JP2007074995A - Modified type 2-deoxyribose 5-phosphate aldolase and its use - Google Patents

Abstract

<P>PROBLEM TO BE SOLVED: To provide a new use of 2-deoxyribose 5-phosphate aldolase (DERA) and to provide a modified type DERA suitable for the new use and to provide a nucleic acid, etc., encoding the DERA. <P>SOLUTION: The method for synthesis of a β-ketol by one step aldol reaction uses the DERA as a catalyst. The modified type DERA comprises an amino acid sequence in which one or more amino acids corresponding to the amino acids selected from a group comprising amino acids on 73th, 76th, 139th, 238th and 239th position of an amino acid sequence in the wild type DERA having a specific sequence, are substituted. The nucleic acid encodes the modified DERA. <P>COPYRIGHT: (C)2007,JPO&INPIT

Description

  The present invention relates to a novel utilization form of 2-deoxyribose 5-phosphate aldolase (hereinafter also referred to as “DERA”), a modified form of DERA (hereinafter also referred to as “modified DERA”), and a nucleic acid encoding the same And a design method of modified DERA.

2-Deoxyribose 5-phosphate aldolase (DERA: EC 4.1.2.1) is a kind of glycolytic enzyme, and is reversible between D-glyceraldehyde 3-phosphate and acetaldehyde in vivo. Catalyze aldol reaction.
On the other hand, DERA has been reported to catalyze a one-step aldol reaction (Non-Patent Document 1 (J. Am. Chem. Soc. 112, 2014-2016 (1990)). Describes that the aldol reaction between phenyl aldehyde as an acceptor substrate and acetaldehyde as a donor substrate does not catalyze, so DERA derived from E. coli is a highly hydrophobic compound containing a benzene ring It was thought that the aldol reaction using phosphine as a substrate could not be catalyzed.

WO03 / 0777868 pamphlet J. et al. Am. Chem. Soc. 112, 2014-2016 (1990)

  An object of the present invention is to provide a novel usage form of DERA, and to provide a modified DERA suitable for the new usage form, a nucleic acid encoding the same, and the like.

Based on the above background, the present inventors tried to use DERA for the synthesis of a compound that is difficult to chemically synthesize, and conducted synthetic experiments using various acceptor substrates and donor substrates. As a result, surprisingly, DERA catalyzes a one-step aldol reaction using benzyloxyacetaldehyde as an acceptor substrate and acetone as a donor substrate, and is useful as a pharmaceutical and agrochemical intermediate (S) -5-benzyloxy. It has been found that -4-hydroxy-2-pentanone ((S) -5-benzyloxy-4-hydroxy-2-pentaneone, hereinafter also referred to as “(S) -BHP”) can be synthesized. This finding is an unexpected discovery in light of previous reports that DERA derived from E. coli can catalyze a one-step aldol reaction with a benzene ring and a highly hydrophobic compound as an acceptor substrate. Create new utility value of DERA derived from E. coli. That is, it can be expected that the use of DERA derived from Escherichia coli will be greatly expanded by the results of the present inventors.
Here, the synthesis of (S) -BHP by aldolase has not been reported so far. (S) -BHP is useful as an optically active intermediate when a compound having physiological activity or the like is synthesized. For example, by the following reaction (see Tetrahedron Lett. 33,2557-2560 (1992)), from (S) -BHP, an antibacterial compound synthesis raw material (J. Org. Chem. 48, 5017-5022 (1983)) The chiral 1,2,4-pentanetriol used in 1) is obtained.
As described above, (S) -BHP is a useful compound as a pharmaceutical intermediate. However, synthesis using asymmetric catalysts that are currently generally used requires a large amount of catalyst and is a reaction under extremely low temperature conditions ( For example, see J. Am. Chem. Soc. 121, 669-685 (1999)), which is a problem from the viewpoint of green chemistry. Therefore, (S) -BHP production under mild reaction conditions is desired. The results of the present inventors have revealed that it is possible to synthesize (S) -BHP using DERA, opening the way to solve the problems of the current synthesis method. That is, it is possible to efficiently synthesize (S) -BHP under mild reaction conditions.

Further research was conducted and the synthesis activity and stereoselectivity of DERA derived from Escherichia coli in the synthesis of (S) -BHP were examined, and there was room for improvement. Therefore, an attempt was made to introduce a mutation into the wild-type enzyme in order to improve the synthesis activity and stereoselectivity of DERA derived from E. coli. When a unique new modeling technique was adopted in determining the position of introduction of mutation in the amino acid sequence, that is, designing the modified enzyme, a plurality of modified enzymes having improved synthetic activity and stereoselectivity were successfully obtained. This not only means that a promising modified enzyme could be obtained for practical use or industrial use, but also supports that the employed modeling technique is effective for modifying DERA. In general, proteins having the same catalytic function generally have similar positions and structures of the active site and the region involved in substrate specificity. For example, DERA of the hyperthermophile Aeropyrum pernix has a low amino acid homology of 29%, but it is reported that the three-dimensional structure and amino acids around the substrate are similar (J. Biol. Chem. 278, 10799-). 10806 (2003)). Therefore, the information obtained regarding the effect of substitution of a specific amino acid in DERA derived from a specific E. coli strain is naturally applicable to DERA derived from the same genus E. coli, and is expected to be applicable to DERA derived from other microorganisms. It was done.
In addition, in the international publication 03/0777868 pamphlet (patent document 1), although the optimization of E. coli origin DERA is reported for the purpose of improving the activity with respect to deoxyribose, mention about the synthesis | combination of (S) -BHP. There is no.

The present invention is mainly based on the above results, and includes the following modified DERA, a method for designing modified DERA, such as a gene encoding modified DERA, and a method for synthesizing a compound using a one-step aldol reaction by DERA. provide.
[1] In the amino acid sequence of wild-type 2-deoxyribose 5-phosphate aldolase, selected from the group consisting of amino acids at positions 73, 76, 139, 238, and 239 of the amino acid sequence shown in SEQ ID NO: 1. A modified 2-deoxyribose 5-phosphate aldolase comprising an amino acid sequence in which amino acids corresponding to one or more amino acids are substituted, wherein the amino acids after substitution at positions 238 and / or 239 are as follows:
The substituted amino acid at position 238 is tyrosine, glycine, arginine or alanine;
The amino acid after substitution at position 239 is methionine, asparagine, glycine or leucine.
[2] The modified 2-deoxyribose 5 according to [1], wherein the wild-type 2-deoxyribose 5-phosphate aldolase is 2-deoxyribose 5-phosphate aldolase derived from E. coli. -Phosphate aldolase.
[3] The modified type according to [1], wherein the amino acid sequence of the wild-type 2-deoxyribose 5-phosphate aldolase is an amino acid sequence having 80% or more homology with the amino acid sequence shown in SEQ ID NO: 1. 2-Deoxyribose 5-phosphate aldolase.
[4] The modified 2-deoxyribose 5-phosphate aldolase according to [1], wherein the amino acid sequence of the wild-type 2-deoxyribose 5-phosphate aldolase is the amino acid sequence shown in SEQ ID NO: 1.
[5] The modified 2-deoxyribose according to [4], wherein the amino acid at position 73 and / or 76 is substituted in the amino acid sequence shown in SEQ ID NO: 1, and the amino acid after substitution is as follows: 5-phosphate aldolase:
The substituted amino acid at position 73 is proline, cysteine, threonine, serine or tryptophan;
The amino acid after substitution at position 76 is arginine, tyrosine or tryptophan.
[6] The modified 2-deoxyribose 5-phosphate aldolase according to [4], wherein the amino acid at position 139 is substituted in the amino acid sequence shown in SEQ ID NO: 1, and the substituted amino acid is valine or methionine .
[7] The modified 2-deoxyribose according to [4], wherein the amino acid at position 238 and / or 239 is substituted in the amino acid sequence shown in SEQ ID NO: 1, and the amino acid after substitution is as follows: 5-phosphate aldolase:
The substituted amino acid at position 238 is tyrosine, glycine, arginine or alanine;
The amino acid after substitution at position 239 is methionine, asparagine, glycine or leucine.
[8] The modified 2-deoxyribose 5-phosphate aldolase according to [1], comprising the amino acid sequence of any one of the following (1) to (18):
(1) in the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which position 73 valine is substituted with proline;
(2) in the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which valine 73 is substituted with cysteine and phenylalanine 76 is substituted with arginine;
(3) an amino acid sequence obtained by substituting threonine for position 73 in the amino acid sequence of SEQ ID NO: 1;
(4) in the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which valine 73 is substituted with threonine and phenylalanine 76 is substituted with tyrosine;
(5) in the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which valine 73 is substituted with serine and phenylalanine 76 is substituted with tryptophan;
(6) an amino acid sequence obtained by replacing position 73 valine with cysteine in the amino acid sequence of SEQ ID NO: 1;
(7) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which valine 73 is substituted with proline and phenylalanine 76 is substituted with tyrosine;
(8) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which position 73 valine is substituted with tryptophan and position 76 phenylalanine is replaced with tryptophan;
(9) an amino acid sequence obtained by substituting isoleucine at position 139 with valine in the amino acid sequence of SEQ ID NO: 1;
(10) an amino acid sequence obtained by substituting isoleucine at position 139 with methionine in the amino acid sequence of SEQ ID NO: 1;
(11) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence obtained by substituting 238th serine with tyrosine and 239th serine with methionine;
(12) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence obtained by substituting 238th serine with glycine and 239th serine with asparagine;
(13) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which the 238th serine is substituted with arginine and the 239th serine is substituted with glycine;
(14) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which serine at position 238 is substituted with alanine and serine at position 239 is substituted with leucine;
(15) an amino acid sequence obtained by substituting serine 239 with leucine in the amino acid sequence of SEQ ID NO: 1;
(16) In the amino acid sequence of SEQ ID NO: 1, the amino acid sequence obtained by substituting serine 238 with glycine. (17) In the amino acid sequence of SEQ ID NO: 1, valine 73 is substituted with proline, and phenylalanine 76 is tyrosine. An amino acid sequence in which serine at position 238 is substituted with arginine and serine at position 239 is substituted with glycine;
(18) In the amino acid sequence of SEQ ID NO: 1, valine at position 73 is substituted with proline, phenylalanine at position 76 is substituted with tyrosine, serine at position 238 is substituted with alanine, and serine at position 239 is substituted with leucine An array.
[9] An isolated nucleic acid encoding the modified 2-deoxyribose 5-phosphate aldolase according to any one of [1] to [8].
[10] A vector carrying the nucleic acid according to [9].
[11] A transformant having the nucleic acid according to [9].
[12] An acceptor substrate composed of benzyloxyacetaldehyde having a substituent on the benzene ring or unsubstituted, a donor substrate composed of a ketone having 3 to 6 carbon atoms, and 2-deoxyribose 5-phosphate aldolase as a catalyst A method for synthesizing β-ketol, wherein the synthesis is performed by an aldol reaction.
[13] The synthesis method according to [12], wherein the 2-deoxyribose 5-phosphate aldolase is the modified 2-deoxyribose 5-phosphate aldolase according to any one of [1] to [8]. .
[14] The synthesis method according to [12] or [13], wherein the acceptor substrate is a compound represented by the following chemical formula:
In the formula, R is a substituent on the benzene ring and is a hydrogen atom, a halogen atom, a hydroxyl group, an alkyl group, an alkoxy group, a nitro group, or a cyano group.
[15] The synthesis method according to [12] or [13], wherein the substrate is benzyloxyacetaldehyde and the donor substrate is acetone.
[16] One or more selected from the group consisting of the amino acid at position 73, the amino acid at position 76, the amino acid at position 139, the amino acid at position 238, and the amino acid at position 239 in the amino acid sequence of 2-deoxyribose 5-phosphate aldolase A method for designing a modified 2-deoxyribose 5-phosphate aldolase, comprising constructing an amino acid sequence in which the amino acids are substituted.
[17] A method for designing a modified 2-deoxyribose 5-phosphate aldolase, comprising the following steps:
(1) A step of preparing three-dimensional structure information of wild-type or modified 2-deoxyribose 5-phosphate aldolase during catalytic reaction when 2-deoxyribose 5-phosphate is used as a substrate;
(2) a step of substituting the target substrate from 2-deoxyribose 5-phosphate in the three-dimensional structure information;
(3) performing a molecular mechanics calculation of wild-type or modified 2-deoxyribose 5-phosphate aldolase to calculate an energy minimized structure;
(4) comparing the structures before and after the calculation, and selecting amino acids in which side chain movement is recognized as substitution candidates;
(5) A step of constructing an amino acid sequence in which the selected amino acid is substituted in the amino acid sequence of wild-type or modified 2-deoxyribose 5-phosphate aldolase.
[18] Before the step (4), amino acids within 3 mm from the target substrate are extracted from the amino acids constituting the wild-type 2-deoxyribose 5-phosphate aldolase, and the extraction is performed in the step (4). The design method according to [17], wherein substitution candidates are selected from the amino acids obtained.
[19] The design method according to [17] or [18], wherein the target substrate is β-ketol.

