gyrB

Summary

Gene Symbol: gyrB
Description: DNA gyrase, subunit B
Alias: Cou, ECK3691, JW5625, acrB, himB, hisU, hopA, nalC, parA, pcbA, pcpA
Species: Escherichia coli str. K-12 substr. MG1655

Top Publications

  1. pmc Novobiocin and coumermycin inhibit DNA supercoiling catalyzed by DNA gyrase
    M Gellert
    Proc Natl Acad Sci U S A 73:4474-8. 1976
  2. ncbi DNA gyrase: structure and function
    R J Reece
    Department of Biochemistry, University of Leicester, UK
    Crit Rev Biochem Mol Biol 26:335-75. 1991
  3. pmc DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences
    Y Yang
    Department of Biochemistry, University of California, Berkeley 94720
    Proc Natl Acad Sci U S A 85:8850-4. 1988
  4. ncbi On the advantages of imperfect energetic linkage
    T S Leyh
    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Methods Enzymol 308:48-70. 1999
  5. pmc GyrI: a counter-defensive strategy against proteinaceous inhibitors of DNA gyrase
    Monalisa Chatterji
    Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
    EMBO Rep 3:261-7. 2002
  6. pmc DNA gyrase: purification and catalytic properties of a fragment of gyrase B protein
    M Gellert
    Proc Natl Acad Sci U S A 76:6289-93. 1979
  7. ncbi Crystal structure of an N-terminal fragment of the DNA gyrase B protein
    D B Wigley
    Department of Chemistry, York University, Heslington, UK
    Nature 351:624-9. 1991
  8. pmc Effects of DNA gyrase inhibitors in Escherichia coli topoisomerase I mutants
    G J Pruss
    J Bacteriol 168:276-82. 1986
  9. pmc Modulation of transcription by DNA supercoiling: a deletion analysis of the Escherichia coli gyrA and gyrB promoters
    R Menzel
    Proc Natl Acad Sci U S A 84:4185-9. 1987
  10. pmc DNA gyrase subunit stoichiometry and the covalent attachment of subunit A to DNA during DNA cleavage
    A Sugino
    Nucleic Acids Res 8:3865-74. 1980

Scientific Experts

  • Andrew Travers
  • A D Bates
  • John Herrick
  • Emmanuelle Cambau
  • D A Ostrov
  • James Berger
  • Yu Zheng
  • E Adam
  • A Maxwell
  • R Loris
  • C J Dorman
  • Brian J Peter
  • Daniel Lafitte
  • Marc Drolet
  • M Ashiuchi
  • Marcelo Nollmann
  • Muhammad Malik
  • S C Kampranis
  • N L Williams
  • Andrew B Smith
  • Trudy H Grossman
  • Christian H Gross
  • Liane Saiz-Urra
  • Tranum Kaur
  • Allyn J Schoeffler
  • Ekambaram Ramesh
  • Alan I Derman
  • F Luzzaro
  • Manuel Saavedra De Bast
  • N R Cozzarelli
  • Nancy J Crisona
  • Saeed M Hashimi
  • Elena Lopez
  • Helena Gradisar
  • Keith Champion
  • L Brino
  • Karl Drlica
  • Laurence Van Melderen
  • Nicholas R Cozzarelli
  • Paola B Arimondo
  • Kyeong Soo Jeong
  • Karen H Schmidt
  • Ya Han Hsu
  • W C Lu
  • Boris P Belotserkovskii
  • Ryosuke L Ohniwa
  • Sylvain Mitelheiser
  • Jennifer Reineke Pohlhaus
  • Jonathan D Parsons
  • Erik P Johnson
  • Minh Hoa Dao-Thi
  • A B Khodursky
  • Lionel Costenaro
  • John H Tran
  • Majda Valjavec-Gratian
  • E L Zechiedrich
  • Alexander J Ruthenburg
  • Paul S Charifson
  • Gitte Ebersbach
  • Kenn Gerdes
  • Jakob Møller-Jensen
  • R Schneider
  • Jonathan G Heddle
  • A J Howells
  • Kenichi Kakinuma
  • Gianfranco Grompone
  • Jan A Olsson
  • Olivier A Pierrat
  • Shun Adachi
  • Christian G Noble
  • Monalisa Chatterji
