WO2007120657A3 - Crystals of a bacterial metabolite-sensing ribozyme and use thereof for antibiotic discovery - Google Patents

Crystals of a bacterial metabolite-sensing ribozyme and use thereof for antibiotic discovery Download PDF

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Publication number
WO2007120657A3
WO2007120657A3 PCT/US2007/008834 US2007008834W WO2007120657A3 WO 2007120657 A3 WO2007120657 A3 WO 2007120657A3 US 2007008834 W US2007008834 W US 2007008834W WO 2007120657 A3 WO2007120657 A3 WO 2007120657A3
Authority
WO
WIPO (PCT)
Prior art keywords
glms
ribozyme
crystals
sensing
structural representation
Prior art date
Application number
PCT/US2007/008834
Other languages
French (fr)
Other versions
WO2007120657A2 (en
Inventor
Daniel J Klein
Amare Adrian R Ferre-Di
Original Assignee
Hutchinson Fred Cancer Res
Daniel J Klein
Amare Adrian R Ferre-Di
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Hutchinson Fred Cancer Res, Daniel J Klein, Amare Adrian R Ferre-Di filed Critical Hutchinson Fred Cancer Res
Publication of WO2007120657A2 publication Critical patent/WO2007120657A2/en
Publication of WO2007120657A3 publication Critical patent/WO2007120657A3/en

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/111—General methods applicable to biologically active non-coding nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/12—Type of nucleic acid catalytic nucleic acids, e.g. ribozymes
    • C12N2310/121—Hammerhead
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2320/00—Applications; Uses
    • C12N2320/10—Applications; Uses in screening processes
    • C12N2320/11—Applications; Uses in screening processes for the determination of target sites, i.e. of active nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2330/00—Production
    • C12N2330/10—Production naturally occurring

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  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Biomedical Technology (AREA)
  • Chemical & Material Sciences (AREA)
  • Molecular Biology (AREA)
  • Organic Chemistry (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Wood Science & Technology (AREA)
  • Microbiology (AREA)
  • Plant Pathology (AREA)
  • Physics & Mathematics (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Saccharide Compounds (AREA)

Abstract

A crystalline GlmS ribozyme, optionally but in some embodiments preferably in dehydrated (including partially dehydrated) form is described, along with the crystal structure thereof. The invention provides a method of identifying a GlmS binding compound (or compound that facilitates or inhibits cleavage of GlmS), comprising: (a) providing in a computer a three-dimensional structural representation of GlmS or a glucosamine-6-phosphate (GlcN6P) and/or glucose-6-phosphate (Glc6P) binding portion thereof; and (b) screening in the computer a candidate compound for an ability to bind to said three-dimensional structural representation. In some embodiments the three-dimensional structural representation is provided at a resolution of from 4.0 or 3.0 Å, to 2.0 or 1.0 Å.
PCT/US2007/008834 2006-04-10 2007-04-10 Crystals of a bacterial metabolite-sensing ribozyme and use thereof for antibiotic discovery WO2007120657A2 (en)

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US79083606P 2006-04-10 2006-04-10
US60/790,836 2006-04-10
US79641606P 2006-05-01 2006-05-01
US60/796,416 2006-05-01

Publications (2)

Publication Number Publication Date
WO2007120657A2 WO2007120657A2 (en) 2007-10-25
WO2007120657A3 true WO2007120657A3 (en) 2008-11-13

Family

ID=38610132

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2007/008834 WO2007120657A2 (en) 2006-04-10 2007-04-10 Crystals of a bacterial metabolite-sensing ribozyme and use thereof for antibiotic discovery

Country Status (1)

Country Link
WO (1) WO2007120657A2 (en)

Families Citing this family (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN105960410B (en) * 2013-11-21 2020-12-04 硒瑞恩生物科技有限公司 Method for determining structure of selenium-derived nucleic acid complex
CN110643561A (en) * 2019-10-30 2020-01-03 上海市农业科学院 Application of glms gene in lactobacillus biosafety screening marker

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
BARRICK J. ET AL.: "New RNA motifs suggest an expanded scope for ribotswitches in bacterial genetic control", PROC. NATL. ACAD. SCI., vol. 101, 2004, pages 6421 - 6426, XP002450913 *
KLEIN D.J. ET AL.: "Structural Basis of glms Ribozyme Activation by Glucosamine-6-Phosphate", SCIENCE, vol. 313, 2006, pages 1752 - 1756, XP008107972, DOI: doi:10.1126/science.1129666 *

Also Published As

Publication number Publication date
WO2007120657A2 (en) 2007-10-25

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