(Modified DERA)
The first aspect of the present invention relates to a modified 2-deoxyribose 5-phosphate aldolase (modified DERA). The present invention has found the fact that wild-type DERA catalyzes the aldol reaction between benzyloxyacetaldehyde and acetone to synthesize β-ketol (see Examples below), and the specific amino acid of wild-type DERA Based on the knowledge that substitution is effective in improving DERA synthetic activity and substrate specificity (see Examples below), modified DERA with β-ketol synthetic activity improved over wild-type DERA is provided. To do. The modified DERA of the present invention has an amino acid sequence in which a specific amino acid is substituted in the amino acid sequence of the corresponding wild-type enzyme. The modified DERA of the present invention is typically produced or designed by substituting some amino acids with other amino acids in the naturally occurring DERA, ie, wild-type DERA. Thus, the DERA that is the basis (derived from) the modified DERA of the present invention is expressed as “wild type DERA” in the present specification. In addition, among the amino acids constituting the wild type DERA, the amino acid to be substituted (that is, among the amino acids constituting the wild type DERA, a difference is recognized as compared with the modified DERA). Or “substitution amino acid”.

  Specific examples of wild-type DERA include E. coli. and DERA produced by E. coli K-12. The amino acid sequence constituting the wild type DERA is shown in SEQ ID NO: 1. E. In addition to wild-type DERA produced by E. coli K-12 strain, E. Examples thereof include DERA having high homology with wild-type DERA produced by E. coli K-12 strain. The amino acid sequence homology here is preferably 80% or more, more preferably 90% or more, and still more preferably 95% or more. For example, E.I. Coli CFTO 73 (100%), E.C. Coli O157: H7 (99%), Shigella flexneri 2a str. 301 (99%), Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150 (96%), Salmonella enterica subsp. enterica serovar Typhi Ty2 (96%), Klebsiella pneumoniae (94%), Vibrio cholerae 01 biovartor str. DERA produced by N16961 (83%), Vibrio parahaemolyticus RIMD 2210633 (82%), Vibrio vulnificus YJ016 (81%), etc. The amino acid sequence has a very high homology with DERA produced by E. coli K-12, and can be said to be a suitable wild-type DERA. The numbers in parentheses following the microorganism name are E. The homology to E. coli K-12-derived DERA is shown.

  The amino acid to be substituted in the present invention is an amino acid corresponding to the amino acid at positions 73, 76, 139, 238, or 239 of the amino acid sequence shown in SEQ ID NO: 1 in the amino acid sequence constituting wild-type DERA. It is. Here, the term “corresponding” when used for amino acid residues in the present specification means that the protein (enzyme) to be compared has an equivalent contribution to the performance of its function, and in particular, Means equal contribution to substrate specificity. For example, the amino acid sequence to be compared can be optimally compared with the reference amino acid sequence (that is, the amino acid sequence of SEQ ID NO: 1) while considering partial homology of the primary structure (that is, amino acid sequence). When a sequence is aligned (the gap may be introduced as necessary to optimize alignment), the amino acid at the position corresponding to the specific amino acid in the reference amino acid sequence is identified as the “corresponding amino acid”. can do. Also included are amino acids that have the same spatial positions as positions 238 and 239 extracted in step (4) of the modified DERA design method below and positions 73, 76, and 139 extracted in step (a).

  The modified DERA of the present invention has an amino acid sequence in which one or more of the substitution target amino acids are substituted in the amino acid sequence of wild-type DERA. For example, in one embodiment of the present invention, a modified DERA in which substitution at position 73 and substitution at position 76 is performed is provided. In another embodiment of the present invention, a modified DERA in which substitution at position 228 and substitution at position 239 is performed is provided.

  Here, the type of amino acid after substitution is not particularly limited. For example, proline, cysteine, threonine, serine or tryptophan is substituted at position 73, arginine, tyrosine or tryptophan is substituted at position 76, and valine or methionine is substituted at position 139. The substitution at position 238 is tyrosine, glycine, arginine or alanine, and the substitution at position 239 is methionine, asparagine, glycine or leucine.

Specific examples of the modified DERA of the present invention include those having the following amino acid sequences. These amino acid sequences are amino acid sequences in which a specific amino acid sequence is substituted in the amino acid sequence of SEQ ID NO: 1 (amino acid sequence of wild-type DERA of Escherichia coli K-12 strain). Corresponds to type DERA (variants 1-18).
(1) An amino acid sequence obtained by substituting proline at position 73 in the amino acid sequence of SEQ ID NO: 1 (variant 1)
(2) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which position 73 valine is substituted with cysteine and position 76 phenylalanine is replaced with arginine (variant 2)
(3) An amino acid sequence obtained by substituting threonine at position 73 in the amino acid sequence of SEQ ID NO: 1 (variant 3)
(4) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which valine 73 is substituted with threonine and phenylalanine 76 is substituted with tyrosine (variant 4)
(5) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which position 73 valine is substituted with serine and position 76 phenylalanine is replaced with tryptophan (variant 5)
(6) Amino acid sequence obtained by substituting cysteine at position 73 for cysteine in the amino acid sequence of SEQ ID NO: 1 (variant 6)
(7) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which position 73 valine is substituted with proline and position 76 phenylalanine is replaced with tyrosine (variant 7)
(8) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which position 73 valine is replaced with tryptophan and position 76 phenylalanine is replaced with tryptophan (variant 8)
(9) Amino acid sequence obtained by substituting 139 isoleucine with valine in the amino acid sequence of SEQ ID NO: 1 (variant 9)
(10) An amino acid sequence obtained by substituting isoleucine at position 139 with methionine in the amino acid sequence of SEQ ID NO: 1 (variant 10)
(11) Amino acid sequence obtained by substituting serine at position 238 with tyrosine and substituting serine at position 239 with methionine in the amino acid sequence of SEQ ID NO: 1 (variant 11)
(12) An amino acid sequence in which the 238th serine is substituted with glycine and the 239th serine is substituted with asparagine in the amino acid sequence of SEQ ID NO: 1 (variant 12)
(13) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence obtained by substituting 238th serine with arginine and 239th serine with glycine (variant 13)
(14) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which the serine at position 238 is substituted with alanine and the serine at position 239 is replaced with leucine (variant 14)
(15) Amino acid sequence obtained by substituting serine 239 with leucine in the amino acid sequence of SEQ ID NO: 1 (variant 15)
(16) An amino acid sequence obtained by substituting serine 238 with glycine in the amino acid sequence of SEQ ID NO: 1 (variant 16)
(17) In the amino acid sequence of SEQ ID NO: 1, valine at position 73 is substituted with proline, phenylalanine at position 76 is substituted with tyrosine, serine at position 238 is substituted with arginine, and serine at position 239 is substituted with glycine Sequence (variant 17)
(18) In the amino acid sequence of SEQ ID NO: 1, valine at position 73 is substituted with proline, phenylalanine at position 76 is substituted with tyrosine, serine at position 238 is substituted with alanine, and serine at position 239 is substituted with leucine Sequence (variant 18)

  As shown in Examples described later, the above modified DERA can provide a high yield in the synthesis of (S) -BHP using benzyloxyacetaldehyde as an acceptor substrate, and has a high enantiomeric excess (ee). Especially in variant 4, it is 96.4% ee.

The modified DERA of the present invention has an amino acid sequence in which the specific amino acid substitution is performed in the amino acid sequence of the wild-type DERA, but some amino acid modifications other than the position related to the specific amino acid substitution May be performed. As described above, the present invention provides a protein (hereinafter referred to as “homologous protein”) that has the same function but has a different amino acid sequence when compared with the modified DERA having the amino acid sequence in which the specific amino acid substitution has been performed. Is also provided). “Partially differing amino acid sequences” typically means deletion, substitution, or addition, insertion or insertion of one to several amino acids, or these. It means that the amino acid sequence is mutated (changed) by the combination. The difference in the amino acid sequence here is permissible as long as the characteristics relating to the aldol reaction are not significantly reduced (preferably within the limit that is substantially maintained). As long as this condition is satisfied, the positions where the amino acid sequences are different are not particularly limited, and differences may occur at a plurality of positions. The term “plurality” as used herein refers to, for example, a number corresponding to less than about 30% of all amino acids, preferably a number corresponding to less than about 20%, and more preferably a number corresponding to less than about 10%. The number is preferably less than about 5%, and most preferably less than about 1%. That is, the homologous protein is, for example, about 70% or more, preferably about 80% or more, more preferably about 90% or more, with any one of the amino acid sequences ((1) to (18)) of the modified DERA (variants 1 to 18). Even more preferably about 95% or more, most preferably about 99% or more.
Preferably, homologous proteins are obtained by making conservative amino acid substitutions at amino acid residues that are not involved in the aldol reaction. As used herein, “conservative amino acid substitution” refers to substitution of a certain amino acid residue with an amino acid residue having a side chain having the same properties. Depending on the side chain of the amino acid residue, a basic side chain (eg, lysine, arginine, histidine), an acidic side chain (eg, aspartic acid, glutamic acid), an uncharged polar side chain (eg, asparagine, glutamine, serine, threonine, tyrosine, cysteine) ), Non-polar side chains (eg glycine, alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), β-branched side chains (eg threonine, valine, isoleucine), aromatic side chains (eg tyrosine, phenylalanine, Like tryptophan), it is classified into several families. A conservative amino acid substitution is preferably a substitution between amino acid residues within the same family.

