific cyclodextrin per minute. Cyclodextrin formation was also determined under conventional industrial production process conditions. A precooked 10% amylopectin solution in 0.5 mM
CaCI2 at pH 5.5 was incubated with 50 NU of CGTase per gram of substrate, at
60ºC and for 24 hours. Samples are regularly withdrawn and boiled for 10 minutes at a pH of 2.5-3 prior to analysis by HPLC.
The results of these experiments are discussed and presented in tables 23-25, below. In Table 25, the figures are the ratio at maximum total level of cyclodextrin.
Oligonucleotide Primers
The following oligonudeotides were synthesized in order to initiate the site- directed mutagenesis (the numbers indicate positions according to the CGTase numbering):
A1: 143-151(G R AGTN P G);
5'-AATCATACATCTGGACGAGCAGGTACCAACCCGACTTTGGGGAA- AATGGTAC-3'; A2: 87-94(1 KYSG-VN N) + 143-151(G RAGTNPG);
Using the B9 variant (87-94(1 K Y S G - V N N)), described in Example 6 below, as starting point, the 143-151 (G RAGTNPG) mutations was introduced using the A1 primer;
A3: F195Y+ 143-151(G R AGTN PG);
5'-TTACCGTAATTTATATGACTTAGCAG-3' was used to introduce the F195Y mutation and using this variant as starting point, the 87-94(1 KY S G - V N N) mutations was introduced using the A1 primer;
A4: F195Y + 87-94(1 KYSG-VN N) + 143-151(G RAGTN PG);
The Spe I - Bst X I fragment of A2 was ligated into the CGTase gene holding the F195Y mutation. The F195Y was introduced by the use of the A3 primer; A5: P143G-A144R-S145W;
5'-ATCATACATCCGGACGATGGGAGACAGACCCTACC-3';
A6: 87-94(l N D S G - V N N);
5'-CATTTACGCAGTTATCAATGATTCCGGAGTTAACAATACATCCTA-TCATGG- 3';
A7: 87-94(l N D S G - V N N) + 146-150(S D Q P S);
Using the A6 variant (87-94(1 N D S G - V N N)) as starting point, the 146-150(S D Q P S) mutations were introduced using the primer 5'-CTCCTGCATC- ATCTGATCAACCGTCCTTTGGGGAAAATGG-3'; A8: 143-148(G R G P A A);
5'-CAAATCATACATCTGGACGAGGACCGGCCGCACCTACCTATGGGG-3';
A9: 143-148(G R A P A A);
5'-CAAATCATACATCTGGACGAGCACCGGCCGCACCTACCTATGGGG-3';
A10: 143-148(G R A * * A);
5'-CAAATCATACATCTGGACGAGCAGCACCTACCTATGGGG-3';
A11 : 143-148(G R P A A A);
5'-CAAATCATACATCTGGACGACCTGCAGCAGCTCCTACCTATGGGG-3';
A12: G180S;
5'-CCATCATTACGGATCCACTAA T T T T T CATC-3'; A13: A144R;
5'-CATACATCTCCTCGATCGGAGACAGACCC-3';
A14: P143A-A144R;
5'-CATACATCTGCTCGATCGGAGACAGACCC-3'; A15: G180N;
5'-CCATCATTACGGAAACACTAAT T T T TCATC-3';
A16: G180D;
5'-CCATCATTACGGAGACACTAAT T T T TCATC-3'; A17: G180N + P143G-A144R-S145W;
Using the A5 variant (P143G-A144R-S145W) as starting point, the G180N mutation was introduced using the primer 5'-CCATCATTACGGAAACACTA- AT T T T TCATC-3';
A18: G180D + P143G-A144R-S145W;
Using the A5 variant (P143G-A144R-S145W) as starting point, the G180N mutation was introduced using the primer 5'-CCATCATTACGGAGACACTAA- T T T T TCATC-3';
A19: G179N;
5'-CCATCATTATAATGGAACTAAT T T T TCATC-3'; A20: G179S;
5'-CCATCATTATAGTGGAACTAAT T T T TCATC-3';
A21: G179D;
5'-CCATCATTATGATGGAACTAAT T T T TCATC-3';
A22: G179N + P143G-A144R-S145W;
Using the A5 variant (P143G-A144R-S145W) as starting point, the G180N mutation was introduced using the primer 5'-CCATCATTATAATGGAACTAA- T T T T TCATC-3';
A23: G179S + P143G-A144R-S145W; Using the A5 variant (P143G-A144R-S145W) as starting point, the G180N mutation was introduced using the primer 5'-CCATCATTATAGTGGAACTAA- T T T T T CATC-3'; and
A24: G179D + P143G-A144R-S146W;
Using the A5 variant (P143G-A144R-S145W) as starting point, the G180N mutation was introduced using the primer 5'-CCATCATTATGATGGAACTAA- T T T T T CATC-3'.
Results
The variants of this example were designed in order to increase α-cyclodextrin formation.
In experiment A1 , the loop at positions 143 to 151 was replaced by (G R A G T N P G) in order to increase the interactions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J (cf. Fig. 1 ). The initial rate of both β-CD formation and of γ-CD formation has decreased. In the CD-production assay, the ratio of α-CD has increased, whereas the β-CD ratio has decreased.
In experiment A2, the loop at positions 87 to 94 was replaced by (I K Y S G * V N N), and simultaneously the loop at positions 143 to 151 was replaced by (G R A G T N P G) in order to increase the interactions between the enzyme and glucose units E, F and H, and in order to decrease the interactions between the enzyme and glucose units I and J (cf. Fig. 1). The initial rate of both β-CD formation and of γ-CD formation has decreased.
In experiment A3, the loop at positions 143 to 151 was replaced by (G R A G T N P G) in order to increase the interactions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J (cf. Fig. 1 ). Simultaneously, the F195 was replaced by 195Y in order to decrease the contact between enzyme and substrate. The initial rate of both β-CD formation and of γ-CD formation has decreased. In the CD-production assay, the ratio of α-CD has increased whereas the β-CD ratio has decreased.
In experiment A4, the loop at positions 87-94 was replaced by (I K Y S G * V N N), and simultaneously the loop at positions 143 to 151 was replaced by (G R A G T N P G) in order to increase the interactions between the enzyme and glucose units E, F and H, and in order to decrease the interactions between the enzyme and glucose units I and J (cf. Fig. 1). Simultaneously, the F195 was replaced by 195Y in order to decrease the contact between enzyme and substrate. The initial rate of β-CD formation has decreased. In the CD-production assay, the β-CD ratio has decreased.
In experiment A5, the region at positions 143 to 145 was replaced by (G R W) in order to increase the interactions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J by making a sterical hindrance (cf. Fig. 1 ). The initial rate of α-CD formation has increased, whereas the initial rate of both β-CD formation and of γ-CD formation has decreased. In the CD-production assay, the ratio of α-CD has increased whereas the β-CD ratio has decreased.
In experiment A6, the loop at positions 87-94 was replaced by (I K D S G * V N N) in order to increase the interactions between the enzyme and glucose units E and F (cf. Fig. 1).
In experiment A7, the loop at positions 87-94 was replaced by (I K D S G * V N N), and simultaneously the loop at positions 146 to 150 was replaced by (S D Q P S) in order to increase the interactions between the enzyme and glucose units E and F, and in order to decrease the interactions between the enzyme and glucose units I and J (cf. Fig. 1).
In experiment A8, the loop at positions 143 to 148 was replaced by (G R G P A A) in order to increase the interactions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J (cf. Fig. 1).
In experiment A9, the loop at positions 143 to 148 was replaced by (G R A P A A) in order to increase the interactions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J (cf. Fig. 1).
In experiment A10, the loop at positions 143 to 148 was replaced by (G R A * * A) in order to increase the interactions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J (cf. Fig. 1 ). In experiment A11 , the region at positions 143 to 148 was replaced by (G R W) in order to increase the interactions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J (cf. Fig. 1). The initial rate of both β-CD formation and of γ-CD formation has decreased more significantly than the initial rate of α-CD formation, which results in an increased ration between α-cd formation and β-CD formation.
In experiment A12, G180 was replaced by 180S in order to increase the interactions between the enzyme and glucose unit H (cf. Fig. 1).
In experiment A13, A144 was replaced by 144R in order to increase the interactions between the enzyme and glucose unit H (cf. Fig. 1).
In experiment A14, P143-A144 was replaced by 143A-144R in order to increase the interactions between the enzyme and glucose unit H (cf. Fig. 1).
In experiment A15, G180 was replaced by 180N in order to increase the interadions between the enzyme and glucose unit H (cf. Fig. 1).
In experiment A16, G180 was replaced by 180D in order to increase the interactions between the enzyme and glucose unit H (cf. Fig. 1).
In experiment A17, G180 was replaced by 180N in order to increase the interactions between the enzyme and glucose unit H (cf. Fig. 1). Simultaneously, the region at positions 143 to 145 was replaced by (G R W) in order to increase the interadions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J by making a sterical hindrance (cf. Fig. 1).
In experiment A18, G180 was replaced by 180D in order to increase the interactions between the enzyme and glucose unit H (cf. Fig. 1). Simultaneously, the region at positions 143 to 145 was replaced by (G R W) in order to increase the interactions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J by making a sterical hindrance (cf. Fig. 1 ).
In experiment A19, G179 was replaced by 179N in order to increase the interactions between the enzyme and glucose unit H (cf. Fig. 1).
In experiment A20, G179 was replaced by 179S in order to increase the interactions between the enzyme and glucose unit H (cf. Fig. 1). In experiment A21 , G179 was replaced by 179D in order to increase the interactions between the enzyme and glucose unit H (cf. Fig. 1).
In experiment A22, G179 was replaced by 179N in order to increase the interactions between the enzyme and glucose unit H (cf. Fig. 1 ). Simultaneously, the region at positions 143 to 145 was replaced by (G R W) in order to increase the interactions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J by making a sterical hindrance (cf. Fig. 1).
In experiment ABBE, G179 was replaced by 179S in order to increase the interadions between the enzyme and glucose unit H (cf. Fig. 1). Simultaneously, the region at positions 143 to 145 was replaced by (G R W) in order to increase the interactions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J by making a sterical hindrance (cf. Fig. 1).
In experiment A24, G179 was replaced by 179D in order to increase the interactions between the enzyme and glucose unit H (cf. Fig. 1). Simultaneously, the region at positions 143 to 145 was replaced by (G R W) in order to increase the interactions between the enzyme and glucose unit H, and in order to decrease the interactions between the enzyme and glucose units I and J by making a sterical hindrance (cf. Fig. 1).
Figure imgf000111_0001
Figure imgf000112_0001
Figure imgf000112_0002
Figure imgf000113_0001
EXAMPLE 6
Construction of β-cyclodextrin ProducingCGTase Variants from Thermoanaerobacter
This example describes the construction of 15 β-cyclodextrin producing CGTase variants (B1-B9), in which site-directed mutagenesis either has lead to an altered number of hydrogen bonds in the subsites of the active cleft or, alternatively, to sterical hindrance in parts of the substrate binding left.
The variants are derived from a Thermoanaerobacter sp. CGTase obtained according to WO 89/03421 , and having the nudeotide and amino acid sequences presented as SEQ ID NOS: 1-2 (i.e. the wild-type enzyme).
Mutations were introduced by a method based on PCR by the use of PWO polymerase. For each mutation, specific oligonudeotides (primers) were developed. The mutations were confirmed by restriction analysis whenever possible, and by sequencing. Mutant proteins were expressed in either Escherichia coli MC1061 [Meissner P S, Sisk W P, Berman M L; Proc. Natl. Acad. Sci. USA 1987 84 4171- 4175], or in the α-amylase and protease negative Bacillus subtilis Strain DB104A [Smith H, de Jong A, Bron S, Venema G; Gene 1988 70 351-361]. Proteins were purified from the media using affinity chromatography (AfC) and/or anion-exchange chromatography (AEC). Enzyme Assays
Enzymatic activity was measured by a slightly modified procedure of the Phadebas amylase test (Pharmacia). Phadebas tablets (Phadebas™ Amylase Test, Pharmacia) are used as substrate. This substrate is a cross-linked insoluble blue- colored starch polymer, which is mixed with bovine serum albumin and a buffer substance. After suspension in water, starch is hydrolyzed by the enzyme, thereby yielding blue fragments. The determination is carried out after incubation at 60°C, pH 6.2, in 0.15 nM calcium for 15 minutes. The absorbance of the resulting blue solution, determined at 620 nm, corresponds the enzymatic activity.
The enzyme activity is compared to that of an enzyme standard, and the activity is expressed in the same unit as that of the enzyme standard. The enzyme standard was Termamyl™ (Novo Nordisk A/D, Denmark), the amylolytic activity of which has been be determined using potato starch as substrate. This method is based on the break-down of modified potato starch by the enzyme, and the reaction is followed by mixing samples of the starch/enzyme solution with an iodine solution. Initially, a blackish-blue color is formed, but during the break-down of the starch the blue color gets weaker and gradually turns into a reddish-brown, which is compared to a colored glass standard.