  • Jozef Adamcik
  • Jacky L Snoep
  • J G Heddle
  • N Smelkova
  • Matheus Froeyen
  • Roderick A Slavcev
  • Qusai Al Abdallah
  • Nafiseh Nafissi
  • Miguel Angel Cabrera
  • Shawn Wettig
  • Barbara E Funnell
  • M Chatterji
  • S J Blance
  • Andrew P May
  • K J Marians
  • Shilpakala Sainath
  • Rathna Durga R S Manian
  • Ragavachary Raghunathan
  • Malathi Raghunathan

Detail Information

Publications126 found, 100 shown here

  1. pmc Novobiocin and coumermycin inhibit DNA supercoiling catalyzed by DNA gyrase
    M Gellert
    Proc Natl Acad Sci U S A 73:4474-8. 1976
    ..We conclude that DNA gyrase controls the supercoiling of DNA in E. coli...
  2. ncbi DNA gyrase: structure and function
    R J Reece
    Department of Biochemistry, University of Leicester, UK
    Crit Rev Biochem Mol Biol 26:335-75. 1991
    ..In this review we summarize the current knowledge concerning DNA gyrase by addressing a wide range of aspects of the study of this enzyme...
  3. pmc DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences
    Y Yang
    Department of Biochemistry, University of California, Berkeley 94720
    Proc Natl Acad Sci U S A 85:8850-4. 1988
    ..In addition, we speculate that these interactions may be of a structural nature, such as involvement in the higher-order structure of the bacterial chromosome...
  4. ncbi On the advantages of imperfect energetic linkage
    T S Leyh
    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York 10461, USA
    Methods Enzymol 308:48-70. 1999
  5. pmc GyrI: a counter-defensive strategy against proteinaceous inhibitors of DNA gyrase
    Monalisa Chatterji
    Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
    EMBO Rep 3:261-7. 2002
    ..Thus, GyrI is an antidote to DNA gyrase-specific proteinaceous poisons encoded by plasmid addiction systems...
  6. pmc DNA gyrase: purification and catalytic properties of a fragment of gyrase B protein
    M Gellert
    Proc Natl Acad Sci U S A 76:6289-93. 1979
    ..The protein, of molecular weight 50,000, appears to be fragment of the DNA gyrase B (Cou) protein (molecular weight, 90,000) as judged by the identical sizes of numerous peptides produced by partial ..
  7. ncbi Crystal structure of an N-terminal fragment of the DNA gyrase B protein
    D B Wigley
    Department of Chemistry, York University, Heslington, UK
    Nature 351:624-9. 1991
    ..The C-terminal domains form the sides of a 20 A hole through the protein dimer which may play a role in DNA strand passage during the supercoiling reaction...
  8. pmc Effects of DNA gyrase inhibitors in Escherichia coli topoisomerase I mutants
    G J Pruss
    J Bacteriol 168:276-82. 1986
    ..Full resistance to oxolinic acid in the presence of the delta topA, gyrB225, and gyrA mutations was conferred by an additional mutation that maps at or near gyrB.
  9. pmc Modulation of transcription by DNA supercoiling: a deletion analysis of the Escherichia coli gyrA and gyrB promoters
    R Menzel
    Proc Natl Acad Sci U S A 84:4185-9. 1987
    Expression of the genes determining the subunits of Escherichia coli DNA gyrase (gyrA and gyrB) is known to be induced by relaxation of the template DNA. In this paper we report a deletion analysis of the gyrA and gyrB promoter regions...