Here, the identity (%) of two amino acid sequences or two nucleic acids (hereinafter, “two sequences” is used as a term including them) can be determined, for example, by the following procedure. First, two sequences are aligned for optimal comparison (eg, a gap may be introduced into the first sequence to optimize alignment with the second sequence). When a molecule (amino acid residue or nucleotide) at a specific position in the first sequence is the same as the molecule at the corresponding position in the second sequence, the molecule at that position is said to be the same. The identity of two sequences is a function of the number of identical positions common to the two sequences (ie, identity (%) = number of identical positions / total number of positions × 100), preferably the optimal alignment Take into account the number and size of gaps required for conversion.
Comparison of two sequences and determination of identity can be accomplished using a mathematical algorithm. Specific examples of mathematical algorithms available for sequence comparison are described in Karlin and Altschul (1990) Proc. Natl. Acad. Sci. USA 87: 2264-68; Karlin and Altschul (1993) Proc. Natl. There is an algorithm modified in Acad. Sci. USA 90: 5873-77, but it is not limited to this. Such an algorithm is incorporated into the NBLAST and XBLAST programs (version 2.0) described in Altschul et al. (1990) J. Mol. Biol. 215: 403-10. In order to obtain an amino acid sequence that is homologous to a certain amino acid sequence, for example, a BLAST polypeptide search may be performed using the XBLAST program with score = 50 and wordlength = 3. Similarly, in order to obtain a nucleotide sequence homologous to a certain nucleic acid, for example, a BLAST nucleotide search may be performed with score = 100 and wordlength = 12, using the NBLAST program. To obtain a gap alignment for comparison, the Gapped BLAST described in Altschul et al. (1997) Amino Acids Research 25 (17): 3389-3402 can be used. When utilizing BLAST and Gapped BLAST, the default parameters of the corresponding programs (eg, XBLAST and NBLAST) can be used. Please refer to http://www.ncbi.nlm.nih.gov for details. Examples of other mathematical algorithms that can be used for sequence comparison include the algorithm described in Myers and Miller (1988) Comput Appl Biosci. 4: 11-17. Such an algorithm is incorporated in the ALIGN program available for example on a GENESTREAM network server (IGH Montpellier, France) or an ISREC server. When using the ALIGN program for comparison of amino acid sequences, for example, a PAM120 residue mass table can be used, with a gap length penalty = 12 and a gap penalty = 4.
The identity of two amino acid sequences, using the Gloss program of the GCG software package, using a Blossom 62 matrix or PAM250 matrix, gap weight = 12, 10, 8, 6, or 4, gap length weight = 2, 3 Or 4 can be determined. In addition, the degree of homology between two nucleic acid sequences can be determined using the GAP program in the GCG software package (available at http://www.gcg.com) with gap weight = 50 and gap length weight = 3. it can.

  The modified DERA of the present invention has improved β-ketol synthesis activity and / or stereoselectivity (substrate specificity) for β-ketol compared to the corresponding wild-type DERA. A preferred form provides a modified DERA in which these two properties are superior to wild-type DERA. The modified DERA of the present invention preferably has β-ketol synthesis activity that is twice or more that of wild-type DERA.

The modified DERA of the present invention can be prepared by expressing a gene encoding it in an appropriate expression system. Hereinafter, an example of a method for preparing a gene encoding modified DERA and an example of a method for preparing modified DERA using the obtained gene will be described.
<Acquisition of gene encoding wild type DERA>
The wild type DERA gene can be obtained from a DERA-producing bacterium. Here, the DERA-producing bacterium refers to a bacterium that originally holds the DERA gene or a bacterium that has been introduced exogenously into the DERA gene. As an example of the former, Escherichia coli K-12 can be mentioned, and as an example of the latter, an Escherichia coli having a vector obtained by cloning the DERA gene of Escherichia coli K-12 can be mentioned.
In order to obtain a DERA gene from a bacterium that inherently holds the DERA gene, for example, PCR using a genomic DNA of the bacterium as a template and a DERA-specific primer may be performed. On the other hand, when a bacterium having a vector in which the DERA gene is cloned can be used, the DERA gene can be extracted and purified from the bacterium according to a conventional method.
In addition, E. coli possessing a vector obtained by cloning DERA of E. coli K-12 and E. coli K-12 can be obtained from a culture collection such as American Type Culture Collection (ATCC).

<Construction of polynucleotide encoding modified DERA>
A gene encoding the desired modified DERA is prepared by adding a mutation to the wild-type DERA gene obtained as described above so that a specific amino acid is substituted in the protein that is the expression product. be able to. Many methods for such position-specific nucleotide sequence substitution are known in the art (see, for example, Molecular Cloning, Third Edition, Cold Spring Harbor Laboratory Press, New York), among which appropriate methods are available. Can be selected and used.

  As a position-specific mutation introducing method, a position-specific amino acid saturation mutation method can be employed. The position-specific amino acid saturation mutation method is a “Semi-rational, semi-random” technique in which a position where a desired function is involved is estimated based on the three-dimensional structure of a protein and an amino acid saturation mutation is introduced (J. Mol. Biol.331, 585-592 (2003)). For example, it is possible to introduce a position-specific amino acid saturation mutation using a kit such as Quick change (Stratagene), Overlap extension PCR (Nucleic Acid Res. 16, 7351-7367 (1988)). As the DNA polymerase used for PCR, Taq polymerase or the like can be used. However, it is preferable to use a highly accurate DNA polymerase such as KOD-PLUS- (Toyobo), Pfu turbo (Stratagene).

  On the other hand, the modified DERA is also encoded by inserting a random mutation into the DERA gene and comparing the substrate specificity of the expression product of each mutant (modified) to select a gene having a preferred substrate specificity. Genes can be created. When introducing such a random mutation, first, a mutation is randomly introduced into a target gene region using, for example, error-pron PCR, and a modified DERA gene library is constructed. Then, clones are selected from the obtained library using enzyme activity and substrate specificity as indices.

(Nucleic acid encoding modified DERA, etc.)
Another aspect of the present invention relates to a nucleic acid related to the modified DERA of the present invention. In this aspect, an isolated nucleic acid encoding modified DERA, a nucleic acid that can be used as a probe for identifying a nucleic acid encoding modified DERA, or amplifying or mutating a nucleic acid encoding modified DERA Nucleic acids that can be used as primers for the purpose are provided.
Nucleic acids encoding modified DERA are typically utilized for the preparation of modified DERA. According to the genetic engineering preparation method using a nucleic acid encoding modified DERA, it is possible to obtain modified DERA in a more homogeneous state. This method can also be said to be a suitable method for preparing a large amount of modified DERA. The use of the nucleic acid encoding modified DERA is not limited to the preparation of modified DERA. For example, the nucleic acid can also be used as an experimental tool for elucidating the mechanism of action of modified DERA, or as a tool for designing or creating a further modified version of DERA.

  The term “nucleic acid” herein includes DNA (including cDNA and genomic DNA), RNA (including mRNA), DNA analogs, and, unless it is clear that it is not intended to include it. Contains RNA analogs. The form of the nucleic acid of the present invention is not limited, that is, it may be either single-stranded or double-stranded. Double-stranded DNA is preferable. Codon degeneracy is also considered. That is, in the case of a nucleic acid encoding a protein, it may have an arbitrary base sequence as long as the protein is obtained as its expression product.

  In the present specification, the “nucleic acid encoding modified DERA” refers to a nucleic acid obtained by expressing the modified DERA, and has a base sequence corresponding to the amino acid sequence of the modified DERA. The nucleic acid includes, of course, a nucleic acid obtained by adding a sequence that does not encode an amino acid sequence to such a nucleic acid.

  As used herein, the term “isolated nucleic acid” refers to nucleic acids that are naturally occurring (eg, nucleic acids in E. coli), typically separated from other nucleic acids that coexist in the natural state. A state nucleic acid. However, some other nucleic acid components such as adjacent nucleic acid sequences in the natural state may be included. For example, a preferred form of “isolated nucleic acid” in the case of genomic DNA is substantially free of other DNA components that coexist in the natural state (including DNA sequences that are contiguous in the natural state).

An “isolated nucleic acid” in the case of a nucleic acid produced by genetic recombination technology, such as a cDNA molecule, preferably refers to a nucleic acid that is substantially free of cell components, culture medium, and the like. Similarly, an “isolated nucleic acid” in the case of a nucleic acid produced by chemical synthesis is preferably substantially free of precursors (raw materials) such as dNTPs and chemical substances used in the synthesis process. Refers to nucleic acid.
Whether the nucleic acid is present as part of a vector or composition or present in a cell as an exogenous molecule, it is an “isolated nucleic acid” as long as it exists as a result of artificial manipulation.
Unless otherwise specified, when simply described as “nucleic acid” in the present specification, it means an isolated nucleic acid.