One Kilo Novo alfa Amylase Unit (KNU) is defined as the amount of enzyme which, under standard conditions (i.e. at 37ºC +/- 0.05; 0.0003 M Ca2+; and pH 5.6) dextrinizes 5.26 g starch dry substance Merck Amylum solubile. Below the activity is expressed in Novo Units (NU) per ml.
CGTase activity was determined by incubating diluted enzyme with substrate in 10 mM sodium citrate, pH 6.0 for 4-10 minutes at 85ºC.
Cyclodextrin forming activity was determined using 5% Paselli™ SA2 (i.e. partially hydrolysed potato starch with an average degree of polymerization of 50, available from AVEBE, Foxhol, The Netherlands) as substrate. The α-cyclodextrin formed was determined with Methyl-orange, the β-cyclodextrin formed was determined with phenolphthalein, and the γ-cyclodextrin formed was determined with bromo cresol green. The activity is expressed in units per mg (U/mg). One unit of enzyme activity is defined as the amount of enzyme able to produce one μmol of the specific cyclodextrin per minute. Cyclodextrin formation was also determined under conventional industrial production process conditions. A precooked 10% amylopectin solution in 0.5 mM
CaCI2 at pH 5.5 was incubated with 50 NU of CGTase per gram of substrate, at
85ºC and for 24 hours. Samples are regularly withdrawn and boiled for 10 minutes at a pH of 2.5-3 prior to analysis by HPLC.
The results of these experiments are discussed and presented in tables 26-28, below. In Table 28, the figures are the ratio at maximum total level of cyclodextrin.
Oligonucleotide Primers
The following oligonudeotides were synthesized in order to initiate the site- directed mutagenesis (the numbers indicate positions according to the CGTase numbering):
Figure imgf000115_0001
Figure imgf000116_0001
This variant is also used in the construction of A2 of Example 5, above;
B10: F195Y + 87-94(1 KYSG-VN N);
5'-TTACCGTAATTTATATGACTTAGCAG-3' was used to introduce the F195Y mutation. Using this variant as starting point, the 87-94(1KYSG-VNN) mutations was introduced using primer B9. Simultaneously, the F195 was replaced by 195Y in order to decrease the contact between enzyme and substrate;
Figure imgf000116_0002
Results
The variants of this example were designed in order to increase β-cyclodextrin formation.
In experiment B1, S145 was replaced by 145A in order to decrease the interactions between the enzyme and glucose unit J (cf. Fig.1). The initial rate of both β-CD formation and of γ-CD formation has increased. In the CD-production assay, the ratio of α-CD has decreased whereas the β-CD ratio has increased.
In experiment B2, E146 was replaced by 146S in order to increase the interactions between the enzyme and glucose unit I (cf. Fig. 1). The initial rate of both β-CD formation and of γ-CD formation has increased. In the CD-production assay, the ratio of α-CD has decreased.
In experiment B3, T147 was replaced by 147A in order to decrease the interactions between the enzyme and glucose unit J (cf. Fig. 1 ). In the CD-production assay, the ratio of α-CD has decreased, whereas the β-CD ratio has increased.
In experiment B4, T147 was replaced by 147L in order to decrease the interactions between the enzyme and glucose unit J (cf. Fig. 1). In the CD-production assay, the ratio of α-CD has decreased, whereas the β-CD ratio has increased.
In experiment B5, D148 was replaced by 148A in order to decrease the interactions between the enzyme and glucose unit J. In the CD-production assay, the ratio of α-CD has decreased, whereas the β-CD ratio has increased.
In experiment B6, D89 was replaced by 89A in order to decrease the interactions between the enzyme and glucose unit F. The initial rate of both β-CD formation and of γ-CD formation has decreased.
In experiment B7, Y91 a was replaced by 91 aA in order to decrease the interactions between the enzyme and glucose unit F. The initial rate of both β-CD formation and of γ-CD formation has decreased.
In experiment B8, Y91a was replaced by Y91a* (deleted) in order to decrease the interactions between the enzyme and glucose unit F. The initial rate of β-CD formation has decreased.
In experiment B9, the loop at positions 87 to 94 was replaced by (I K Y S G * V N N) in order to increase the contacts between the enzyme and glucose units E and F (cf. Fig. 1).
In experiment B10, 5'-TTACCGTAATTTATATGACTTAGCAG-3' was used to introduce the F195Y mutation. Using this variant as starting point, the 87-94(1 K Y S G - V N N) mutations was introduced using primer B9. Simultaneously, the F195 was replaced by 195Y in order to decrease the contact between enzyme and substrate. In experiment B11 , D196 was replaced by 196S in order to decrease the interactions between the enzyme and glucose unit E and glucose unit F.
In experiment B12, D196 was replaced by 196A in order to decrease the interactions between the enzyme and glucose unit E and glucose unit F.
In experiment BBB, D371 was replaced by 371 N in order to decrease the interactions between the enzyme and glucose unit E and glucose unit F,
In experiment B14, D371 was replaced by 371 G in order to decrease the interactions between the enzyme and glucose unit E and glucose unit F.
In experiment B15, D371 was replaced by 371A in order to decrease the interactions between the enzyme and glucose unit E and glucose unit F.
Figure imgf000118_0001
Figure imgf000119_0001
Figure imgf000119_0002
Figure imgf000120_0001
EXAMPLE 7
Construction of β-cyclodextrin ProducingCGTase Variants from Thermoanaerobacter
This example describes the construction of 9 β-cyclodextrin producing CGTase variants (C1-C9), in which site-directed mutagenesis either has lead to an altered number of hydrogen bonds in the subsites of the active cleft or, alternatively, to sterical hindrance in parts of the substrate binding left.
The variants are derived from a Thermoanaerobacter sp. CGTase obtained according to WO 89/03421 , and having the nudeotide and amino acid sequences presented as SEQ ID NOS: 1-2 (i.e. the wild-type enzyme).
Variants were introduced by a method based on Unique Site Elimination (USE), following the protocol from the supplier (Stratagene®). The unique restriction site BsaMI at the plasmid opposite to the CGTase gene was removed by the use of the 5'P-CACTGTTCCTTCGAACGCGTAACCTTAAATACC-3, oligonucleotide. In this oligonucleotide, "P" indicates a 5' phosphorylation necessary for the procedure. For each mutation specific oligonudeotides were developed. The mutations were confirmed by restriction analysis whenever possible, and by sequencing. Mutant proteins were expressed in either Escherichia coli MC1061 [Meissner P S, Sisk W P, Berman M L; Proc. Natl. Acad. Sci. USA 1987 84 4171-4175]. Proteins were purified from the media using affinity chromatography (AfC).
Enzyme Assays
Enzymatic activity was measured by a slightly modified procedure of the Phadebas amylase test (Pharmacia). Phadebas tablets (Phadebas™ Amylase Test, Pharmacia) are used as substrate. This substrate is a cross-linked insoluble blue- colored starch polymer, which is mixed with bovine serum albumin and a buffer substance. After suspension in water, starch is hydrolyzed by the enzyme, thereby yielding blue fragments. The determination is carried out after incubation at 60ºC, pH 6.2, in 0.15 nM calcium for 15 minutes. The absorbance of the resulting blue solution, determined at 620 nm, corresponds the enzymatic activity. The enzyme activity is compared to that of an enzyme standard, and the activity is expressed in the same unit as that of the enzyme standard. The enzyme standard was Termamyl™ (Novo Nordisk A/D, Denmark), the amylolytic activity of which has been be determined using potato starch as substrate. This method is based on the break-down of modified potato starch by the enzyme, and the reaction is followed by mixing samples of the starch/enzyme solution with an iodine solution. Initially, a blackish-blue color is formed, but during the break-down of the starch the blue color gets weaker and gradually turns into a reddish-brown, which is compared to a colored glass standard.
One Kilo Novo alfa Amylase Unit (KNU) is defined as the amount of enzyme which, under standard conditions (i.e. at 37°C +/- 0.05; 0.0003 M Ca2+; and pH 5.6) dextrinizes 5.26 g starch dry substance Merck Amylum solubile. Below the activity is expressed in Novo Units (NU) per ml.
CGTase activity was determined by incubating diluted enzyme with substrate in 10 mM sodium citrate, pH 6.0 for 4-10 minutes at 85ºC.
Cyclodextrin forming activity was determined using 5% Paselli™ SA2 (i.e. partially hydrolysed potato starch with an average degree of polymerization of 50, available from AVEBE, Foxhol, The Netherlands) as substrate. The α-cyclodextrin formed was determined with Methyl-orange, the β-cyclodextrin formed was determined with phenolphthalein and the γ-cyclodextrin formed was determined with bromo cresol green. The activity is expressed in units per mg (U/mg). One unit of enzyme activity is defined as the amount of enzyme able to produce one μmol of the specific cyclodextrin per minute.
Cyclodextrin formation was also determined under conventional industrial production process conditions. A precooked 10% amylopectin solution in 0.5 mM CaCI2 at pH 5.5 was incubated with 50 NU of CGTase per gram of substrate, at 60ºC and for 24 hours. Samples are regularly withdrawn and boiled for 10 minutes at a pH of 2.5-3 prior to analysis by HPLC.
The results of these experiments are discussed and presented in tables 29-31 , below. In Table 31 , the figures are the ratio at maximum total level of cyclodextrin. Oligonucleotide Primers
The following oligonudeotides were synthesized in order to initiate the site- directed mutagenesis (the numbers indicate positions according to the CGTase numbering):
Figure imgf000122_0001
Both primers listed C2 and C5 were used simultaneously. Results
The variants of this example were designed in order to increase β-cyclodextrin formation.
In experiment C1 , N193 were replaced by 193A in order to decrease the interactions between the enzyme and glucose unit H. In the CD-produdion assay, the ratio of α-CD has decreased, and the ratio of β-CD has increased.
In experiment C2, the region at positions 146-150 was replaced by (S D Q P S) in order to decrease the interactions between the enzyme and glucose unit J, and in order to increase the interactions between the enzyme and glucose unit I.
In experiment C3, the region at positions 145-148 was replaced by (A E L A) in order to decrease the interactions between the enzyme and glucose unit J, and in order to increase the interadions between the enzyme and glucose unit I.
In experiment C4, the region at positions 145-148 was replaced by (A E W A) in order to decrease the interactions between the enzyme and glucose unit J, and in order to increase the interactions between the enzyme and glucose unit I.
In experiment C5, the loop at positions 87-94 was replaced by (I N Y S G * V N N) in order to decrease the interactions between the enzyme and glucose unit E and glucose unit F.
In experiment C6, the loop at positions 87-94 was replaced by (H P * S G Y * * *) in order to decrease the interadions between the enzyme and glucose unit E and glucose unit F.
In experiment C7, the region at positions 145-148 was replaced by (L E T N) in order to decrease the interactions between the enzyme and glucose unit J, and in order to increase the interactions between the enzyme and glucose unit I.
In experiment C8, the loop at positions 87-94 was replaced by (H P * S G Y * * *) in order to decrease the interactions between the enzyme and glucose unit E and glucose unit F. Simultaneously, the region at positions 145-148 was replaced by (L E T N) in order to decrease the interactions between the enzyme and glucose unit J, and in order to increase the interactions between the enzyme and glucose unit I.
In experiment C9, the loop at positions 87-94 was replaced by (I N Y S G * V N N) in order to decrease the interactions between the enzyme and glucose unit E and glucose unit F. Simultaneously, the region at positions 145-148 was replaced by (S D Q P S) in order to decrease the interactions between the enzyme and glucose unit J, and in order to increase the interactions between the enzyme and glucose unit I.
Figure imgf000124_0001
Figure imgf000124_0002
Figure imgf000124_0003
SEQUENCE LISTING
Figure imgf000125_0001
Figure imgf000125_0002
Figure imgf000126_0001
Figure imgf000127_0001
Figure imgf000128_0001
Figure imgf000128_0002
Figure imgf000129_0001
Figure imgf000130_0001