  10. pmc DNA gyrase subunit stoichiometry and the covalent attachment of subunit A to DNA during DNA cleavage
    A Sugino
    Nucleic Acids Res 8:3865-74. 1980
    Escherichia coli DNA gyrase contains a 1:1 ratio of protomers coded by the genes gyrA and gyrB. This along with previous results shows that the enzyme has two copies of each protomer and thus a molecular weight of 400,000...
  11. pmc Site-specific interaction of DNA gyrase with DNA
    L M Fisher
    Proc Natl Acad Sci U S A 78:4165-9. 1981
    ..This result supports the view that, in the DNA gyrase--DNA complex, the DNA is largely wrapped on the outside of the enzyme...
  12. ncbi Escherichia coli DNA topoisomerase I mutants have compensatory mutations in DNA gyrase genes
    S DiNardo
    Cell 31:43-51. 1982
    ..Several of these compensatory mutations have been found to map at or near the genes encoding DNA gyrase, gyrA and gyrB. DNA gyrase assays of crude extracts show that strains carrying the mutations have lower gyrase activity...
  13. ncbi Regulation of the genes for E. coli DNA gyrase: homeostatic control of DNA supercoiling
    R Menzel
    Cell 34:105-13. 1983
    ..The results suggest that DNA supercoiling in E. coli is controlled by a homeostatic mechanism. Synthesis of the RecA protein and several other proteins is also increased by treatments that relax intracellular DNA...
  14. ncbi Roles of topoisomerase IV and DNA gyrase in DNA unlinking during replication in Escherichia coli
    E L Zechiedrich
    Department of Molecular and Cell Biology, University of California, Berkeley 94720 3204, USA
    Genes Dev 9:2859-69. 1995
    ..We conclude that catenanes are kinetic intermediates in DNA replication and that the essential role of topo IV is to unlink daughter replicons...
  15. ncbi Immunogold localization of GyrA and GyrB proteins in Escherichia coli
    M Thornton
    School of Biological Sciences, University of Manchester, UK
    Microbiology 140:2371-82. 1994
    Immunogold preparations of Escherichia coli, using anti-GyrA and anti-GyrB antibodies to the subunits of DNA gyrase, showed clear labelling with both secondary antibody and protein A-gold conjugates...
  16. ncbi Contrasting enzymatic activities of topoisomerase IV and DNA gyrase from Escherichia coli
    C Ullsperger
    Department of Molecular and Cellular Biology, Division of Biochemistry and Molecular Biology, University of California, Berkeley, California 94720, USA
    J Biol Chem 271:31549-55. 1996
    ..This ability of Topo IV to selectively unlink catenated molecules mirrors its key role in decatenation of replicating chromosomes in vivo...
  17. ncbi Crystal structure of the breakage-reunion domain of DNA gyrase
    J H Morais Cabral
    Department of Biochemistry, University of Leicester, UK
    Nature 388:903-6. 1997
    ..Mutations that confer resistance to the quinolone antibacterial agents cluster at the new dimer interface, indicating how these drugs might interact with the gyrase-DNA complex...
  18. ncbi In vivo cleavage of Escherichia coli BIME-2 repeats by DNA gyrase: genetic characterization of the target and identification of the cut site
    O Espeli
    Laboratoire de Chimie Bacterienne, UPR 9043, Institut de Biologie Structurale et Microbiologie du CNRS, Marseille, France
    Mol Microbiol 26:767-77. 1997
    ..DNA gyrase cleavage at repetitive BIME-2 elements may have consequences for DNA topology and genomic rearrangements...
  19. ncbi Probing the two-gate mechanism of DNA gyrase using cysteine cross-linking
    N L Williams
    Department of Biochemistry, University of Leicester, U K
    Biochemistry 38:13502-11. 1999
    ..This indicates that passage of DNA through the bottom dimer interface is not essential for this reaction. The mechanistic implications of these results are discussed...