The nucleic acid of the present invention has the following sequence as a preferred embodiment. These base sequences are nucleic acids encoding modified DERA (variants 1 to 18) shown in the examples described later.
(1) A nucleotide sequence in which the portion encoding valine 73 in the nucleotide sequence of SEQ ID NO: 2 is substituted with a nucleotide encoding proline (variant 1)
(2) In the base sequence of SEQ ID NO: 2, a base encoding valine 73 is replaced with a base encoding cysteine, and a base encoding phenylalanine 76 is replaced with a base encoding arginine. Array (variant 2)
(3) A nucleotide sequence in which the portion encoding valine 73 in the nucleotide sequence of SEQ ID NO: 2 is substituted with a nucleotide encoding threonine (variant 3)
(4) In the nucleotide sequence of SEQ ID NO: 2, a base encoding valine 73 is substituted with a base encoding threonine, and a base 76 encoding phenylalanine is replaced with a base encoding tyrosine. Sequence (variant 4)
(5) In the nucleotide sequence of SEQ ID NO: 2, a base encoding 73 position valine is replaced with a serine encoding base, and a 76 position phenylalanine encoding base is replaced with a tryptophan encoding base. Sequence (variant 5)
(6) A base sequence in which the part encoding valine 73 is substituted with a base encoding cysteine in the base sequence of SEQ ID NO: 2 (variant 6)
(7) In the base sequence of SEQ ID NO: 2, a portion encoding 73 position valine is substituted with a base encoding proline, and a portion encoding position 76 phenylalanine is replaced with a base encoding tyrosine. Sequence (variant 7)
(8) In the base sequence of SEQ ID NO: 2, a portion coding for position 73 valine is substituted with a base coding for tryptophan, and a portion coding for position 76 phenylalanine is substituted with a base coding for tryptophan Sequence (variant 8)
(9) A nucleotide sequence obtained by replacing the portion encoding 139 isoleucine with a nucleotide encoding valine in the nucleotide sequence of SEQ ID NO: 2 (variant 9)
(10) A nucleotide sequence in which the portion encoding 139 isoleucine in the nucleotide sequence of SEQ ID NO: 2 is substituted with a nucleotide encoding methionine (variant 10)
(11) A base obtained by substituting the 238th serine-encoding portion with a tyrosine-encoding base and the 239th serine-encoding portion with a methionine-encoding base in the base sequence of SEQ ID NO: 2. Sequence (variant 11)
(12) A base obtained by substituting the base encoding glycine for the 238th serine and the part encoding 239th serine for the asparagine base in the base sequence of SEQ ID NO: 2. Sequence (variant 12)
(13) A base obtained by substituting the 238th serine-encoding portion with a base encoding arginine and the 239th serine-encoding portion with a base encoding glycine in the base sequence of SEQ ID NO: 2. Sequence (variant 13)
(14) A base obtained by substituting the 238-position serine-encoding portion with an alanine-encoding base and the 239-position serine-encoding portion with a leucine-encoding base in the nucleotide sequence of SEQ ID NO: 2. Sequence (variant 14)
(15) A nucleotide sequence obtained by replacing the portion encoding 239th serine with a nucleotide encoding leucine in the nucleotide sequence of SEQ ID NO: 2 (variant 15)
(16) A base sequence in which the part encoding serine 238 in the base sequence of SEQ ID NO: 2 is replaced with a base encoding glycine (variant 16)
(17) In the nucleotide sequence of SEQ ID NO: 2, a portion encoding valine at position 73 is replaced with a base encoding proline, and a portion encoding phenylalanine at position 76 is replaced with a base encoding tyrosine, and position 238 A nucleotide sequence in which the serine-encoding portion is substituted with a base encoding arginine and the 239th serine-encoding portion is substituted with a glycine-encoding base (variant 17)
(18) In the nucleotide sequence of SEQ ID NO: 2, the portion encoding valine at position 73 is substituted with a base encoding proline, and the portion encoding phenylalanine at position 76 is replaced with a base encoding tyrosine, and position 238 A base sequence (variant 18) in which the serine-encoding portion is substituted with an alanine-encoding base, and the 239th serine-encoding portion is substituted with a leucine-encoding base.

  The nucleic acid of the present invention is isolated by using standard genetic engineering techniques, molecular biological techniques, biochemical techniques, etc. with reference to the sequence information disclosed in this specification or the attached sequence listing. Can be prepared.

In another aspect of the present invention, the function of the protein encoded by the nucleic acid ((1) to (18)) encoding the modified DERA (variants 1 to 18) when compared with any of the nucleotide sequences is as follows: Nucleic acids (hereinafter also referred to as “homologous nucleic acids”. In addition, base sequences that define homologous nucleic acids are also referred to as “homologous base sequences”) are provided. Examples of homologous nucleic acids include substitution, deletion, and insertion of one or more bases based on any base sequence of the nucleic acid ((1) to (18)) encoding the modified DERA (variants 1 to 18). And a DNA encoding a protein consisting of a base sequence containing an addition, or an inversion, and having an activity of catalyzing a synthesis reaction of β-ketol. Base substitution or deletion may occur at a plurality of sites. The term “plurality” as used herein refers to, for example, 2 to 40 bases, preferably 2 to 20 bases, more preferably 2 to 10 bases, although it varies depending on the position and type of amino acid residues in the three-dimensional structure of the protein encoded by the nucleic acid. It is.
Such homologous nucleic acids include, for example, restriction enzyme treatment, treatment with exonuclease and DNA ligase, position-directed mutagenesis (Molecular Cloning, Third Edition, Chapter 13, Cold Spring Harbor Laboratory Press, New York) It can be obtained by introducing mutations by a mutation introducing method (Molecular Cloning, Third Edition, Chapter 13, Cold Spring Harbor Laboratory Press, New York). Homologous nucleic acids can also be obtained by other methods such as ultraviolet irradiation.

  Another aspect of the present invention relates to a nucleic acid having a base sequence complementary to the base sequence of any one of the nucleic acids ((1) to (18)) encoding the modified DERA (variants 1 to 18). Still another embodiment of the present invention provides a nucleotide sequence of any one of the nucleic acids ((1) to (18)) encoding the modified DERA (variants 1 to 18) or a nucleotide sequence complementary to any of these. In contrast, nucleic acids having at least about 60%, 70%, 80%, 90%, 95%, 99%, 99.9% identical base sequences are provided.

  Still another embodiment of the present invention is the nucleotide sequence complementary to the nucleotide sequence of any one of the nucleic acids ((1) to (18)) encoding the modified DERA (variants 1 to 18) or a homologous nucleotide sequence thereof. The present invention relates to a nucleic acid having a base sequence that hybridizes under stringent conditions. The “stringent conditions” here are conditions under which so-called specific hybrids are formed and non-specific hybrids are not formed. Such stringent conditions are known to those skilled in the art, such as Molecular Cloning (Third Edition, Cold Spring Harbor Laboratory Press, New York) and Current protocols in molecular biology (edited by Frederick M. Ausubel et al., 1987). Can be set with reference to. As stringent conditions, for example, hybridization solution (50% formamide, 10 × SSC (0.15M NaCl, 15 mM sodium citrate, pH 7.0), 5 × Denhardt solution, 1% SDS, 10% dextran sulfate, 10 μg / ml denaturation Conditions of incubation at about 42 ° C. to about 50 ° C. using salmon sperm DNA, 50 mM phosphate buffer (pH 7.5), and then washing at about 65 ° C. to about 70 ° C. using 0.1 × SSC, 0.1% SDS Can be mentioned. More preferable stringent conditions include, for example, 50% formamide, 5 × SSC (0.15M NaCl, 15 mM sodium citrate, pH 7.0), 1 × Denhardt solution, 1% SDS, 10% dextran sulfate, 10 μg / ml as a hybridization solution. Of denatured salmon sperm DNA, 50 mM phosphate buffer (pH 7.5)).

Still another embodiment of the present invention is the nucleotide sequence of any one of the nucleic acids ((1) to (18)) encoding the modified DERA (variants 1 to 18), or a nucleotide sequence complementary to any of these. Nucleic acids having a portion (nucleic acid fragments) are provided. Such a nucleic acid fragment detects, identifies, and identifies the nucleic acid of the present invention, such as a nucleic acid having any one of the nucleic acids ((1) to (18)) encoding the modified DERA (variants 1 to 18). It can be used for amplification. The nucleic acid fragment is, for example, a nucleotide portion (for example, about 10 to about 100 bases in length, continuous in the base sequence of any one of the nucleic acids ((1) to (18)) encoding the modified DERA (variants 1 to 18), preferably Is designed to include at least a portion that hybridizes to a length of about 20 to about 100 bases, more preferably about 30 to about 100 bases.
When used as a probe, a nucleic acid fragment can be labeled. For labeling, for example, fluorescent substances, enzymes, and radioisotopes can be used.

Still another aspect of the present invention relates to a vector containing the nucleic acid of the present invention (nucleic acid encoding modified DERA or a part thereof or a homologue thereof). As used herein, the term “vector” refers to a nucleic acid molecule capable of transporting a nucleic acid inserted therein into a target such as a cell, and is a plasmid vector, cosmid vector, phage vector, viral vector (adenovirus vector, Adeno-associated virus vectors, retrovirus vectors, herpesvirus vectors, etc.).
An appropriate vector is selected depending on the purpose of use (cloning, protein expression) and in consideration of the type of host cell. M13 phage or a variant thereof, λ phage or a variant thereof, pBR322 or a variant thereof (pB325, pAT153, pUC8, etc.), etc. Examples of vectors using insect cells as hosts include pAc and pVL, and examples of vectors using mammalian cells as hosts include pCDM8 and pMT2PC.

The vector of the present invention is preferably an expression vector. “Expression vector” refers to a vector capable of introducing a nucleic acid inserted therein into a target cell (host cell) and allowing expression in the cell. Expression vectors usually contain a promoter sequence necessary for the expression of the inserted nucleic acid, an enhancer sequence that promotes expression, and the like. An expression vector containing a selectable marker can also be used. When such an expression vector is used, the presence / absence (and extent) of introduction of the expression vector can be confirmed using a selection marker.
Insertion of the nucleic acid of the present invention into a vector, insertion of a selectable marker gene (if necessary), insertion of a promoter (if necessary), etc. are performed using standard recombinant DNA techniques (for example, Molecular Cloning, Third Edition, 1.84, Cold). A known method using a restriction enzyme and DNA ligase, which can be referred to Spring Harbor Laboratory Press, New York.
As the host cell, it is preferable to use a bacterial cell such as Escherichia coli from the viewpoint of easy handling.

  Another aspect of the present invention relates to a host cell (ie, transformant) into which the nucleic acid of the present invention has been introduced. The transformant of the present invention can be obtained by transfection or transformation using the vector of the present invention. Transfection and the like include calcium phosphate coprecipitation, electroporation (Potter, H. et al., Proc. Natl. Acad. Sci. USA 81, 7161-7165 (1984)), lipofection (Felgner, PL et al., Proc Natl. Acad. Sci. USA 84,7413-7417 (1984)) and the like.

The transformant of the present invention can be used for producing the modified DERA of the present invention. That is, another aspect of the present invention provides a method for producing the modified DERA of the present invention using the transformant. The production method of the present invention includes at least a step of culturing the above transformant under conditions under which the modified DERA of the present invention is produced. Usually, in addition to this step, a step of recovering (separating and purifying) the produced protein is performed.
As a nutrient source of the medium used for culturing the transformant, those usually used for culturing the transformant can be used. Any carbon compound that can be assimilated may be used as the carbon source. For example, glucose, sucrose, lactose, maltose, lactose, molasses, pyruvic acid and the like are used. The nitrogen source may be any nitrogen compound that can be used. For example, peptone, meat extract, yeast extract, casein hydrolyzate, soybean cake alkaline extract, and the like are used. In addition, phosphates, carbonates, sulfates, salts such as magnesium, calcium, potassium, iron, manganese, and zinc, specific amino acids, specific vitamins, and the like are used as necessary.

  The transformant is cultured under temperature conditions where the transformant can grow and modified DERA is produced. For example, the culture temperature can be set within a range of 30 ° C. to 40 ° C. (preferably around 37 ° C.). The culture time can be set in consideration of the growth characteristics of the transformant to be cultured and the production characteristics of the modified DERA. The pH of the medium is adjusted so that the transformant grows and DERA is produced. Preferably, the pH of the medium is about 6.0 to 9.0 (preferably around pH 7.0).