Claims

1. A method of modifying the substrate binding and/or product selectivity of a precursor CGTase enzyme, which method comprises substitution, insertion and/or deletion of one or more amino acid residue(s) of the precursor enzyme, which amino acid residue(s) holds a position close to the substrate.
2. The method according to claim 1 , in which the amino add residue(s) hold(s) a position less than 8 A from the substrate.
3. The method according to either of claims 1-2, in which the amino add residue(s) is located in domain A of the enzyme. 4. The method according to either of claims 1-2, in which the amino acid residue(s) is located in domain B of the enzyme. 5. The method according to either of daims 1-2, in which the amino add residue(s) is located in domain C of the enzyme.
6. The method according to either of claims 1-2, in which the amino acid residue(s) is located in domain E of the enzyme.
7. The method according to any of claims 1-6, in which the amino add residues holding a position close to the substrate are the amino acid residues corresponding to the positions listed in Table 2.
8. The method according to any of claims 1-7, in which the amino acid residue(s) is substituted by introducing one or more amino acid residue(s) with more intermolecular interaction(s).
9. The method according to any of claims 1-7, in which the amino acid residue(s) is substituted by introducing one or more amino acid residue(s) with less intermolecular interaction(s).
10. The method according to any of claims 1-9, in which the CGTase is derived from a strain of Bacillus, a strain of Brevibacterium, a strain of Clostridium, a strain of Corynebacterium, a strain of Klebsiella, a strain of Micrococcus, a strain of Thermoanaerobium, a strain of Thermoanaerobacterium, a strain of Thermoanaerobacter, or a strain of Thermoactinomyces.
11. The method according to claim 10, in which the CGTase is derived from a strain of Bacillus autolyticus, a strain of Bacillus cereus, a strain of Bacillus circulans, a strain of Bacillus circulans var. alkalophilus, a strain of Bacillus coagulans, a strain of Bacillus firmus, a strain of Bacillus halophilus, a strain of Bacillus macerans, a strain of Bacillus megaterium, a strain of Bacillus ohbensis, a strain of Bacillus stearothermophilus, or a strain of Bacillus subtilis.
12. The method according to claim 10, in which the CGTase is derived from the strain Bacillus sp. Strain 1011 , the strain Bacillus sp. Strain 38-2, the strain Bacillus sp. Strain 17-1 , the strain Bacillus sp. 1-1 , the strain Bacillus sp. Strain B1018, the strain Bacillus circulans Strain 8, or the strain Bacillus circulans Strain 251 , or a mutant or a variant thereof.
13. The method according to claim 10, in which the CGTase is derived from a strain of Klebsiella pneumonia, a strain of Thermoanaerobacter ethanolicus, a strain of Thermoanaerobacter fmnii, a strain of Clostridium thermoamylolyticum, a strain of Clostridium thermosaccharolyticum, or a strain of Thermoanaerobacterium thermosulfurigenes.
14. The method according to claim 10, in which the CGTase is derived from the strain Bacillus circulans Strain 251.
15. The method according to claim 10, in which the CGTase is derived from the strain Thermoanaerobacter sp. ATCC 53627.
16. A CGTase variant derived from a precursor CGTase enzyme by substitution, insertion and/or deletion of one or more amino acid residue(s), which amino acid residue(s) holds a position close to the substrate.
17. The CGTase variant according to claim 16, in which one or more amino acid residue(s) holding a position less than 8 A from the substrate have been substituted, inserted and/or deleted.
18. The CGTase variant according to either of claims 16-17, in which one or more amino acid residue(s) located in domain A of the enzyme have been substituted, inserted and/or deleted. 19. The CGTase variant according to either of claims 16-17, in which one or more amino acid residue(s) located in domain B of the enzyme have been substituted, inserted and/or deleted.
20. The CGTase variant according to either of claims 16-17, in which one or more amino acid residue(s) located in domain C of the enzyme have been substituted, inserted and/or deleted.
21. The CGTase variant according to either of claims 16-17, in which one or more amino acid residue(s) located in domain E of the enzyme have been substituted, inserted and/or deleted.
22. The CGTase variant according to any of claims 16-21 , in which one or more amino acid residue(s) have been substituted by an amino acid residue with more hydrogen binding potential.
23. The CGTase variant according to any of claims 16-21 , in which one or more amino acid residue(s) have been substituted by an amino add residue with less hydrogen binding potential.
24. The CGTase variant according to any of claims 16-23, which is derived from a strain of Bacillus, a strain of Brevibacterium, a strain of Clostridium, a strain of Corynebacterium, a strain of Klebsiella, a strain of Micrococcus, a strain of Thermoanaerobium, a strain of Thermoanaerobacterium, a strain of Thermoanaerobacter, or a strain of Thermoactinomyces.
25. The CGTase variant according to claim 24, which is derived from a strain of Bacillus autolyticus, a strain of Bacillus cereus, a strain of Bacillus circulans, a strain of Bacillus circulans var. alkalophilus, a strain of Bacillus coagulans, a strain of Bacillus firmus, a strain of Bacillus halophilus, a strain of Bacillus macerans, a strain of Bacillus megaterium, a strain of Bacillus ohbensis, a strain of Bacillus stearothermophilus, or a strain of Bacillus subtilis.
26. The CGTase variant according to claim 24, which is derived from the strain Bacillus sp. Strain 1011, the strain Bacillus sp. Strain 38-2, the strain Bacillus sp. Strain 17-1 , the strain Bacillus sp. 1-1 , the strain Bacillus sp. Strain B1018, the strain Bacillus circulans Strain 8, or the strain Bacillus circulans Strain 251 , or a mutant or a variant thereof.
27. The CGTase variant according to claim 24, which is derived from the strain Bacillus circulans Strain 251.
28. The CGTase variant according to claim 24, which is derived from a strain of Klebsiella pneumonia, a strain of Thermoanaerobacter ethanolicus, a strain of
Thermoanaerobacter fmnii, a strain of Clostridium thermoamylolyticum, a strain of Clostridium thermosaccharolyticum, or a strain of Thermoanaerobacterium thermosulfurigenes.
29. The CGTase variant according to claim 24, which is derived from the strain Thermoanaerobacter sp. ATCC 53627.
30. The CGTase variant according to any of claims 16-29, in which one or more of the amino acid residue(s) corresponding to the positions listed in Table 2 have been substituted, inserted and/or deleted.
31. The CGTase variant according to any of claims 16-29, in which one or more of the amino acid residue(s) corresponding to the positions listed in Table 9 have been substituted, inserted and/or deleted, as indicated in this table.
32. The CGTase variant according to any of claims 16-29, in which one or more of the amino acid residue(s) corresponding to the positions listed in Table 10 have been substituted, inserted and/or deleted, as indicated in this table. 33. The CGTase variant according to any of claims 16-29, in which one or more of the amino acid residue(s) corresponding to the positions listed in Tables 3-5 have been substituted, inserted and/or deleted.
34. The CGTase variant according to any of claims 16-29, in whidi one or more of the amino acid residue(s) corresponding to the positions listed in Table 11 have been substituted, inserted and/or deleted, as indicated in this table.
35. The CGTase variant according to any of claims 16-29, in which one or more of the amino acid residue(s) corresponding to the positions listed in Table 12 have been substituted, inserted and/or deleted, as indicated in this table.
36. The CGTase variant according to any of claims 33-35, which is derived from a strain of Bacillus.
37. The CGTase variant according to claim 36, which is derived from a strain of Bacillus autolyticus, a strain of Bacillus cereus, a strain of Bacillus circulans, a strain of Bacillus circulans var. alkalophilus, a strain of Bacillus coagulans, a strain of Bacillus firmus, a strain of Bacillus halophilus, a strain of Bacillus macerans, a strain of Bacillus megaterium, a strain of Bacillus ohbensis, a strain of Bacillus stearothermophilus, a strain of Bacillus subtilis, the strain Bacillus sp. Strain 1011 , the strain Bacillus sp. Strain 38-2, the strain Bacillus sp. Strain 17-1 , the strain Bacillus sp. 1-1, the strain Bacillus sp. Strain B1018, the strain Bacillus circulans Strain 8, or the strain Bacillus circulans Strain 251 , or a mutant or a variant thereof.
38. The CGTase variant according to claim 36, which is derived from the strain Bacillus circulans Strain 251 , or a mutant or a variant thereof.
39. The CGTase variant according to any of claims 16-29, in which one or more of the amino acid residue(s) corresponding to the positions listed in Tables 6-8 have been substituted, inserted and/or deleted.
40. The CGTase variant according to any of claims 16-29, in which one or more of the amino acid residue(s) corresponding to the positions listed in Table 13 have been substituted, inserted and/or deleted.
41. The CGTase variant according to any of claims 16-29, in which one or more of the amino acid residue(s) corresponding to the positions listed in Table 14 have been substituted, inserted and/or deleted. 42. The CGTase variant according to any of claims 39-41 , which is derived from a strain of Thermoanaerobacter.
43. The CGTase variant according to claim 41 , which is derived from the strain Thermoanaerobacter sp. ATCC 53627, or a mutant or a variant thereof.
44. A CGTase variant according to any of claims 16-29, which variant at position 21 holds a phenylalanine residue (X21 F) or a tyrosine residue (X21Y).
45. A CGTase variant according to any of claims 16-29, which variant at position 47 holds a glutamine residue (X47Q), or an alanine residue (X47A), or a leucine residue (X47L), or a histidine residue (X47H), or an arginine residue (X47R).
46. A CGTase variant according to any of claims 16-29, which variant at position 88 holds a proline residue (X88P) or a lysine residue (X88K).
47. A CGTase variant according to any of claims 16-29, which variant at position 89 holds an aspartic acid residue (X89D), or an alanine residue (X89A), or a glycine residue (X89G).
48. A CGTase variant according to any of claims 16-29, which variant at position 91a (e.g. via insertion) holds an alanine residue (X91 aA or *91aA), or a tyrosine residue (X91 aY or *91 aY), or in which variant position 91 a has been deleted (X91a*). 49. A CGTase variant according to any of claims 16-29, in which variant position 92 has been deleted (X92*). 5O. A CGTase variant according to any of claims 16-29, which variant at position 94 holds a glutamine residue (X94Q), or a lysine residue (X94K), or an arginine residue (X94R), or a tryptophan residue (X94W), or a phenylalanine residue (X94F), or in which variant position 94 has been deleted (X94*).
51. A CGTase variant according to any of claims 16-29, which variant at position 135 holds a leucine residue (X135L). 52. A CGTase variant according to any of claims 16-29, which variant at position 143 holds an alanine residue (X143A), or a glycine residue (X143G). 53. A CGTase variant according to any of claims 16-29, which variant at position 144 holds an arginine residue (X144R), or a lysine residue (X144K), or an aspartic acid residue (X144D).