  20. ncbi The interaction of DNA gyrase with the bacterial toxin CcdB: evidence for the existence of two gyrase-CcdB complexes
    S C Kampranis
    Department of Biochemistry, University of Leicester, Leicester, LE1 7RH, UK
    J Mol Biol 293:733-44. 1999
    ..Incubation of this initial complex with ATP in the presence of GyrB and DNA slowly converts it to a second complex (beta), which has a lower rate of ATP hydrolysis and is unable to ..
  21. ncbi A DNA architectural protein couples cellular physiology and DNA topology in Escherichia coli
    R Schneider
    Institut fur Genetik und Mikrobiologie, LMU Munchen, Maria Ward Str 1a, 80638 Munchen, Germany
    Mol Microbiol 34:953-64. 1999
    ..Here, we show that, in addition, FIS represses the gyrA and gyrB promoters and reduces DNA gyrase activity...
  22. ncbi Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli
    E L Zechiedrich
    Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas 77030, USA
    J Biol Chem 275:8103-13. 2000
    ..09), greatly stimulating transcription from the supercoiling sensitive leu-500 promoter and increasing the number of supercoils trapped by lambda integrase site-specific recombination...
  23. ncbi The additional 165 amino acids in the B protein of Escherichia coli DNA gyrase have an important role in DNA binding
    M Chatterji
    Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
    J Biol Chem 275:22888-94. 2000
    ..The enzyme is a heterotetramer of A(2)B(2) subunit composition. Alignment of the primary sequence of gyrase B (GyrB) from various species shows that they can be grouped into two classes...
  24. ncbi DNA supercoiling in Escherichia coli is under tight and subtle homeostatic control, involving gene-expression and metabolic regulation of both topoisomerase I and DNA gyrase
    Jacky L Snoep
    Department of Molecular Cell Physiology, BioCentrum Amsterdam, Free University, Amsterdam, The Netherlands
    Eur J Biochem 269:1662-9. 2002
    ..3% change of DNA supercoiling only. We conclude that the homeostatic regulation of the nonequilibrium DNA structure in wild-type Escherichia coli is almost complete and subtle (i.e. involving at least three regulatory mechanisms)...
  25. ncbi The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a proposed two metal-ion mechanism
    Christian G Noble
    Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
    J Mol Biol 318:361-71. 2002
    ..We present evidence to support the idea that cleavage of each DNA strand involves two or more metal ions, and suggest a scheme for the DNA cleavage chemistry of DNA gyrase involving two metal ions...
  26. ncbi Glutamate racemase is an endogenous DNA gyrase inhibitor
    Makoto Ashiuchi
    Department of Bioresources Science, Kochi University, Nankoku, Kochi 783 8502, Japan
    J Biol Chem 277:39070-3. 2002
    ..This is the first finding of the enzyme protein participating in both d-amino acid metabolism and DNA processing...
  27. ncbi The action of the bacterial toxin microcin B17. Insight into the cleavage-religation reaction of DNA gyrase
    Olivier A Pierrat
    Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom
    J Biol Chem 278:35016-23. 2003
    ..Based on these results and on the observations that MccB17 only slowly inhibits the supercoiling and relaxation reactions, we suggest a model of the interaction of MccB17 with gyrase...
  28. ncbi Overexpression and purification of bacterial DNA gyrase
    A Maxwell
    Department of Biochemistry, University of Leicester, UK
    Methods Mol Biol 94:135-44. 1999
  29. ncbi Nucleotide binding to DNA gyrase causes loss of DNA wrap
    Jonathan G Heddle
    Department of Biological Chemistry, John Innes Centre, Colney, Norwich NR4 7UH, UK
    J Mol Biol 337:597-610. 2004
    ....
  30. ncbi Bacterial mitosis: partitioning protein ParA oscillates in spiral-shaped structures and positions plasmids at mid-cell
    Gitte Ebersbach
    Department of Biochemistry and Molecular Biology, Campusvej 55, DK 5230 Odense M, University of Southern Denmark, Denmark
    Mol Microbiol 52:385-98. 2004
    The par2 locus of Escherichia coli plasmid pB171 encodes oscillating ATPase ParA, DNA binding protein ParB and two cis-acting DNA regions to which ParB binds (parC1 and parC2)...