Although the culture solution containing the cells producing the modified DERA can be used as an enzyme solution as it is, or after concentration, removal of impurities, etc., in general, once the modified DERA is temporarily used from the culture solution or the cells. to recover. If the produced modified DERA is a secreted protein, it can be recovered from the culture solution, and otherwise it can be recovered from the microbial cells. When recovering from the culture solution, for example, the culture supernatant is filtered and centrifuged to remove insolubles, followed by concentration under reduced pressure, membrane concentration, salting out using ammonium sulfate or sodium sulfate, methanol, ethanol, acetone, etc. Fractionation methods such as fractional precipitation, dialysis, heat treatment, isoelectric point treatment, gel filtration, adsorption chromatography, ion exchange chromatography, affinity chromatography, etc. (eg Sephadex gel (Pharmacia Biotech) gel) Separation and purification by combining filtration, DEAE Sepharose CL-6B (Pharmacia Biotech), Octyl Sepharose CL-6B (Pharmacia Biotech), CM Sepharose CL-6B (Pharmacia Biotech)), etc. Obtainable. On the other hand, when recovering from the microbial cells, the microbial cells are collected by filtering, centrifuging, etc., and then the microbial cells are subjected to mechanical methods such as pressure treatment, ultrasonic treatment, or enzymatic methods such as lysozyme. After disruption by the method, purified DERA can be obtained by separation and purification in the same manner as described above.
The purified enzyme obtained as described above can be provided by pulverization, for example, by freeze drying, vacuum drying or spray drying. At that time, the purified enzyme may be dissolved in a phosphate buffer, triethanolamine buffer, Tris-HCl buffer or GOOD buffer in advance. Preferably, a phosphate buffer or a triethanolamine buffer can be used. In addition, PIPES, MES, or MOPS is mentioned as a GOOD buffer here.

(Method for synthesizing β-ketol using DERA as a catalyst)
As another aspect, the present invention provides a method for synthesizing β-ketol using DERA as a catalyst. In the synthesis method of the present invention, a benzene ring-substituted or unsubstituted benzyloxyacetaldehyde (the following chemical formula) is used as an acceptor substrate, a ketone having 3 to 6 carbon atoms is used as a donor substrate, and DERA is catalyzed. Β-ketol is synthesized by combining the two in the aldol reaction. In addition, it is preferable to add 0.5-10 equivalent of donor substrates with respect to an acceptor substrate, and to react. In the case of a substrate that does not dissolve in water, it is preferable to use dimethyl sulfoxide (DMSO) or the like as an emulsifier.
In the formula, R is a substituent on the benzene ring and is a hydrogen atom, a halogen atom, a hydroxyl group, an alkyl group, an alkoxy group, a nitro group, or a cyano group.

In a preferred embodiment of the present invention, benzyloxyacetaldehyde shown below is used as an acceptor substrate.

On the other hand, acetone is preferably used for the donor substrate. A synthesis reaction of β-ketol using acetone as a donor substrate is shown below.
In the formula, R is a substituent on the benzene ring and is a hydrogen atom, a halogen atom, a hydroxyl group, an alkyl group, an alkoxy group, a nitro group, or a cyano group.

In the most preferred embodiment of the present invention, as shown in the following reaction formula, optically active 5-benzyloxy-4-hydroxy-2-pentanone ((S) —) is obtained by a one-step aldol reaction using benzyloxyacetaldehyde and acetone. BHP) is synthesized.

  In the synthesis method of the present invention, DERA is used as a catalyst. DERA may be a wild type or a modified type. Preferably, the modified DERA of the present invention is used as a catalyst. High yields can be expected by using the modified DERA of the present invention. In addition, as will be apparent from the examples described later, some modified DERAs provide a higher enantiomeric excess (ee) than the corresponding wild-type DERA. Therefore, the use of modified DERA is preferable from the viewpoint of stereoselectivity.

This reaction can be carried out in a state where benzyloxyacetaldehyde and acetone as substrates are dissolved or dispersed in a buffer solution such as a Tris-HCl buffer solution or a triethanolamine buffer solution. Here, the hydrogen ion concentration (pH) of the buffer solution is, for example, 3 to 12, and preferably 5 to 9.
In this reaction, an organic solvent having compatibility with water such as methanol, ethanol, acetone, dimethyl sulfoxide (DMSO), dimethylformamide (DMF) or the like may be added in order to increase the solubility of the substrate in the buffer solution. it can. The amount of these organic solvents used is preferably 0.01 to 30% by weight with respect to the buffer solution.
In addition, this reaction can be performed in a two-phase system using an organic solvent that is not compatible with water, such as toluene, diethyl ether, hexane, or ethyl acetate, and the buffer solution. The reaction can also be carried out in these organic solvents without using the buffer solution.

Commercially available benzyloxyacetaldehyde (above (Formula 3)) used in the present invention can be used, but 2-benzyloxyethanol is oxidized according to the method described in JP-A-2000-290214. Can also be manufactured.
The concentration of benzyloxyacetaldehyde (above (Chemical Formula 3)) in the reaction solution is not particularly limited, but is usually preferably 0.01 to 20% by weight.
Moreover, as acetone, a commercially available thing can be used. The usage-amount of acetone is 0.5-20 mol with respect to 1 mol of benzyloxyacetaldehyde, Preferably it is 2-10 mol.

The method for adding benzyloxyacetaldehyde (formula (1)) and acetone, which are substrates for this reaction, is not particularly limited, and can be added all at once or dividedly. These substrates can also be added by dissolving in advance in water or the organic solvent.
The reaction temperature of this reaction varies depending on the thermal stability of the aldolase used, but is usually 1 to 80 ° C.
Isolation and purification of 5-benzyloxy-4-hydroxy-2-pentanone ((S) -BHP) produced by this reaction can be performed by a known method such as extraction, distillation or column chromatography.

(Design method for modified DERA)
The present invention provides, as yet another aspect, a method for designing a modified DERA. A modified DERA can be produced (prepared) based on the structural information obtained by the design method of the present invention.
The present invention roughly provides two types of design methods. The first design method is based on the fact that the yield and the substrate specificity can be improved by performing a specific amino acid substitution on wild-type DERA. The amino acid of 2-deoxyribose 5-phosphate aldolase One or more amino acids selected from the group consisting of amino acid at position 73, amino acid at position 76, amino acid at position 139, amino acid at position 238, and amino acid at position 239 in the sequence are substituted with other amino acids. .
On the other hand, the second design method of the present invention includes a modeling method on a computer based on experimental confirmation of the effectiveness of the method employed by the present inventors when acquiring modified DERA. . Specifically, the following steps (1) to (5) are included.
(1) Step of preparing three-dimensional structure information of wild-type 2-deoxyribose 5-phosphate aldolase during catalytic reaction using 2-deoxyribose 5-phosphate (hereinafter also referred to as “2DR5P”) as a substrate .
(2) A step of substituting a substrate portion from 2-deoxyribose 5-phosphate with a target substrate in the three-dimensional structure information.
(3) A step of calculating an energy-minimized structure by performing molecular mechanics calculation under conditions where the main chain of wild-type 2-deoxyribose 5-phosphate aldolase is fixed and only the side chain vibrates.
(4) A step of comparing structures before and after calculation and selecting amino acids in which side chain movement is recognized as substitution candidates.
(5) A step of constructing an amino acid sequence in which the selected amino acid is substituted in the amino acid sequence of wild-type 2-deoxyribose 5-phosphate aldolase.

In step (1), the three-dimensional structure information of wild type DERA when acting on 2-deoxyribose 5-phosphate which is the original substrate is obtained. The three-dimensional structure information of wild-type DERA can be acquired from, for example, Protein Data Bank (http://www.pdbj.org/index_j.html). The origin of wild-type DERA is not particularly limited, and for example, three-dimensional structure information (for example, 1 JCL) of wild-type DERA derived from E. coli (for example, E. coli K-12 strain) is obtained.
After obtaining the three-dimensional structure information, the substrate and the active center amino acid (lysine at position 167) may be extracted.

In step (2), the substrate is rewritten (replaced). That is, the original substrate 2-deoxyribose 5-phosphate is rewritten to the target substrate. For example, in step (1), the information on the three-dimensional structure of the complex is acquired. In step (2), the information on the substrate portion is deleted from the three-dimensional structure information on the complex, and then the three-dimensional structure information on the target substrate is applied. . Here, it is preferable to perform molecular mechanics calculation on the target substrate and apply the obtained energy minimized structure. This is because, in step (4), the three-dimensional position comparison including the substrate of the initial structure and the energy minimization structure is performed.
Examples of the target substrate include various β-ketols (for example, (S) -BHP).

  In step (3), molecular mechanics calculation is performed on the entire complex of the target substrate and wild type DERA, and an energy minimized structure is calculated. The molecular mechanics calculation is preferably performed under the condition that the main chain of wild type DERA is fixed and only the side chain vibrates. The goal is to improve selectivity to the target substrate by optimizing amino acids near the substrate. Therefore, in order to focus on the space near the substrate, the calculation is performed under the condition that only the side chain vibrates.

  In step (4), the structures before and after the molecular mechanics calculation in step (3) are compared. That is, the structure of the wild type DERA before the energy minimization is compared with the structure of the wild type DERA after the energy minimization. As a result, among the constituent amino acids of wild-type DERA, amino acids in which side chain movement was observed before and after energy minimization were selected as substitution candidates. Here, when the target substrate is set to (S) -BHP, among the amino acids in the hydrophilic region facing the benzene ring of (S) -BHP, amino acids in which side chain movement was observed before and after the calculation were substituted candidates It is good to select as. The movement of the side chain indicates a part that affects the configuration, and it may be possible to optimize the target substrate by substitution of the corresponding amino acid.

  Prior to step (4), amino acids within 3Å are extracted from the target substrate from among the amino acids constituting wild-type DERA, and in step (4), substitution candidates are selected from the extracted amino acids. It is preferable. Thus, if amino acids that can directly act on a substrate are extracted in advance, substitution candidates that act effectively can be selected efficiently.

  In step (5), the amino acid selected in step (4) is substituted with another amino acid in the amino acid sequence of wild-type DERA. In this manner, an amino acid sequence in which a specific amino acid is substituted in the amino acid sequence of wild-type DERA is constructed and used as an amino acid sequence constituting the modified DERA.

Here, the donor substrate in the reaction of DERA against the original substrate 2DR5P is acetaldehyde, while the donor substrate in the one-step aldol reaction with DERA in the present invention is a ketone (usually acetone). Therefore, when the donor substrates of both reactions are compared, a change from a hydrogen atom to a methyl group is observed. In one aspect of the present invention, in view of this change, in order to design a modified DERA having a high catalytic ability for a one-step aldol reaction, in place of steps (2) to (4), preferably step (4), or In addition to these steps, the following step (a) is performed.
(A) A step of selecting amino acids located around the terminal methyl group of β-ketol, which is a target substrate, among the constituent amino acids of wild-type 2-deoxyribose 5-phosphate aldolase as substitution candidates.
Specifically, for example, when the target substrate is set to (S) -BHP, the hydrophobic amino acid facing the terminal methyl group of (S) -BHP, which is located near the active center amino acid of the enzyme, is a candidate for substitution. It is good to select as.
Even before this step (a), amino acids within 3 mm are extracted from the target substrate from among the amino acids constituting the wild-type DERA. In step (a), substitution is made from the extracted amino acids. It is preferable to select candidates.

  The above design method can be performed using, for example, software Insight II (manufactured by Axcelis), and an energy-minimized structure can be calculated by molecular mechanics calculation using the Discover 3 module.