54. A CGTase variant according to any of claims 16-29, which variant at position 145 holds an alanine residue (X145A), or a glutamic acid (X145E), or a tryptophan residue (X145W), or a glycine residue (X145G), or a phenylalanine residue (X145F), or a tyrosine residue (X145Y), or a leucine residue (X145L), or a proline residue (X145P). 55. A CGTase variant according to any of claims 16-29, which variant at position 145a (e.g. via insertion) holds an isoleucine residue (X145al or *145al). 56. A CGTase variant according to any of claims 16-29, which variant at position 146 holds a proline residue (X146P), or a serine residue (X146S), or an isoleucine residue (X146I), or a glutamine residue (X146Q), or a tryptophan residue (X146W), or an arginine residue (X146R), or a glutamic acid residue (X146E). 57. A CGTase variant according to any of claims 16-29, which variant at position 147 holds an isoleucine residue (X147I), or a leucine residue (X147L), or an alanine residue (X147A), or a serine residue (X147S), or a tryptophan residue (X147W). 58. A CGTase variant according to any of claims 16-29, which variant at position 147a (e.g. via insertion) holds an alanine residue (X147aA or *147aA). 59. A CGTase variant according to any of claims 16-29, which variant at position 148 holds an alanine residue (X148A), or a glycine residue (X148G), or a glutamic acid residue (X148E), or an asparagine residue (X148N).
60. A CGTase variant according to any of claims 16-29, which variant at position 149 holds an isoleucine residue (X149I). 61. A CGTase variant according to any of claims 16-29, which variant at position 167 holds a phenylalanine residue (X167F).
62. A CGTase variant according to any of claims 16-29, which variant at position 185 holds an arginine residue (X185R), or a glutamic acid residue (X185E), or an aspartic acid residue (X185D).
63. A CGTase variant according to any of claims 16-29, which variant at position 186 holds an alanine residue (X186A).
64. A CGTase variant according to any of claims 16-29, which variant at position 193 holds a glycine residue (X193G), or an alanine residue (X193A), or an aspartic acid residue (X193D), or a glutamic acid residue (X193E).
65. A CGTase variant according to any of claims 16-29, which variant at position 196 holds an alanine residue (X196A), or a leucine residue (X196L).
66. A CGTase variant according to any of claims 16-29, which variant at position 197 holds an aspartic acid residue (X197D), or a glutamic acid residue (X197E).
67. A CGTase variant according to any of claims 16-29, which variant at position 232 holds a glutamine residue (X232Q), or an asparagine residue (X232N), or an alanine residue (X232A), or a leucine residue (X232L).
68. A CGTase variant according to any of claims 16-29, which variant at position 233 holds a glutamine residue (X233Q).
69. A CGTase variant according to any of claims 16-29, which variant at position 259 holds a phenylalanine residue (X259F).
70. A CGTase variant according to any of claims 16-29, which variant at position 264 holds a glutamine residue (X264Q), or an alanine residue (X264A), or an asparagine residue (X264N), or a leucine residue (X264L).
71. A CGTase variant according to any of claims 16-29, which variant at position 268 holds an alanine residue (X268A).
72. A CGTase variant according to any of claims 16-29, which variant at position 371 holds a glycine residue (X371 G), or an asparagine residue (X371 N), or an alanine residue (X371 A), or a leucine residue (X371 L),, or a glutamic acid residue (X371 E).
73. A CGTase variant according to any of claims 16-29, which variant at position 375 holds a proline residue (X375P), or a glycine residue (X375G), or a glutanine residue (X375Q), or an asparagine residue (X375N), or an alanine residue (X375A), or a leucine residue (X375L).
74. A CGTase variant according to any of claims 16-29, which variant at position 599a (e.g. via insertion) holds a proline residue (X599aP or *599aP), or an arginine residue (X599aR or *599aR), or a histidine residue (X599aH or *599aH). 75. A CGTase variant according to any of claims 16-29, which variant at position 600 has been substituted for a different amino acid residue, in particular a tryptophan residue (X600W), a phenylalanine residue (X600F), a tyrosine residue (X600Y), an arginine residue (X600R), a proline residue (X600P), a leucine residue (X600L), or an asparagine residue (X600N). 76. A CGTase variant according to any of claims 16-29, which variant at position 616 holds an alanine residue (X616A).
77. A CGTase variant according to any of claims 16-29, which variant at position 633 holds an alanine residue (X633A).
78. A CGTase variant according to any of claims 16-29, which variant at position 662 holds an alanine residue (X662A).
79. A CGTase variant according to any of claims 16-29, which variant at position 47 holds a histidine residue or an arginine residue, and/or at position 135 holds a leucine residue (X47H/X135L or X47R/X136L).
80. A CGTase variant according to any of claims 16-29, which variant at position 88 holds a proline residue, and at position 143 holds a glycine residue (X88P/X143G).
81. A CGTase variant according to any of daims 16-29, which variant at position 89 holds an aspartic acid residue, and at position 146 holds a proline residue (X89D/X146P).
82. A CGTase variant according to any of claims 16-29, in which variant at positions 92 and 94 have been deleted (X92VX94*).
83. A CGTase variant according to any of claims 16-29, which variant at position 143 holds an alanine residue, and at position 144 holds an arginine residue
(X143A/X144R).
84. A CGTase variant according to any of claims 16-29, which variant at position 143 holds a glycine residue, and at position 144 holds an arginine residue, and at position 145 holds a tryptophan residue (X143G/X144R/X145W). 85. A CGTase variant according to any of claims 16-29, which variant at positions 143-148 comprises the partial amino acid sequence GRA**A, the partial amino acid sequence GRAAAA, the partial amino acid sequence GRAPAA, or the partial amino acid sequence GRGPAA.
86. A CGTase variant according to any of claims 16-29, which variant at position 144 holds an arginine residue, at position 145 holds an alanine residue, and at position 146 holds a proline residue (X144R/X145A/X146P).
87. A CGTase variant according to any of claims 16-29, which variant at position 145 holds an alanine residue, and at position 145a (e.g. via insertion) holds an isoleucine residue (X145A/X145al or X145A/*145al).
88. A CGTase variant according to any of claims 16-29, which variant at position 145 holds an alanine residue, and at position 146 holds a glydne residue (X145A/X146G).
89. A CGTase variant according to any of claims 16-29, which variant at position 145 holds a leucine residue, and at position 148 holds an asparagine residue (X145L/X148N).
90. A CGTase variant according to any of daims 16-29, which variant at position 145 holds a glutamic acid residue, and in position 146 holds a proline residue or a glutamine residue (X145E/X146P or X145E/X146Q). 91. A CGTase variant according to any of claims 16-29, which variant at position 145 holds a tryptophan residue, and in position 146 holds a tryptophan residue, or an isoleucine residue, or an arginine residue (X145W/X146W or X145W/X146l or X146W/X146R).
92. A CGTase variant according to any of claims 16-29, which variant at position 145 holds an alanine residue, at position 145a (e.g. via insertion) holds an isoleucine residue, and at position 148 holds a glutamic add residue (X145A/X145al/X148E or X145AΛ145al/X148E).
93. A CGTase variant according to any of daims 16-29, which variant at position 145a (e.g. via insertion) holds an isoleucine residue, and at position 148 holds a glutamic acid residue (X145al/X148E or *145al/X148E).
94. A CGTase variant according to any of claims 16-29, which variant at position 616 holds an alanine residue, and at position 662 holds an alanine residue (X616A/X662A).
95. A CGTase variant according to any of claims 16-29, which variant at positions 87-94 comprises the partial amino acid sequence IKYSGVNN, and/or at positions 143-161 comprises the partial amino acid sequence GRAGTNPGF, or at positions 143-145 comprises the partial amino acid sequence GRW.
96. A CGTase variant according to any of claims 16-29, which variant at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAETWPAF.
97. A CGTase variant according to any of claims 16-29, which variant at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-151 comprises the partial amino acid sequence PAAETWPAF, and which variant at position 195 holds a leucine residue (X195L).
98. A CGTase variant according to any of claims 16-29, which variant at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-151 comprises the partial amino acid sequence PALETNPNF, or at positions 143-161 comprises the partial amino acid sequence PAAEADPNF.
99. A CGTase variant according to any of claims 16-29, which variant at positions 87-94 comprises the partial amino acid sequence HP*SGY**, and/or at positions 143-161 comprises the partial amino acid sequence PALETNPNF, or at positions 143-161 comprises the partial amino acid sequence PAAEADPNF, and which variant at position 195 holds a leudne residue (X195W).
100. A CGTase variant according to any of claims 44-99, which variant is derived from a strain of a strain of Bacillus autolyticus, a strain of Bacillus cereus, a strain of Bacillus circulans, a strain of Bacillus circulans var. alkalophilus, a strain of Bacillus coagulans, a strain of Bacillus firmus, a strain of Bacillus halophilus, a strain of Bacillus macerans, a strain of Bacillus megaterium, a strain of Bacillus ohbensis, a strain of Bacillus stearothermophilus, or a strain of Bacillus subtilis.
101. A CGTase variant according to any of claims 44-99, which variant is derived from the strain Bacillus sp. Strain 1011 , the strain Bacillus sp. Strain 38-2, the strain Bacillus sp. Strain 17-1 , the strain Bacillus sp. 1-1, the strain Bacillus sp. Strain B1018, the strain Bacillus circulans Strain 8, or the strain Bacillus circulans Strain 251 , or a mutant or a variant thereof.
102. A CGTase variant according to any of daims 44-99, which variant is derived from a strain of Thermoanaerobacter sp.
103. A CGTase variant according to any of claims 44-99, which variant is derived from the strain Thermoanaerobacter sp. ATCC 53627, or a mutant or a variant thereof.
104. A DNA construct encoding a CGTase variant according to any of claims 16-103.
105. The DNA construct according to claim 104, comprising one or more of the partial oligonucleotide sequences describes as primers in examples 3-7. 106. A recombinant expression vedor comprising the DNA construct according to either of claims 104-106.
107. A host cell comprising a DNA construct according to either of claims 104- 10δ, or the recombinant expression vector according to claim 106.
108. A method of producing a CGTase variant according to any of daims 16- 103, which method comprises culturing the cell according to claim 107 under conditions permitting the production of the CGTase variant, and recovering the enzyme from the culture.
109. Use of a CGTase variant according to any of claims 16-103, in a process for the manufacture of cyclodextrins.
110. The use according to claim 109, of the CGTase variant in a process for the manufacture of α-, β- and γ-cyclodextrins, or mixtures hereof.
111. The use according to claim 109, of the CGTase variant in a process for the manufacture of δ-, ε-, and ζ-cyclodextrins, or mixtures hereof. 112. Use of a CGTase variant according to any of claims 16-98, in a process for the manufacture of linear oligosaccharides.
113. Use of a CGTase variant according to any of claims 16-98, in a process for in situ generation of cyclodextrins.
114. The use according to claim 113, of the CGTase variant in a process for the manufacture of a baked product.
115. The use according to claim 113, of the CGTase variant in a process for stabilizing chemical products during their manufacture.
116. Use of a CGTase variant according to any of daims 16-98, in a process for in situ generation of linear oligosaccharides.
PCT/DK1996/000179 1995-04-21 1996-04-22 Cyclomaltodextrin glucanotransferase variants WO1996033267A1 (en)