  31. ncbi DNA supercoiling - a global transcriptional regulator for enterobacterial growth?
    Andrew Travers
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
    Nat Rev Microbiol 3:157-69. 2005
    ....
  32. ncbi Small-angle X-ray scattering reveals the solution structure of the full-length DNA gyrase a subunit
    Lionel Costenaro
    Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom
    Structure 13:287-96. 2005
    ..The uniqueness of gyrase is due to the ability of the GyrA-CTDs to wrap DNA. Their position within the GyrA structure strongly suggests a large conformation change of the enzyme upon DNA binding...
  33. ncbi Thirty years of Escherichia coli DNA gyrase: from in vivo function to single-molecule mechanism
    Marcelo Nollmann
    Department of Molecular and Cell Biology, University of California, 16 Barker Hall, Berkeley, CA 94720 3204, USA
    Biochimie 89:490-9. 2007
    ..Here, we review the biological roles of gyrase in vivo and its mechanism in vitro...
  34. pmc Fusions of the Escherichia coli gyrA and gyrB control regions to the galactokinase gene are inducible by coumermycin treatment
    R Menzel
    J Bacteriol 169:1272-8. 1987
    ..When the DNA encoding the gyrA and gyrB genes is relaxed, both genes are expressed at a high level; in negatively supercoiled DNA they are expressed at a ..
  35. ncbi Crystal structure of CcdB, a topoisomerase poison from E. coli
    R Loris
    Laboratorium voor Ultrastructuur, Vlaams Interuniversitair Instituut voor Biotechnologie, Vrije Universiteit Brussel, Paardenstraat 65, Sint Genesius Rode, B 1640, Belgium
    J Mol Biol 285:1667-77. 1999
    ..We propose that the CcdB dimer binds into the central hole of the 59 kDa N-terminal fragment of GyrA, after disruption of the head dimer interface of GyrA...
  36. pmc Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays
    A B Khodursky
    Department of Molecular and Cell Biology, University of California, Berkeley 94720, USA
    Proc Natl Acad Sci U S A 97:9419-24. 2000
    ..Topo IV activity was sufficient to prevent accumulation of (+) supercoils in plasmid DNA in vivo, suggesting that topo IV can promote replication by removing (+) supercoils in front of the chromosomal fork...
  37. pmc Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli
    Brian J Peter
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720 3204, USA
    Genome Biol 5:R87. 2004
    ..In turn, supercoiling influences local DNA structure and can affect gene expression. We used microarrays representing nearly the entire genome of Escherichia coli MG1655 to examine the dynamics of chromosome structure...
  38. ncbi Molecular basis of gyrase poisoning by the addiction toxin CcdB
    Minh Hoa Dao-Thi
    Laboratorium voor Ultrastructuur, Vrije Universiteit Brussel and Department of Molecular and Cellular Interactions, Vlaams Instituut voor Biotechnologie, Building E, Pleinlaan 2, B 1050 Brussels, Belgium
    J Mol Biol 348:1091-102. 2005
    ..Overexpression of GyrA14 protects Escherichia coli cells against CcdB, mimicking the action of the antidote CcdA...
  39. ncbi Cloning of the DNA gyrase genes under tac promoter control: overproduction of the gyrase A and B proteins
    P Hallett
    Department of Biochemistry, University of Leicester, U K
    Gene 93:139-42. 1990
    The construction of plasmids which over-produce the Escherichia coli DNA gyrase A and B proteins (GyrA and GyrB) is described...
  40. ncbi Tus-mediated arrest of DNA replication in Escherichia coli is modulated by DNA supercoiling
    Majda Valjavec-Gratian
    National Center for Biotechnology Information, US National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
    Mol Microbiol 58:758-73. 2005
    ..Introduction of gyrB mutations in combination with the topA869 mutation restored supercoiling density to normal values and also restored ..