(Activity measurement method)
In the present invention, “aldolase activity” refers to the activity of degrading 2-deoxyribose 5-phosphate (2DR5P) into D-glyceraldehyde 3-phosphate and acetaldehyde. The method for measuring the aldolase activity is in accordance with a previously reported method (Eur. J. Biochem. 125, 561-566 (1982), J. Am. Chem. Soc. 117, 3333-3339 (1995)). The principle of the method for measuring aldolase activity, the reagents used, and the measurement conditions are shown below.
<Measurement principle>
Acetaldehyde generated by the degradation reaction of 2DR5P by DERA is converted to ethanol by alcohol dehydrogenase. At this time, 2DR5P degrading activity is calculated from the amount of NADH (nicotinamide adenine dinucleotide reduced form) that decreases in a coupled manner.
<Reagent>
Activity measurement solution: 100 mM Tris-HCl (pH 7.5), 0.2 mM 2DR5P, 200 U Alcohol dehydrogenase (Sigma) derived from Saccharomyces cerevisiae, 0.1 mM NADH
<Measurement conditions>
The enzyme solution is added to 1 ml of the activity measurement solution, and the decrease in absorbance at a wavelength of 340 nm accompanying the decrease in NADH at 40 ° C. is measured for 2 minutes. The amount of enzyme that decreases 1 μmol of NADH per minute is defined as 1 unit (U) of enzyme activity. The mmol extinction coefficient of NADH at 340 nm is 6.22 mM ⁻¹ cm ⁻¹ .

  Unless otherwise specified, genetic engineering operations in this specification are, for example, Molecular Cloning (Third Edition, Cold Spring Harbor Laboratory Press, New York) or Current protocols in molecular biology (edited by Frederick M. Ausubel et al., 1987).

1. Synthesis of (S) -BHP by wild-type DERA In order to find a novel use of 2-deoxyribose 5-phosphate aldolase (DERA), the catalytic activity of DERA in a synthetic reaction system using various acceptor substrates and donor substrates was investigated. We searched exhaustively. Specifically, using DERA freeze-dried powder derived from Escherichia coli K-12 described in the following examples, 0.5 M acetone and 0.05 M various aldehydes were added in triethanolamine buffer (pH 7.3), and a catalyst was added. Activity was examined. As a result of the search, it was surprisingly found that DERA catalyzes the synthesis of (S) -BHP by a one-step aldol reaction using benzyloxyacetaldehyde as an acceptor substrate and acetone as a donor substrate. Although there has been a report that DERA derived from Escherichia coli catalyzes a one-step aldol reaction, DERA derived from Escherichia coli does not catalyze a reaction that binds phenylaldehyde and acetaldehyde. It was expected that the aldol reaction using a compound having a high hydrophobicity as a substrate could not be catalyzed. The above synthesis reaction found by the present inventors is contrary to this expectation and provides a novel use of DERA.
As a result of the study by the present inventors, it was found that (S) -BHP can be synthesized with a synthesis yield of 95% and an enantiomeric excess of about 80% by reacting under the following conditions.
(1) Composition of reaction solution 200 ml of buffer solution containing 0.5 M acetone and 0.05 M benzyloxyacetaldehyde (0.1 M triethanolamine pH 7.3 (including 1 mM EDTA))
(2) Amount of enzyme 3000 U of DERA derived from E. coli K-12
(3) Reaction temperature 30 ° C
(4) Reaction time 72 hours

2. 2. Preparation of modified DERA 2-1. Acquisition of E. coli-derived aldolase gene E. coli cited in a report by Chen et al. (J. Am. Chem. Soc. 114, 741-748 (1992)). E. coli harboring a vector (referred to as pBR322 / dera) in which the DERA gene derived from E. coli K-12 is cloned. E. coli ATCC 86963 strain was obtained from American Type Culture Collection (ATCC).
In LB liquid medium (polypeptone 1%, yeast extract 0.5%, sodium chloride 0.5% (pH 7.0)). E. coli ATCC86963 strain was inoculated and cultured with shaking at 37 ° C. for 18 hours. The culture solution was centrifuged to obtain wet cells as a precipitate. The plasmid vector pBR322 / dera was purified from the wet cells using a Wizard Plus SV Minipreps (Promega) kit.

2-2. Cloning of DERA gene derived from E. coli The DERA gene was amplified by PCR from the purified pBR322 / dera and cloned from the multiple cloning site Hind III of the expression vector pUC18 into EcoRI.
PCR was carried out using primers (pUC18EcoRI-F primer, pUC18HindIII-RV primer) provided with HindIII upstream of the DERA gene terminal and EcoRI linker downstream, and the target fragment was amplified. Using KOD-Plus-DNA polymerase (Toyobo), PCR was performed according to the following procedure. That is, 5 μl of buffer solution, 2 μl of magnesium sulfate adjusted to 25 mM, 5 μl of dNTP mixed solution adjusted to 2 mM each, 1.5 μl of the primer DNA adjusted to 10 μM, 1 ng of pBR322 / dera, 1 μl of the DNA polymerase In addition, the total volume was adjusted to 50 μl. After reacting at 94 ° C. for 2 minutes with a commercially available temperature cycling apparatus (Thermal cycler Takara), 25 temperature cycles of 94 ° C. for 15 seconds, 55 ° C. for 30 seconds, and 68 ° C. for 60 seconds were performed. .
After completion of the reaction, the reaction solution was subjected to agarose gel electrophoresis and separated, and then the target fragment was excised and the gene was purified using MinElute Extraction Kit (QIAGEN).
pUC18EcoRI-F primer: 5'-GGGGAATTCGATGACTGATCTGA (SEQ ID NO: 3)
pUC18HindIII-RV primer: 5'-GGGAAGCTTTTAGTAGCTGC (SEQ ID NO: 4)

The obtained gene was treated with restriction enzymes Hind III and EcoRI (both from NEB), and subjected to agarose gel electrophoresis to purify the target fragment in the same manner as described above. pUC18 (Toyobo Co., Ltd.) was treated with the same restriction enzyme and ligated with the above gene. Using the obtained recombinant plasmid (hereinafter referred to as pUC18 / dera), E. coli was used. E. coli JM109 was transformed and LB plate agar medium (50 μg / ml ampicillin, 0.1 mM IPTG: isopropyl-β-D-thiogalactopyranoside, 40 μg / ml X-Gal: 5-bromo-4-chloro-3-indolyl -Containing β-D-galactoside). Subsequently, the agar medium was allowed to stand at 37 ° C. and cultured. Among the grown E. coli colonies, white colonies were selected.
White colonies were inoculated into LB liquid medium (containing 50 μg / ml ampicillin), and plasmid pUC18 / dera was purified as described above. The nucleotide sequence was determined by the following procedure using the purified plasmid. First, using M13 Universal Primer (M13 M4 Primer (SEQ ID NO: 5) or M13 RV Primer (SEQ ID NO: 6) (Takara)) and Big Dye Terminator Cycle Sequencing Kit (Perkin Elmer Applied Biosystems) The gene was amplified. Subsequently, the base sequence was analyzed using ABI PISM 310 Genetic Analyzer (Perkin Elmer Applied Biosystems).
The obtained sequence data was analyzed, and it was confirmed that the insert matched the gene sequence derived from E. coli of SEQ ID NO: 2. That is, the base sequence of the insert coincided with the DERA (gene name deoC) gene sequence published in databases such as GenBank and EMBAL as SEQ ID NO: X03224.
M13 M4 primer; 5'-GTTTTCCCAGTCACGAC (SEQ ID NO: 5)
M13 RV primer; 5'-CAGGAAACAGCATTGAC (SEQ ID NO: 6)

2-3. Cultivation of pUC18 / dera recombinant bacteria The culture of pUC18 / dera recombinant E. coli was carried out using a terrific broth medium containing 50 μg / ml ampicillin (tryptone 1.2%, yeast extract 2.4%, glycerol 40 ml / l, dihydrogen phosphate). Inoculate colonies grown on LB agar medium (containing 50 μg / ml ampicillin) in 20 ml of potassium 0.231%, dipotassium hydrogenphosphate 1.254% (phosphoric acid is separately sterilized), Cultured with shaking at 37 ° C. for 18 hours. The main culture was added to 1000 ml of a terrific broth medium containing 50 μg / ml ampicillin, cultured at 37 ° C. until OD660 = 0.6, IPTG was added to a final concentration of 1 mM, and the culture was further continued for 6 hours. . After completion of the culture, the cells were collected by centrifugation (5000 g, 10 minutes), washed with 0.85% NaCl, and further centrifuged to obtain wet cells.
The crude purification of the enzyme was performed with reference to the report of Wong et al. (J. Am. Chem. Soc., 114, 741-748 (1992)). The suspension was suspended in 100 mM Tris-HCl (pH 7.3) buffer solution (containing 1 mM EDTA) 5 times the weight of wet bacteria, and after ultrasonic disruption, centrifuged, and the supernatant was collected. 1% (w / v) streptomycin sulfate was added to the supernatant and allowed to stand for 20 minutes, followed by centrifugation to remove nucleic acid as a precipitated fraction. Ammonium sulfate was added to the obtained supernatant, and a fraction that precipitated at 30 to 80% (w / v) was obtained by centrifugation. After adding the said buffer solution and suspending to the obtained precipitation, it moved to the dialysis tube (Wako Pure Chemical Industries), and dialyzed with respect to distilled water. After dialysis, preliminary freezing was performed with liquid nitrogen, followed by freeze drying with a freeze dryer (Tokyo Rika Kikai Co., Ltd.) to obtain a crude enzyme powder.

2-4.2 Measurement of DR5P degradation activity The amount of NADH (nicotinamide adenine dinucleotide reduced form) that decreases as a result of conversion of acetaldehyde generated by the degradation reaction of 2DR5P by DERA into ethanol with alcohol dehydrogenase. 2DR5P degrading activity was calculated.
Add the enzyme solution to the activity measurement solution (100 mM Tris-HCl (pH 7.5), 0.2 mM 2DR5P, 200 U budding yeast alcohol dehydrogenase (Sigma), 0.1 mM NADH) to make 1 ml, and decrease NADH at 40 ° C. The decrease in absorbance at a wavelength of 340 nm accompanying the measurement was measured for 2 minutes. The amount of enzyme that decreased 1 μmol NADH per minute at 40 ° C. was defined as 1 unit (U) of enzyme activity. The mmol extinction coefficient of NADH at 340 nm was 6.22 mM ⁻¹ cm ⁻¹ .

2-5. Preparation of racemic BHP synthetic standard Am. Chem. Soc. 118, 4322-4343 (1996), a racemic synthetic preparation was prepared by the following reaction.