Priority Applications (5)

Application Number Priority Date Filing Date Title
EP96910915A EP0822982B1 (en) 1995-04-21 1996-04-22 Cyclomaltodextrin glucanotransferase variants
DE69635515T DE69635515T2 (en) 1995-04-21 1996-04-22 VARIANTS OF CYCLOMALTODEXTRIN GLUCANOTRANSFERASE
AT96910915T ATE311439T1 (en) 1995-04-21 1996-04-22 VARIANTS OF CYCLOMALTODEXTRIN GLUCANOTRANSFERASE
JP53141396A JP4057055B2 (en) 1995-04-21 1996-04-22 Cyclomaltodextrin glucanotransferase mutant
AU53968/96A AU5396896A (en) 1995-04-21 1996-04-22 Cyclomaltodextrin glucanotransferase variants

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
DK47795 1995-04-21
DK0477/95 1995-04-21
DK117395 1995-10-17
DK1173/95 1995-10-17
DK128195 1995-11-16
DK1281/95 1995-11-16

Related Child Applications (1)

Application Number Title Priority Date Filing Date
US08/947,965 Continuation US6004790A (en) 1995-04-21 1997-10-09 Cyclomaltodextrin glucanotransferase variants

Publications (1)

Publication Number Publication Date
WO1996033267A1 true WO1996033267A1 (en) 1996-10-24

Family

ID=27220709

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/DK1996/000179 WO1996033267A1 (en) 1995-04-21 1996-04-22 Cyclomaltodextrin glucanotransferase variants