  41. pmc his operons of Escherichia coli and Salmonella typhimurium are regulated by DNA supercoiling
    K E Rudd
    Proc Natl Acad Sci U S A 84:517-21. 1987
    ..Several lines of evidence, including high transduction linkage to recF, suggest that hisU1820 is an allele of gyrB. Finally, well-characterized gyrA and gyrB alleles of E. coli are also his regulatory mutations...
  42. pmc Inhibition of deoxyribonucleic acid gyrase: effects on nucleic acid synthesis and cell division in Escherichia coli K-12
    N F Fairweather
    J Bacteriol 142:153-61. 1980
    ..clorobiocin are also coumermycin resistant, and the mutation to resistance in at least one mutant was mapped near gyrB. We conclude, therefore, that clorobiocin inhibits deoxyribonucleic acid gyrase, and the drug was used to probe the ..
  43. ncbi The 43-kilodalton N-terminal fragment of the DNA gyrase B protein hydrolyzes ATP and binds coumarin drugs
    J A Ali
    Department of Biochemistry, University of Leicester, U K
    Biochemistry 32:2717-24. 1993
    ..The implications of these results with respect to the mechanism of supercoiling by DNA gyrase and the inhibition of gyrase by coumarin drugs are discussed...
  44. ncbi Expression in Escherichia coli of Y5-mutant and N-terminal domain-deleted DNA gyrase B proteins affects strongly plasmid maintenance
    L Brino
    Institut de Genetique et de Biologie Moleculaire et Cellulaire, CNRS, INSERM, ULP, Illkirch, France
    Plasmid 38:188-201. 1997
    Escherichia coli DNA gyrase B subunit (GyrB) is composed of a 43-kDa N-terminal domain containing an ATP-binding site and a 47-kDa C-terminal domain involved in the interaction with the gyrase A subunit (GyrA)...
  45. ncbi gyrB-225, a mutation of DNA gyrase that compensates for topoisomerase I deficiency: investigation of its low activity and quinolone hypersensitivity
    J G Heddle
    Department of Biochemistry, University of Leicester, Leicester, LE1 7RH, UK
    J Mol Biol 309:1219-31. 2001
    The B subunit of DNA gyrase (GyrB) consists of a 43 kDa N-terminal domain, containing the site of ATP binding and hydrolysis, and a 47 kDa C-terminal domain that is thought to play a role in interactions with GyrA and DNA...
  46. ncbi Effect of bacteria growth temperature on the distribution of supercoiled DNA and its thermal stability
    Jozef Adamcik
    Department of Biochemistry, Faculty of Sciences, P J Sárik University, Kosice, Kosice, Slovakia
    Electrophoresis 23:3300-9. 2002
    ..Temperature gradient gel electrophoresis (TGGE) and atomic force microscopy (AFM) were used to study the effect of bacteria growth temperature on the distribution of supercoiled DNA and its thermal stability...
  47. pmc Mutants suppressing novobiocin hypersensitivity of a mukB null mutation
    Shun Adachi
    Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Konoe, Yoshida, Sakyo, Kyoto 606 8501, Japan
    J Bacteriol 185:3690-5. 2003
    ..All suppressor mutations are localized in or near the gyrB gene, and the four tested clones have an amino acid substitution in the DNA gyrase beta subunit...
  48. ncbi Antibiotic-mediated recombination: ciprofloxacin stimulates SOS-independent recombination of divergent sequences in Escherichia coli
    Elena Lopez
    Departamento de Biotecnologia Microbiana, Centro Nacional de Biotecnologia CSIC, Campus UAM Cantoblanco, 28049 Madrid, Spain
    Mol Microbiol 64:83-93. 2007
    ....
  49. doi ParAB-mediated intermolecular association of plasmid P1 parS sites
    Tranum Kaur
    School of Pharmacy, University of Waterloo, Waterloo, Ontario, Canada N2L 3G1
    Virology 421:192-201. 2011
    The P1 plasmid partition system depends on ParA-ParB proteins acting on centromere-like parS sites for a faithful plasmid segregation during the Escherichia coli cell cycle. In vivo we placed parS into host E...