3 g of benzyloxyacetaldehyde and 2.6 g of isopropynyloxyTMS were dissolved in 100 ml of methylene chloride. Boron trifluoride diethyl etherate was added dropwise to the resulting solution at −78 ° C. under an argon atmosphere. After stirring for 10 minutes, 50 ml of saturated sodium carbonate solution was added, and the temperature was raised to room temperature. The reaction solvent was extracted with ethyl acetate (150 ml × 3), washed with saturated brine, dried over anhydrous magnesium sulfate, and concentrated under reduced pressure. The residue was purified by silica gel column chromatography (developing solvent toluene / ethyl acetate = 4/1) to obtain BHP (1.2 g, yield 29%).
Literature values (J. Am. Chem. Soc. 121, 669-685 (1999))
¹ H NMR (400 MHz CDCl ₃ ): δ 7.34 (m, 5H), 4.57 (d, J = 12.2Hz, 1H), 4.54 (d, J = 12.2Hz, 1H), 4.23 (quintet, J = 5.6Hz , 1H), 3.49 (dd, J = 4.6, 9.6Hz, 1H), 3.44 (dd, J = 6.0, 9.6Hz, 1H), 2.99 (br s, 1H), 2.69 (dd, J = 7.3, 17.0Hz , 1H), 2.63 (dd, J = 4.4, 17.1Hz, 1H), 2.18 (s, 3H, Me)

2-6. Evaluation of synthetic yield of BHP The detection and quantification of the compounds were carried out under the following conditions using a gas chromatograph. A gas chromatograph chart of the racemic synthetic sample is shown in FIG.
Equipment: Shimadzu GC-1700
Column: DB-1 (15m x 0.53mm ID, J & W SCIENTIFIC INC)
Column temperature: 200 ° C (4 minutes)
Injection temperature: 250 ° C
Detector temperature: 290 ° C
Linear velocity: 30m / s
Detection: Hydrogen flame ionization detector (FID)

2-7. Method for measuring optical purity of BHP Am. Chem. Soc. 121, 669-685 (1999), the optical purity of the compound was measured using HPLC under the following conditions. An HPLC chart of the racemic synthetic sample is shown in FIG.
Pump: Shimadzu Corporation LC-10AD
Mobile phase: n-hexane / isopropanol = 95/5
Flow rate: 1 ml / min
Column: CHIRALCELL OJ 0.46cm × 25cm (Daicel)
Column temperature: 40 ° C
Detection: Shimadzu Corporation SPD-10A, 210 nm

2-8. Acquisition of protein three-dimensional structure of aldolase enzyme and determination of mutation position The three-dimensional structure of DERA derived from E. coli has already been reported (Science 294, 369-374, (2001)). The corresponding three-dimensional structure data (PDB ID: 1JCJ) was obtained from Protein Data Bank (http://www.pdbj.org/index_j.html). Substrate 2DR5P in the three-dimensional structure was replaced with (S) -BHP. In the three-dimensional structure after substrate substitution, calculation by molecular mechanics method (force field: CVFF, protein main chain fixation) using InsightII (Accelrys) was performed to calculate an energy minimized structure (see FIG. 3). Based on the calculation results, the mutation positions were determined as follows.
(1) From the change in protein three-dimensional structure before and after the calculation within 3 cm from the substrate (S) -BHP, paying attention to the amino acids located near the benzene ring of the substrate, the 238th serine and the 239th serine were selected as mutation positions (See FIG. 4).
(2) Focusing on the amino acid surrounding the terminal methyl group of the substrate (S) -BHP, which is located near the active center (102 position asparagine, 167 position lysine, 201 position lysine), position 73 valine, position 76 Phenylalanine and 139-position isoleucine were selected as mutation positions (see FIG. 4).

Amino acid saturation mutagenesis at positions 2-9238 and 239 Attempts were made to substitute amino acids at positions 238 and 239 of wild-type DERA by site-specific amino acid saturation mutagenesis using the Overlap extension PCR method. In addition, the position-specific amino acid saturation mutation method is known as a “Semi-rational, semi-random” method for introducing amino acid saturation mutation by estimating the position where a desired function is involved from the three-dimensional structure of a protein. It has been used for modification (J. Mol. Biol. 331, 585-592 (2003)).

First, a fragment for mutagenesis 1 (upstream fragment) and a fragment for mutagenesis 2 (downstream fragment including a mutated portion) were prepared by PCR. The primer sets used for the preparation of each fragment are as follows.
(Primer set 1 for amplifying mutation-introducing fragment 1)
M13 RV primer: 5'-CAGGAAACAGCATTGAC (SEQ ID NO: 6)
238 & 239_RV primer: 5'-AGCGCCAAAGCGGTAGTGACGC (SEQ ID NO: 8)
(Primer set 2 for amplifying mutation-introducing fragment 2)
M13 M4 primer: 5'-GTTTTCCCAGTCACGAC (SEQ ID NO: 5)
238 & 239_F primer: 5'-GTCACTACCGCTTTGGCGCTNNSNNSCTGCTGGCAAGCCTGCTGAA (SEQ ID NO: 7)

  PUC18 / dera was used as the template DNA for each PCR reaction. The thermal cycle was performed at 94 ° C. for 2 minutes, and then a reaction cycle consisting of 94 ° C. for 15 seconds, 55 ° C. for 30 seconds, and 68 ° C. for 60 seconds was performed 25 times. The conditions not mentioned were the same as the above (column 2-2).

The obtained PCR product was subjected to agarose gel electrophoresis and purified. The purification operation was the same as described above (column 2-2.).
Then, overlap extension PCR was performed using the obtained fragments 1 and 2 for mutagenesis as primers, and a modified DERA gene having amino acids 238 and 239 as mutation positions was obtained. For the reaction, KOD-Plus-DNA polymerase (Toyobo Co., Ltd.) was used and the following procedure was used. That is, 2.5 μl of buffer solution, 1 μl of 25 mM magnesium sulfate, 2.5 μl of each 2 mM dNTP mixed solution, 1 ng of each of the fragments 1 and 2 for mutagenesis, and 0.5 μl of the DNA polymerase were added. Adjusted to 25 μl. After reacting at 94 ° C for 2 minutes with a commercially available temperature cycling device (Thermal cycler Takara), a total of 10 reaction cycles consisting of 94 ° C for 15 seconds, 55 ° C for 30 seconds, and 68 ° C for 60 seconds were performed. It was.
After completion of the reaction, PCR was carried out by adding the following reaction solution. That is, M13 M4 primer (SEQ ID NO: 5) and M13 RV primer (SEQ ID NO: 5) adjusted to 2.5 μl of buffer solution, 1 μl of 25 mM magnesium sulfate, and 2.5 μl and 10 μM of each 0.2 mM dNTP mixed solution. 6) was added in an amount of 1.5 μl and the DNA polymerase was added in an amount of 0.5 μl to adjust the amount of the reaction solution added to 25 μl. After reacting at 94 ° C for 2 minutes with a commercially available temperature cycling device (Thermal cycler Takara), a total of 20 reaction cycles consisting of 94 ° C for 15 seconds, 55 ° C for 30 seconds, and 68 ° C for 60 seconds were performed. It was.
The obtained PCR product was subjected to agarose gel electrophoresis, and the target gene was extracted and purified. The extracted / purified gene was treated with a restriction enzyme in the same manner as described above and cloned into the corresponding cloning site of pUC18 to obtain pUC18 / dera238 & 239. Using the vector, E. coli JM109 was transformed in the same manner as described above to construct a modified DERA library having the amino acid positions 238 and 239 as mutation positions.

Amino acid saturation mutagenesis at positions 2-10.73 and 76 The amino acid saturation mutagenesis for positions 73 and 76 was carried out in the same procedure as when the amino acids 238 and 239 were used as mutation positions. However, the following primer sets were used for the production of fragments for specifically introducing mutations at positions 73 and 76 (mutation introduction fragments 1 and 2).
(Primer set 1 for amplifying mutation-introducing fragment 1)
M13 RV primer: 5'-CAGGAAACAGCATTGAC (SEQ ID NO: 6)
73 & 76_RV primer: 5'-CGTAGCGATACGGATTTCC (SEQ ID NO: 10)
(Primer set 2 for amplifying mutation-introducing fragment 2)
M13 M4 primer: 5'-GTTTTCCCAGTCACGAC (SEQ ID NO: 5)
73 & 76_F primer: 5'-GGAAATCCGTATCGCTACGNNSACCAACNNSCCACACGGTAACGACGACA (SEQ ID NO: 9)

  The obtained gene was cloned in the same manner as described above (column 2-9) to obtain pUC18 / dera73 & 76. Escherichia coli JM109 was transformed with the vector to obtain a modified DERA library having amino acids 73 and 76 as mutation positions.

Amino acid saturation mutagenesis at the 2-11.139 position Amino acid saturation mutagenesis targeting the 139th position was carried out in the same procedure as when the 238th amino acid and the 239th amino acid were used as mutation positions. However, the following primer sets were used for the preparation of fragments for specifically introducing mutations at position 139 (fragment introducing fragments 1 and 2).
(Primer set 1 for amplifying mutation-introducing fragment 1)
M13 RV primer; 5'-CAGGAAACAGCATTGAC (SEQ ID NO: 6)
139_R primer, 5'-CACTTTCAGCAGTACATTCG (SEQ ID NO: 12)
(Primer set 2 for amplifying mutation-introducing fragment 2)
M13 M4 primer; 5'-GTTTTCCCAGTCACGAC (SEQ ID NO: 5)
139_F primer, 5'-CGAATGTACTGCTGAAAGTGNNSATCGAAACCGGCGAACTGAA (SEQ ID NO: 11)

  On the other hand, pUC18 / dera was used as template DNA. The obtained gene was cloned in the same manner as described above to obtain pUC18 / dera139. Escherichia coli JM109 was transformed with the vector to obtain a modified DERA library with the amino acid at position 139 as the mutation position.

Mutation crossing between mutations at positions 2-12.73 and 76 and mutations at positions 238 and 239 In the same manner as in the case where the amino acid at position 238 and the amino acid at position 239 are used as mutation positions, the mutation at position 73 and / or 76 at position DERA Mutation combinations of (variants 1 to 8) and 238 and / or 239 mutation DERA (variants 11 to 16) were performed. However, the following primer sets were used for the preparation of gene fragments containing mutations at positions 73 and / or 76, and displacement fragments containing displacements at positions 238 and / or 239 (mutation combination fragments 1 and 2, respectively).

(Primer set 1 for amplifying fragment 1 for mutation combination, template: variants 1 to 8)
M13 RV primer: 5'-CAGGAAACAGCATTGAC (SEQ ID NO: 6)
alover-R1 primer: 5'-ACGGTTTTTTCTACGCCCAT (SEQ ID NO: 13)

(Primer set 2 for amplifying fragment 2 for mutation combination: variants 11 to 16)
alover-F1 primer: 5'-ATGATGGAAGTGATCCGTGA (SEQ ID NO: 14)
M13 M4 primer: 5'-GTTTTCCCAGTCACGAC (SEQ ID NO: 5)

  The obtained gene was cloned in the same manner as described above (column 2-9) to obtain pUC18 / dera73 & 76 & 238 & 239. Escherichia coli JM109 was transformed with the vector to obtain a modified DERA library having amino acid positions 73, 76, 238, and 239 as mutation positions.