Country Status (11)

Country Link
US (1) US6004790A (en)
EP (2) EP1632566A3 (en)
JP (1) JP4057055B2 (en)
KR (1) KR19990007930A (en)
AR (1) AR001678A1 (en)
AT (1) ATE311439T1 (en)
AU (1) AU5396896A (en)
CA (1) CA2217876A1 (en)
DE (1) DE69635515T2 (en)
DK (1) DK0822982T3 (en)
WO (1) WO1996033267A1 (en)

Cited By (31)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP0802259A1 (en) * 1996-04-18 1997-10-22 Consortium für elektrochemische Industrie GmbH Cyclodextrin glucosyltransferases for the production of gamma-cyclodextrin
WO1998050511A1 (en) * 1997-05-05 1998-11-12 Henkel Kommanditgesellschaft Auf Aktien Method for preventing colours from running in textiles during washing
WO1999015633A1 (en) * 1997-09-24 1999-04-01 Novo Nordisk A/S Novel cyclomaltodextrin glucanotransferase variants
WO1999043793A1 (en) * 1998-02-27 1999-09-02 Novo Nordisk A/S Amylolytic enzyme variants
WO1999043794A1 (en) 1998-02-27 1999-09-02 Novo Nordisk A/S Maltogenic alpha-amylase variants
WO2001016349A1 (en) * 1999-09-01 2001-03-08 Novozymes A/S Method for production of maltose and/or enzymatically modified starch
WO2002044350A2 (en) * 2000-11-28 2002-06-06 Henkel Kommanditgesellschaft Auf Aktien Cyclodextrin glucanotransferase (cgtase), obtained from bacillus agaradherens (dsm 9948) and detergents and cleaning agents containing said novel cyclodextrin glucanotransferase
US6472192B1 (en) 1996-04-18 2002-10-29 Consortium für elektrochemische Industrie GmbH Cyclodextrin glycosyl transferases for producing γ-cyclodextrin
EP1284293A2 (en) * 2001-07-11 2003-02-19 Nihon Shokuhin Kako Co., Ltd. Gene coding for cyclodextrin glucanotransferase chiefly producing gamma-cyclodextrin and use thereof
WO2003024242A1 (en) 2001-09-18 2003-03-27 Novozymes A/S Enzymatic treatment of starchy food products for shortening the tempering step
WO2005003337A1 (en) * 2003-07-01 2005-01-13 Novozymes A/S Cgtase variants
US6876932B1 (en) 1998-02-27 2005-04-05 Novozymes A/S Maltogenic alpha-amylase variants
WO2005116180A1 (en) 2004-05-17 2005-12-08 The Procter & Gamble Company Bleaching composition comprising a carbohydrate oxidase
EP1710303A1 (en) * 1998-02-27 2006-10-11 Novozymes A/S Amylolytic enzyme variants
EP2031066A1 (en) * 2006-06-08 2009-03-04 Nihon Shokuhin Kako Co., Ltd. Mutant and gene encoding the same
WO2011005830A1 (en) 2009-07-09 2011-01-13 The Procter & Gamble Company Laundry detergent composition comprising low level of sulphate
WO2011005623A1 (en) 2009-07-09 2011-01-13 The Procter & Gamble Company Laundry detergent composition comprising low level of bleach
US8017371B2 (en) 2004-08-02 2011-09-13 Novozymes A/S Hybrid polypeptide of a maltogenic alpha-amylase and a cyclodextrin glucanotransferase
US8088722B2 (en) 2009-05-26 2012-01-03 The Procter & Gamble Company Aqueous liquid composition for pre-treating soiled dishware
WO2012121297A1 (en) 2011-03-07 2012-09-13 株式会社林原 METHOD FOR PRODUCING 2-O-α-D-GLUCOSYL-L-ASCORBIC ACID ANHYDROUS CRYSTAL-CONTAINING POWDER
WO2016113399A1 (en) * 2015-01-16 2016-07-21 Novozymes A/S Method to improve sliceability of baked goods
WO2018089211A1 (en) 2016-11-08 2018-05-17 Ecolab Usa Inc. Non-aqueous cleaner for vegetable oil soils
WO2019045113A1 (en) 2017-09-04 2019-03-07 昭和電工株式会社 Mixture of inositol derivatives
WO2019045112A1 (en) 2017-09-04 2019-03-07 昭和電工株式会社 Method for producing inositol derivative
EP3456809A1 (en) 2012-10-04 2019-03-20 Ecolab USA, Inc. Pre-soak technology for laundry and other hard surface cleaning
WO2021030676A1 (en) 2019-08-14 2021-02-18 Ecolab Usa Inc. Methods of cleaning and soil release of highly oil absorbing substrates employing optimized extended chain nonionic surfactants
US11103118B2 (en) 2014-08-01 2021-08-31 Ecolab Usa Inc. Method of manual surface cleaning using cleaning textiles and of washing said cleaning textiles
WO2022010911A1 (en) 2020-07-06 2022-01-13 Ecolab Usa Inc. Foaming mixed alcohol/water compositions comprising a structured alkoxylated siloxane
WO2022010906A1 (en) 2020-07-06 2022-01-13 Ecolab Usa Inc. Peg-modified castor oil based compositions for microemulsifying and removing multiple oily soils
WO2022010893A1 (en) 2020-07-06 2022-01-13 Ecolab Usa Inc. Foaming mixed alcohol/water compositions comprising a combination of alkyl siloxane and a hydrotrope/solubilizer
WO2024020445A1 (en) 2022-07-20 2024-01-25 Ecolab Usa Inc. Novel nonionic extended surfactants, compositions and methods of use thereof

Families Citing this family (12)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
JP3934851B2 (en) * 2000-05-23 2007-06-20 日本食品化工株式会社 Novel cyclodextrin gluconotransferase, method for producing the same, and method for producing cyclodextrin using the enzyme
US7700338B2 (en) * 2000-07-19 2010-04-20 Novozymes A/S CGTase and DNA sequence encoding same
WO2003068976A2 (en) * 2002-02-14 2003-08-21 Novozymes A/S Process for producing starch hydrolysate
GB0305685D0 (en) * 2003-03-12 2003-04-16 Danisco Enzyme
EP2248907A1 (en) * 2009-05-08 2010-11-10 Rijksuniversiteit Groningen Gluco-oligosaccharides comprising (alpha 1-->4) and (alpha 1-->6) glycosidic bonds, use thereof, and methods for providing them
CN103740669A (en) * 2013-04-26 2014-04-23 江南大学 Method for improving beta-cyclodextrin production capability of cyclodextrin glycosyltransferase by calcium ion binding site amino acid residue mutation
CN103602641B (en) * 2013-11-20 2015-05-20 广西大学 Beta-cyclodextrin glucosyl tranferase enzyme mutant for producing gamma-cyclodextrin and use thereof
CN104293743B (en) * 2014-09-26 2016-09-07 江南大学 A kind of cyclodextrin glycosyltransferase mutant weakened by Product inhibiton
CN108034645B (en) * 2018-01-15 2020-05-08 江南大学 Preparation and application of cyclodextrin glucosyltransferase mutant
CN111411097B (en) * 2018-12-07 2022-02-15 江南大学 Cyclodextrin glucosyltransferase mutant S90G
CN113493747A (en) * 2020-04-02 2021-10-12 青岛蔚蓝生物集团有限公司 Mutant strain of high-yield cyclodextrin glucosyltransferase and application thereof
CN111534498B (en) * 2020-05-28 2022-03-25 江南大学 Cyclodextrin glucosyltransferase mutant with improved disproportionation specific activity and AA-2G yield

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1989003421A1 (en) * 1987-10-15 1989-04-20 Novo Industri A/S Thermostable cyclodextrin glycosyl transferase, its production and use
WO1991014770A2 (en) * 1990-03-27 1991-10-03 Consortium für elektrochemische Industrie GmbH η-CGTase
US5278059A (en) * 1985-12-04 1994-01-11 Kabushiki Kaisha Hayashibara Seibutsu Kagaki Kenkyujo Polypeptide possessing cyclomaltodextrin glucanotransferase activity
EP0614971A2 (en) * 1993-02-09 1994-09-14 Amano Pharmaceutical Co., Ltd. Novel cyclodextrin glucanotransferase, process for producing the same and process for producing cyclodextrin using the same
EP0630967A1 (en) * 1993-06-24 1994-12-28 Consortium für elektrochemische Industrie GmbH Cyclodextrin glycosyltransferase for the production of gamma-cyclodextrin

Family Cites Families (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5162210A (en) * 1990-06-29 1992-11-10 Iowa State University Research Foundation Process for enzymatic hydrolysis of starch to glucose
JPH0541985A (en) * 1991-03-04 1993-02-23 Oji Koonsutaac Kk Mutant cyclomaltodextrin glucanotransferase
JP3155324B2 (en) * 1992-02-04 2001-04-09 武司 魚住 Cyclodextrin glucanotransferase, method for producing the same, and gene encoding the enzyme
JPH05244945A (en) * 1992-03-04 1993-09-24 Nippon Shokuhin Kako Co Ltd Production of alpha-cyclodextrin
JPH0740938B2 (en) * 1993-03-04 1995-05-10 工業技術院長 Mutant saccharide hydrolase, mutant gene of the enzyme, and method for producing oligosaccharide using the enzyme
JPH0723781A (en) * 1993-06-25 1995-01-27 Oji Koonsutaac Kk Modified cgtase, its production and use