  50. ncbi Neutron and light-scattering studies of DNA gyrase and its complex with DNA
    S Krueger
    National Institute of Standards and Technology, Gaithersburg, MD 20899
    J Mol Biol 211:211-20. 1990
    ..No appreciable change in structure is found with the addition of ADPNP. However, the higher-angle SANS data indicate a slight rearrangement of the enzyme in the presence of nucleotide...
  51. ncbi The DNA gyrase of Escherichia coli participates in the formation of a spontaneous deletion by recA-independent recombination in vivo
    A Miura-Masuda
    Institute of Medical Science, University of Tokyo, Japan
    Mol Gen Genet 220:345-52. 1990
    ..These results indicate that the DNA gyrase of E. coli participated in the in vivo deletion formation resulting from the direct repeats...
  52. ncbi The expression of the DNA ligase gene of Escherichia coli is stimulated by relaxation of chromosomal supercoiling
    J C Liebart
    Institut Jacques Monod, Paris, France
    Mol Microbiol 3:269-73. 1989
    ..coli ligts251 mutation can be phenotypically suppressed by mutations which map close to, or in, the gyrB gene and which affect the degree of DNA supercoiling...
  53. ncbi Increased production of a knotted form of plasmid pBR322 DNA in Escherichia coli DNA topoisomerase mutants
    K Shishido
    Department of Life Science, Faculty of Science, Tokyo Institute of Technology, Yokohama, Japan
    J Mol Biol 195:215-8. 1987
    ..deletion of the DNA topoisomerase I gene (delta topA) with a compensatory mutation of the DNA gyrase gene (gyrA or gyrB) and from their TopA+ transductants was analyzed by agarose gel electrophoresis followed by electron microscopy, ..
  54. ncbi A water-soluble form of penicillin-binding protein 2 of Escherichia coli constructed by site-directed mutagenesis
    H Adachi
    Department of Agricultural Chemistry, University of Tokyo, Japan
    FEBS Lett 226:150-4. 1987
    ..this indicates that the removed hydrophobic segment is an uncleaved signal sequence required for translocation of PBP2 across the cytoplasmic membrane, and also suggests that the segment anchors the protein to the membrane...
  55. pmc The nature of inhibition of DNA gyrase by the coumarins and the cyclothialidines revealed by X-ray crystallography
    R J Lewis
    Laboratory of Molecular Biophysics, University of Oxford, UK
    EMBO J 15:1412-20. 1996
    ..These crystal structures consequently describe a chemically well characterized ligand binding surface and provide useful information to assist in the design of novel ligands...
  56. ncbi Hydrolysis of ATP at only one GyrB subunit is sufficient to promote supercoiling by DNA gyrase
    S C Kampranis
    Department of Biochemistry, University of Leicester, University Road, Leicester, LE1 7RH, United Kingdom
    J Biol Chem 273:26305-9. 1998
    ..With only one ATP molecule hydrolyzed at a time, gyrase could still perform supercoiling, but the limit of this reaction was lower than that observed when both subunits can hydrolyze the nucleotide...
  57. pmc A model for the mechanism of strand passage by DNA gyrase
    S C Kampranis
    Department of Biochemistry, University of Leicester, Leicester LE1 7RH, United Kingdom
    Proc Natl Acad Sci U S A 96:8414-9. 1999
    ..This mechanism is concerted, in that capture of the transported segment by the ATP-operated clamp induces opening of the DNA gate, which in turn stimulates ATP hydrolysis...
  58. pmc Temperature-sensitive suppressor mutations of the Escherichia coli DNA gyrase B protein
    S J Blance
    Department of Biochemistry, University of Leicester, United Kingdom
    Protein Sci 9:1035-7. 2000
    Escherichia coli strain LE316 contains a mutation in gyrB that results in the substitution of Val164 to Gly and confers both chlorobiocin resistance and temperature sensitivity...