2-13. Screening method for modified enzyme
48-well culture plate (Nippon Gene) supplemented with 1 ml medium (Terrific broth (containing 50 μg / ml ampicillin, 0.1 mM IPTG)) of E. coli (modified DERA library) grown on LB plate agar medium containing 50 μg / ml ampicillin Tys) was inoculated. The inoculated culture plate was cultured with shaking in a 37 ° C. constant temperature bath. 18 hours after the start of the culture, 100 μl of the culture solution was dispensed into a 96-well microplate, and the turbidity was measured with a spectrometer (Tecan) (wavelength 620 nm). The remaining culture solution was centrifuged (5000 g, 20 minutes) to remove the supernatant, and the cells were obtained as a precipitate. 100 μl CellLytic (SIGMA) was added to the collected wet cells and lysed to obtain a crude enzyme solution.
Crude enzyme solution (25 μl), buffer solution (containing 100 mM Bis-Tris pH7.3 1 mM EDTA), substrate (100 μl DMSO dissolved in 250 μmol acetone and 25 μmol benzyloxyacetaldehyde) were added to a new 48-well culture plate for 24 hours. The reaction was carried out by shaking at 30 ° C. After completion of the reaction, 50 μl of 5N hydrochloric acid and 3 ml of acetone (containing internal standard 0.75 mg / ml 3 ′, 4′-dimethoxyacetophenone) were added. After mixing, the plate was centrifuged, and the supernatant was subjected to gas chromatographic analysis (see 2-6) and HPLC analysis (see 2-7). From these analysis results, a strain producing a modified DERA with high synthetic activity and excellent substrate selectivity was identified.
The modified DERA (variants 1-18) obtained as a result of the above screening is shown in the table of FIG. As shown in this table, a total of 18 types of modified DERA with high synthesis efficiency and excellent stereoselectivity were successfully obtained. All of these variants have improved yields compared to the wild type. Many variants also show improved enantiomeric excess. This result shows that amino acid substitutions at positions 73, 76, 139, 238, and 239 are effective in improving DERA characteristics. On the other hand, variants 1 to 4 have an enantiomeric excess of 90% or more, and the yield is significantly improved over the wild type. From this result, it can be said that the substitution at positions 73 and 76 is particularly effective.

  Here, in variant 1 or variant 7, the amino acid at position 73 is substituted with proline. Since the amino acid at position 73 of wild-type DERA is valine, the codon at position 73 is replaced from GTA to CCC. That is, these modified DERAs were obtained as a result of the three base substitutions. Such substitution is made possible by carrying out position-specific amino acid saturation mutation, and it is difficult to introduce mutations of two or more consecutive bases by random mutation such as error-pron PCR. Thus, it can be said that at least a part of modified DERA can be obtained for the first time by adopting position-specific amino acid saturation mutation as a method for introducing amino acid substitution.

  According to the present invention, a modified DERA in which a part of the amino acid sequence of a wild-type enzyme is substituted is provided. The modified DERA of the present invention exhibits excellent catalytic ability for a one-step aldol reaction using benzyloxyacetaldehyde as an acceptor substrate. The modified DERA of the present invention can be suitably used as a catalyst for the synthesis of β-ketol.

The present invention is not limited to the description of the embodiments and examples of the invention described above. Various modifications may be included in the present invention as long as those skilled in the art can easily conceive without departing from the description of the scope of claims.
The contents of papers, published patent gazettes, patent gazettes, and the like specified in this specification are incorporated by reference in their entirety.

It is a gas chromatograph chart of a racemic BHP synthetic standard. It is an HPLC chart of a racemic BHP synthetic standard. It is a figure which shows typically the three-dimensional structure around the substrate (BHP) before and after energy minimization calculation. BHP was displayed with a stick. It is a figure which shows typically the amino acid residue side chain and substrate around a substrate (BHP) after energy minimization calculation. The BHP part is shaded. It is the table | surface which put together the amino acid sequence of the modified DERA which was acquired successfully, the yield in (S) -BHP synthesis | combination, and enantiomeric excess (ee). A blank in the table indicates the same amino acid as the wild type. The yield is shown as a relative value when the yield of the wild-type enzyme is 1.

Claims (19)

One selected from the group consisting of amino acids 73, 76, 139, 238, and 239 of the amino acid sequence shown in SEQ ID NO: 1 in the amino acid sequence of wild-type 2-deoxyribose 5-phosphate aldolase A modified 2-deoxyribose 5-phosphate aldolase comprising an amino acid sequence in which amino acids corresponding to the above amino acids are substituted, wherein the amino acids after substitution at positions 238 and / or 239 are as follows:
The substituted amino acid at position 238 is tyrosine, glycine, arginine or alanine;
The amino acid after substitution at position 239 is methionine, asparagine, glycine or leucine.   The modified 2-deoxyribose 5-phosphate according to claim 1, wherein the wild-type 2-deoxyribose 5-phosphate aldolase is 2-deoxyribose 5-phosphate aldolase derived from E. coli. Aldolase.   The modified 2-deoxy according to claim 1, wherein the amino acid sequence of the wild-type 2-deoxyribose 5-phosphate aldolase is an amino acid sequence having 80% or more homology with the amino acid sequence shown in SEQ ID NO: 1. Ribose 5-phosphate aldolase.   The modified 2-deoxyribose 5-phosphate aldolase according to claim 1, wherein the amino acid sequence of the wild-type 2-deoxyribose 5-phosphate aldolase is the amino acid sequence shown in SEQ ID NO: 1. The modified 2-deoxyribose 5-phosphorus according to claim 4, wherein the amino acid at position 73 and / or 76 in the amino acid sequence shown in SEQ ID NO: 1 is substituted, and the amino acid after substitution is as follows: Acid aldolase:
The substituted amino acid at position 73 is proline, cysteine, threonine, serine or tryptophan;
The amino acid after substitution at position 76 is arginine, tyrosine or tryptophan.   The modified 2-deoxyribose 5-phosphate aldolase according to claim 4, wherein the amino acid at position 139 is substituted in the amino acid sequence shown in SEQ ID NO: 1, and the substituted amino acid is valine or methionine. The modified 2-deoxyribose 5-phosphorus according to claim 4, wherein the amino acid at position 238 and / or 239 is substituted in the amino acid sequence shown in SEQ ID NO: 1, and the amino acid after substitution is as follows: Acid aldolase:
The substituted amino acid at position 238 is tyrosine, glycine, arginine or alanine;
The amino acid after substitution at position 239 is methionine, asparagine, glycine or leucine. The modified 2-deoxyribose 5-phosphate aldolase according to claim 1, comprising any one of the following amino acid sequences (1) to (18):
(1) in the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which position 73 valine is substituted with proline;
(2) in the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which valine 73 is substituted with cysteine and phenylalanine 76 is substituted with arginine;
(3) an amino acid sequence obtained by substituting threonine for position 73 in the amino acid sequence of SEQ ID NO: 1;
(4) in the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which valine 73 is substituted with threonine and phenylalanine 76 is substituted with tyrosine;
(5) in the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which valine 73 is substituted with serine and phenylalanine 76 is substituted with tryptophan;
(6) an amino acid sequence obtained by replacing position 73 valine with cysteine in the amino acid sequence of SEQ ID NO: 1;
(7) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which valine 73 is substituted with proline and phenylalanine 76 is substituted with tyrosine;
(8) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which position 73 valine is substituted with tryptophan and position 76 phenylalanine is replaced with tryptophan;
(9) an amino acid sequence obtained by substituting isoleucine at position 139 with valine in the amino acid sequence of SEQ ID NO: 1;
(10) an amino acid sequence obtained by substituting isoleucine at position 139 with methionine in the amino acid sequence of SEQ ID NO: 1;
(11) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence obtained by substituting 238th serine with tyrosine and 239th serine with methionine;
(12) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence obtained by substituting 238th serine with glycine and 239th serine with asparagine;
(13) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which the 238th serine is substituted with arginine and the 239th serine is substituted with glycine;
(14) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence in which serine at position 238 is substituted with alanine and serine at position 239 is substituted with leucine;
(15) an amino acid sequence obtained by substituting serine 239 with leucine in the amino acid sequence of SEQ ID NO: 1;
(16) In the amino acid sequence of SEQ ID NO: 1, an amino acid sequence obtained by substituting 238th serine with glycine;
(17) In the amino acid sequence of SEQ ID NO: 1, valine at position 73 is substituted with proline, phenylalanine at position 76 is substituted with tyrosine, serine at position 238 is substituted with arginine, and serine at position 239 is substituted with glycine Sequence;
(18) In the amino acid sequence of SEQ ID NO: 1, valine at position 73 is substituted with proline, phenylalanine at position 76 is substituted with tyrosine, serine at position 238 is substituted with alanine, and serine at position 239 is substituted with leucine An array.   An isolated nucleic acid encoding the modified 2-deoxyribose 5-phosphate aldolase according to claim 1.   A vector carrying the nucleic acid according to claim 9.   A transformant having the nucleic acid according to claim 9.   Aldol reaction using 2-deoxyribose 5-phosphate aldolase as a catalyst for an acceptor substrate composed of benzyloxyacetaldehyde having a substituent on the benzene ring or unsubstituted and a donor substrate composed of a ketone having 3 to 6 carbon atoms A method for synthesizing β-ketol.   The synthesis method according to claim 12, wherein the 2-deoxyribose 5-phosphate aldolase is the modified 2-deoxyribose 5-phosphate aldolase according to any one of claims 1 to 8. The synthesis method according to claim 12 or 13, wherein the acceptor substrate is a compound represented by the following chemical formula:
In the formula, R is a substituent on the benzene ring and is a hydrogen atom, a halogen atom, a hydroxyl group, an alkyl group, an alkoxy group, a nitro group, or a cyano group.   The synthesis method according to claim 12 or 13, wherein the substrate is benzyloxyacetaldehyde and the donor substrate is acetone.   At least one amino acid selected from the group consisting of amino acid at position 73, amino acid at position 76, amino acid at position 139, amino acid at position 238, and amino acid at position 239 in the amino acid sequence of 2-deoxyribose 5-phosphate aldolase; A method for designing a modified 2-deoxyribose 5-phosphate aldolase, comprising constructing a substituted amino acid sequence. A method for designing a modified 2-deoxyribose 5-phosphate aldolase comprising the following steps:
(1) A step of preparing three-dimensional structure information of wild-type or modified 2-deoxyribose 5-phosphate aldolase during catalytic reaction when 2-deoxyribose 5-phosphate is used as a substrate;
(2) a step of substituting the target substrate from 2-deoxyribose 5-phosphate in the three-dimensional structure information;
(3) performing a molecular mechanics calculation of wild-type or modified 2-deoxyribose 5-phosphate aldolase to calculate an energy minimized structure;
(4) comparing the structures before and after the calculation, and selecting amino acids in which side chain movement is recognized as substitution candidates;
(5) A step of constructing an amino acid sequence in which the selected amino acid is substituted in the amino acid sequence of wild-type or modified 2-deoxyribose 5-phosphate aldolase.   Before the step (4), amino acids within 3 Å from the target substrate are extracted from among the amino acids constituting the wild-type 2-deoxyribose 5-phosphate aldolase, and in the step (4), the extracted amino acids The design method according to claim 17, wherein substitution candidates are selected from among amino acids.   The design method according to claim 17 or 18, wherein the target substrate is β-ketol.