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5278059A (en) * 1985-12-04 1994-01-11 Kabushiki Kaisha Hayashibara Seibutsu Kagaki Kenkyujo Polypeptide possessing cyclomaltodextrin glucanotransferase activity
WO1989003421A1 (en) * 1987-10-15 1989-04-20 Novo Industri A/S Thermostable cyclodextrin glycosyl transferase, its production and use
WO1991014770A2 (en) * 1990-03-27 1991-10-03 Consortium für elektrochemische Industrie GmbH η-CGTase
EP0614971A2 (en) * 1993-02-09 1994-09-14 Amano Pharmaceutical Co., Ltd. Novel cyclodextrin glucanotransferase, process for producing the same and process for producing cyclodextrin using the same
EP0630967A1 (en) * 1993-06-24 1994-12-28 Consortium für elektrochemische Industrie GmbH Cyclodextrin glycosyltransferase for the production of gamma-cyclodextrin

Non-Patent Citations (11)

* Cited by examiner, † Cited by third party
Title
BIOCHEMISTRY, Volume 33, 1994, AKIRA NAKAMURA et al., "Four Aromatic Residues in the Active Center of Cyclodextrin Glucanotransferase from Alkalophilic Bacillus Sp. 1011: Effects of Replacements on Substrate Binding and cyclization Characteristics", pages 9929-9936. *
BIOCHEMISTRY, Volume 34, 1995, DIRK PENNINGA et al., "Site-Directed Mutations in Tyrosine 195 of Cyclodextrin Glycosyl Transferase from Bacillus Circulans Strain 251 Affect Activity and Product Specificity", pages 3368-3376. *
DIALOG INFORMATION SERVICES, File 155, MEDLINE, Dialog Accession No. 07973781, Medline Accession No. 92111781, NAKAMURA A., "Functional Relationships Between Cyclodextrin Glucanotransferase from an Alkalophilic Bacillus and alpha-Amylases. Site-Directed Mutagenesis of the Conserved two Asp and on Glu Residues"; & FEBS LETT., *
DIALOG INFORMATION SERVICES, File 155, MEDLINE, Dialog Accession No. 08610037, Medline Accession No. 93320037, NAKAMURA A., "Three Histidine Residues in the Active Center of Cyclodextrin, Glucanotransferase from Alkalophilic Bacillus Sp. 1011: Effects of the Replacement on Ph Dependence and Transition-State Stabilization"; & *
DIALOG INFORMATION SERVICES, File 155, MEDLINE, Dialog Accession No. 09231397, Medline Accession No. 95161397, STROKOPYTOV B., "X-Ray Structure of Cyclodextrin Glycosyltransferase Complexed with Acarbose, Implications for the Catalytic Mechanism of Glycosidases"; & BIOCHEMISTRY, (UNITED STATES), 21 Feb. 1995, 34(7), *
DIALOG INFORMATION SERVICES, File 155, MEDLINE, Dialog Accession No. 09572717, Medline Accession No. 96094317, KNEGTEL R.M. et al., "Crystallographic Studies of the Interaction of Cyclodextrin Glycosyltransferase from Bacillus Circulans Strain 251 with Natural Substrates and Products"; & J. BIOL. CHEM., (UNITED *
DIALOG INFORMATION SERVICES, File 351, DERWENT WPI, Dialog Accession No. 009410097, WPI Accession No. 93-103608/13, OJI CORN STARCH CO LTD., "Mutated Cyclo Malto Dextran Glucan Transferase CGTase - Prepd. by Culturing Transformants Contg. CGTase Expression Vector Using Starch-Contg. Medium and Sepg. gamma *
DIALOG INFORMATION SERVICES, File 351, DERWENT WPI, Dialog Accession No. 009653923, WPI Accession No. 93-347473/44, NIPPON SHOKUHIN KAKO KK, "New alpha-Cyclodextrin Prepn. by Substituting Tyrosine for Phenylalanine of Cyclo Malto-Dextrin Glucano-Transferase"; & JP,A,05 244 945, (24-09-93). *
DIALOG INFORMATION SERVICES, File 351, DERWENT WPI, Dialog Accession No. 010199689, WPI Accession No. 95-100943/14, OJI CORN STARCH CO LTD., "Modified Cyclo-Malto-Dextrin Glucano-Transferase and Corresp. Gene- Useful in the Prodn. of gamma-Dextrin"; & JP,A,07 023 781, (27-01-95). *
JOURNAL OF BACTERIOLOGY, Volume 174, No. 22, 1992, SHINSUKE FUJIWARA et al., "Analysis of Mutations in Cyclodextrin Glucanotransferase from Bacillus Stearothermophilus Which Affect Cyclization Characteristics and Thermostability", pages 7478-7481. *
JOURNAL OF BIOTECHNOLOGY, Volume 32, 1994, KYEONG-A SIN et al., "Replacement of an Amino Acid Residue of Cyclodextrin Glucano Transferase of Bacillus Ohbensis Doubles the Production of Y-Cyclodextrin", pages 283-288. *

Cited By (54)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US6472192B1 (en) 1996-04-18 2002-10-29 Consortium für elektrochemische Industrie GmbH Cyclodextrin glycosyl transferases for producing γ-cyclodextrin
EP0802259A1 (en) * 1996-04-18 1997-10-22 Consortium für elektrochemische Industrie GmbH Cyclodextrin glucosyltransferases for the production of gamma-cyclodextrin
WO1998050511A1 (en) * 1997-05-05 1998-11-12 Henkel Kommanditgesellschaft Auf Aktien Method for preventing colours from running in textiles during washing
US6271010B1 (en) 1997-09-24 2001-08-07 Novzymes A/S Cyclomaltodextrin glucanotransferase variants
WO1999015633A1 (en) * 1997-09-24 1999-04-01 Novo Nordisk A/S Novel cyclomaltodextrin glucanotransferase variants
EP1571206A1 (en) * 1997-09-24 2005-09-07 Novozymes A/S Cyclomaltodextrin glucanotransferase variants
US6777215B2 (en) 1997-09-24 2004-08-17 Novozymes A/S Cyclomaltodextrin glucanotransferase variants
WO1999043794A1 (en) 1998-02-27 1999-09-02 Novo Nordisk A/S Maltogenic alpha-amylase variants
US8828460B2 (en) 1998-02-27 2014-09-09 Novozymes A/S Method for preparing maltogenic alpha-amylase variants
US6162628A (en) * 1998-02-27 2000-12-19 Novo Nordisk A/S Maltogenic alpha-amylase variants
US6482622B1 (en) 1998-02-27 2002-11-19 Novozymes A/S Amylolytic enzyme variants
US7908094B2 (en) 1998-02-27 2011-03-15 Novozymes A/S Method for preparing maltogenic alpha-amylase variants
EP2305799A2 (en) 1998-02-27 2011-04-06 Novozymes A/S Maltogenic alpha-amylase variants
EP2316929A2 (en) 1998-02-27 2011-05-04 Novozymes A/S Maltogenic alpha-amylase variants
EP1710303A1 (en) * 1998-02-27 2006-10-11 Novozymes A/S Amylolytic enzyme variants
US8232086B2 (en) 1998-02-27 2012-07-31 Novozymes A/S Method for preparing maltogenic alpha-amylase variants
US8546099B2 (en) 1998-02-27 2013-10-01 Novozymes A/S Processes for preparing a dough or a baked product using maltogenic alpha-amylase variants
US6876932B1 (en) 1998-02-27 2005-04-05 Novozymes A/S Maltogenic alpha-amylase variants
WO1999043793A1 (en) * 1998-02-27 1999-09-02 Novo Nordisk A/S Amylolytic enzyme variants
WO2001016349A1 (en) * 1999-09-01 2001-03-08 Novozymes A/S Method for production of maltose and/or enzymatically modified starch
WO2002044350A3 (en) * 2000-11-28 2003-03-13 Henkel Kgaa Cyclodextrin glucanotransferase (cgtase), obtained from bacillus agaradherens (dsm 9948) and detergents and cleaning agents containing said novel cyclodextrin glucanotransferase
WO2002044350A2 (en) * 2000-11-28 2002-06-06 Henkel Kommanditgesellschaft Auf Aktien Cyclodextrin glucanotransferase (cgtase), obtained from bacillus agaradherens (dsm 9948) and detergents and cleaning agents containing said novel cyclodextrin glucanotransferase
US7888104B2 (en) 2000-11-28 2011-02-15 Henkel Ag & Co. Kgaa Cyclodextrin glucanotransferase (CGTase), obtained from<I>Bacillus agaradherens<λ>(DSM 9948) and detergents and cleaning agents containing said novel cyclodextrin glucanotransferase
US6960461B2 (en) 2001-07-11 2005-11-01 Nihon Shokuhin Kako Co., Ltd. Gene coding for cyclodextrin glucanotransferase chiefly producing γ-cyclodextrin and use thereof
EP1284293A3 (en) * 2001-07-11 2003-11-05 Nihon Shokuhin Kako Co., Ltd. Gene coding for cyclodextrin glucanotransferase chiefly producing gamma-cyclodextrin and use thereof
EP1284293A2 (en) * 2001-07-11 2003-02-19 Nihon Shokuhin Kako Co., Ltd. Gene coding for cyclodextrin glucanotransferase chiefly producing gamma-cyclodextrin and use thereof
WO2003024242A1 (en) 2001-09-18 2003-03-27 Novozymes A/S Enzymatic treatment of starchy food products for shortening the tempering step
WO2005003337A1 (en) * 2003-07-01 2005-01-13 Novozymes A/S Cgtase variants
EP1983045A3 (en) * 2003-07-01 2008-12-17 Novozymes A/S CGTase Variants
WO2005116180A1 (en) 2004-05-17 2005-12-08 The Procter & Gamble Company Bleaching composition comprising a carbohydrate oxidase
US8017371B2 (en) 2004-08-02 2011-09-13 Novozymes A/S Hybrid polypeptide of a maltogenic alpha-amylase and a cyclodextrin glucanotransferase
US8309337B2 (en) 2004-08-02 2012-11-13 Novozymes A/S Hybrid polypeptide of a maltogenic alpha-amylase and a cyclodextrin glucanotransferase
EP2031066A4 (en) * 2006-06-08 2009-11-18 Japan Maize Prod Mutant and gene encoding the same
EP2031066A1 (en) * 2006-06-08 2009-03-04 Nihon Shokuhin Kako Co., Ltd. Mutant and gene encoding the same
US8088722B2 (en) 2009-05-26 2012-01-03 The Procter & Gamble Company Aqueous liquid composition for pre-treating soiled dishware
WO2011005830A1 (en) 2009-07-09 2011-01-13 The Procter & Gamble Company Laundry detergent composition comprising low level of sulphate
WO2011005623A1 (en) 2009-07-09 2011-01-13 The Procter & Gamble Company Laundry detergent composition comprising low level of bleach
US10603333B2 (en) 2009-09-03 2020-03-31 Hayashibara Co., Ltd. Process for producing a particulate composition comprising an hydrous crystalline 2-o-alpha-d-glucosyl-ascorbic acid
US9186368B2 (en) 2009-09-03 2015-11-17 Hayashibara Co., Ltd. Process for producing a particulate composition comprising an hydrous crystalline 2-O-α-D-glucosyl-L-ascorbic acid
US9265781B2 (en) 2009-09-03 2016-02-23 Hayashibara Co., Ltd. Process for producing a particulate composition comprising anhydrous crystalline 2-O-alpha-D-glucosyl-L-ascorbic acid
US9872872B2 (en) 2009-09-03 2018-01-23 Hayashibara Co., Ltd. Process for producing a particulate composition comprising an hydrous crystalline 2-O-α-D-glucosyl-L-ascorbic acid
KR20140039177A (en) 2011-03-07 2014-04-01 가부시기가이샤하야시바라 Method for producing 2-o-a-d-glucosyl-l-ascorbic acid anhydrous crystal-containing powder
WO2012121297A1 (en) 2011-03-07 2012-09-13 株式会社林原 METHOD FOR PRODUCING 2-O-α-D-GLUCOSYL-L-ASCORBIC ACID ANHYDROUS CRYSTAL-CONTAINING POWDER
EP3456809A1 (en) 2012-10-04 2019-03-20 Ecolab USA, Inc. Pre-soak technology for laundry and other hard surface cleaning
US11103118B2 (en) 2014-08-01 2021-08-31 Ecolab Usa Inc. Method of manual surface cleaning using cleaning textiles and of washing said cleaning textiles
WO2016113399A1 (en) * 2015-01-16 2016-07-21 Novozymes A/S Method to improve sliceability of baked goods
WO2018089211A1 (en) 2016-11-08 2018-05-17 Ecolab Usa Inc. Non-aqueous cleaner for vegetable oil soils
WO2019045113A1 (en) 2017-09-04 2019-03-07 昭和電工株式会社 Mixture of inositol derivatives
WO2019045112A1 (en) 2017-09-04 2019-03-07 昭和電工株式会社 Method for producing inositol derivative
WO2021030676A1 (en) 2019-08-14 2021-02-18 Ecolab Usa Inc. Methods of cleaning and soil release of highly oil absorbing substrates employing optimized extended chain nonionic surfactants
WO2022010911A1 (en) 2020-07-06 2022-01-13 Ecolab Usa Inc. Foaming mixed alcohol/water compositions comprising a structured alkoxylated siloxane
WO2022010906A1 (en) 2020-07-06 2022-01-13 Ecolab Usa Inc. Peg-modified castor oil based compositions for microemulsifying and removing multiple oily soils
WO2022010893A1 (en) 2020-07-06 2022-01-13 Ecolab Usa Inc. Foaming mixed alcohol/water compositions comprising a combination of alkyl siloxane and a hydrotrope/solubilizer
WO2024020445A1 (en) 2022-07-20 2024-01-25 Ecolab Usa Inc. Novel nonionic extended surfactants, compositions and methods of use thereof

Also Published As

Publication number Publication date
JP4057055B2 (en) 2008-03-05
KR19990007930A (en) 1999-01-25
EP1632566A2 (en) 2006-03-08
EP0822982A1 (en) 1998-02-11
CA2217876A1 (en) 1996-10-24
EP1632566A3 (en) 2006-08-16
AR001678A1 (en) 1997-11-26
AU5396896A (en) 1996-11-07
EP0822982B1 (en) 2005-11-30
DE69635515T2 (en) 2006-08-10
DK0822982T3 (en) 2006-02-13
ATE311439T1 (en) 2005-12-15
JPH11503906A (en) 1999-04-06
US6004790A (en) 1999-12-21
DE69635515D1 (en) 2006-01-05

Similar Documents

Publication Publication Date Title
EP0822982B1 (en) Cyclomaltodextrin glucanotransferase variants
Penninga et al. Site-directed mutations in tyrosine 195 of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 affect activity and product specificity
Tonkova Bacterial cyclodextrin glucanotransferase
Gawande et al. Purification and properties of a novel raw starch degrading cyclomaltodextrin glucanotransferase from Bacillus firmus
Gawande et al. Purification and properties of a novel raw starch degrading-cyclodextrin glycosyltransferase from Klebsiella pneumoniae AS-22
EP0605040A1 (en) Pullulanase, micro-organisms producing the same, method for preparation thereof as well as its use
Takada et al. Biochemical and genetic analyses of a novel γ-cyclodextrin glucanotransferase from an alkalophilic Bacillus clarkii 7364
Larsen et al. Purification and characterisation of cyclodextrin glycosyltransferase from Paenibacillus sp. F8
Jemli et al. A β-cyclodextrin glycosyltransferase from a newly isolated Paenibacillus pabuli US132 strain: purification, properties and potential use in bread-making
Wind et al. Engineering of factors determining α‐amylase and cyclodextrin glycosyltransferase specificity in the cyclodextrin glycosyltransferase from Thermoanaerobacterium thermosulfurigenes EM1
WO1995034642A1 (en) Novel transferase and amylase, process for producing the enzymes,use thereof, and gene coding for the same
Rahman et al. Molecular cloning of a cyclodextrin glucanotransferase gene from alkalophilic Bacillus sp. TS1-1 and characterization of the recombinant enzyme
Moriwaki et al. Production and characterization of a new cyclodextrin glycosyltransferase from Bacillus firmus isolated from Brazilian soil
US5474917A (en) Modified cyclodextrin glycosyltransferases for producing γ-cyclodextrins
EP1017793B1 (en) Novel cyclomaltodextrin glucanotransferase variants
Chang et al. Effects of mutations in the starch-binding domain of Bacillus macerans cyclodextrin glycosyltransferase
Charoensakdi et al. Cloning and expression of cyclodextrin glycosyltransferase gene from Paenibacillus sp. T16 isolated from hot spring soil in northern Thailand
JP3155324B2 (en) Cyclodextrin glucanotransferase, method for producing the same, and gene encoding the enzyme
Hyun-Dong et al. Site-directed mutagenesis and functional analysis of maltose-binding site of β-cyclodextrin glucanotransferase from Bacillus firmus var. alkalophilus
US5804426A (en) Recombinant cyclodextran glucanotransferase mutants
Thombre et al. Cyclodextrin Glycosyl Transferase (CGTase): An overview of their production and biotechnological applications
JP4989922B2 (en) Mutant and gene encoding the same
Rojtinnakorn et al. Immunoaffinity purification and characterization of cyclodextrin glycosyltransferase from Bacillus circulans A11
Alcalde et al. Effect of Chemical Modification of Cyclodextrin Glycosyltransferase (CGTase) from Thermoanaerobacter sp. on Its Activity and Product Selectivitya
Keadsin Construction of Chimeric Cyclodextrin Glucanotransferases by Homologous Recombination and Study of Their Activites

Legal Events

Date Code Title Description
AK Designated states

Kind code of ref document: A1

Designated state(s): AL AM AT AU AZ BB BG BR BY CA CH CN CZ DE DK EE ES FI GB GE HU IS JP KE KG KP KR KZ LK LR LS LT LU LV MD MG MK MN MW MX NO NZ PL PT RO RU SD SE SG SI SK TJ TM TR TT UA UG US UZ VN AM AZ BY KG KZ MD RU TJ TM

AL Designated countries for regional patents

Kind code of ref document: A1

Designated state(s): KE LS MW SD SZ UG AT BE CH DE DK ES FI FR GB GR IE IT LU MC NL PT SE BF BJ CF CG CI CM GA GN

DFPE Request for preliminary examination filed prior to expiration of 19th month from priority date (pct application filed before 20040101)
121 Ep: the epo has been informed by wipo that ep was designated in this application
WWE Wipo information: entry into national phase

Ref document number: 1996910915

Country of ref document: EP

ENP Entry into the national phase

Ref document number: 2217876

Country of ref document: CA

Ref country code: CA

Ref document number: 2217876

Kind code of ref document: A

Format of ref document f/p: F

WWE Wipo information: entry into national phase

Ref document number: 08947965

Country of ref document: US

ENP Entry into the national phase

Ref country code: JP

Ref document number: 1996 531413

Kind code of ref document: A

Format of ref document f/p: F

WWE Wipo information: entry into national phase

Ref document number: 1019970707453

Country of ref document: KR

WWP Wipo information: published in national office

Ref document number: 1996910915

Country of ref document: EP

REG Reference to national code

Ref country code: DE

Ref legal event code: 8642

WWP Wipo information: published in national office

Ref document number: 1019970707453

Country of ref document: KR

WWR Wipo information: refused in national office

Ref document number: 1019970707453

Country of ref document: KR

WWG Wipo information: grant in national office

Ref document number: 1996910915

Country of ref document: EP