  59. ncbi DNA gyrase interaction with coumarin-based inhibitors: the role of the hydroxybenzoate isopentenyl moiety and the 5'-methyl group of the noviose
    Daniel Lafitte
    UMR CNRS 6032, UFR de Pharmacie, 27 Bd Jean Moulin, 13385 Marseille Cedex 5, France
    Biochemistry 41:7217-23. 2002
    ..We also demonstrate the crucial role of both the hydroxybenzoate isopentenyl moiety and the 5'-alkyl group on the noviose of the coumarins in the binding affinity for gyrase...
  60. ncbi Detection and identification of Escherichia coli, Shigella, and Salmonella by microarrays using the gyrB gene
    Kenichi Kakinuma
    Genomics Research Institute, SRL, Inc, 5 6 50 Shinmachi, Hino shi, Tokyo 191 0002, Japan
    Biotechnol Bioeng 83:721-8. 2003
    ..However, it may not always be applicable for distinguishing closely related bacteria. Therefore, we selected gyrB genes that encode the subunit B protein of DNA gyrase (a topoisomerase type II protein) as target genes...
  61. pmc Segmentally variable genes: a new perspective on adaptation
    Yu Zheng
    Bioinformatics Graduate Program, Boston University, Boston, Massachusetts, USA
    PLoS Biol 2:E81. 2004
    ..Discerning their function and identifying their binding partners may offer biologists new insights into the basic mechanisms of adaptation, context-dependent evolution, and the interaction between microbes and their environment...
  62. pmc Distribution of gyrase and topoisomerase IV on bacterial nucleoid: implications for nucleoid organization
    Ya Han Hsu
    Department and Graduate Institute of Microbiology, School of Medicine, National Taiwan University, No 1, Section 1, Jen Ai Road, Taipei 10018, Taiwan, ROC
    Nucleic Acids Res 34:3128-38. 2006
    ..In sum, our study suggests a potential role of Topo IIs in the arrangement of DNA supercoiling loop domains in prokaryotic cells...
  63. ncbi Topoisomerase action on short DNA duplexes reveals requirements for gate and transfer DNA segments
    Boris P Belotserkovskii
    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720 3402, USA
    J Biol Chem 281:25407-15. 2006
    ..Topo IV cleaved the DNA-DNA duplex, but not the DNA-RNA duplex implying that the DNA-RNA duplex can be a T-segment but not a G-segment...
  64. ncbi Lethal fragmentation of bacterial chromosomes mediated by DNA gyrase and quinolones
    Muhammad Malik
    Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA
    Mol Microbiol 61:810-25. 2006
    ..Instability of type II topoisomerase-DNA complexes may be a general phenomenon that can be exploited to kill cells...
  65. ncbi Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque
    Marcelo Nollmann
    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Nat Struct Mol Biol 14:264-71. 2007
    ..A third mode is responsible for the ATP-independent relaxation of negative supercoils. We present a branched kinetic model that quantitatively accounts for all of our single-molecule results and agrees with existing biochemical data...
  66. ncbi [Fluoroquinolones and Gram-negative bacteria: antimicrobial activity and mechanisms of resistance]
    F Luzzaro
    Ospedale di Circolo e Università dell Insubria, Varese, Italy
    Infez Med 16:5-11. 2008
    ..this mechanism of action, bacteria have developed resistance mechanisms consisting in some target mutations (GyrA/GyrB for DNA gyrase and ParC/ParE for topoisomerase IV) or in a reduced access to the target itself, by either decreased ..
  67. doi Synthesis and antibacterial property of quinolines with potent DNA gyrase activity
    Ekambaram Ramesh
    Department of Organic Chemistry, Guindy Campus, University of Madras, Chennai 600025, India
    Bioorg Med Chem 17:660-6. 2009
    ..5 mg/mL against Escherichia coli...
  68. pmc A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function
    Allyn J Schoeffler
    Department of Molecular and Cell Biology, California Institute for Quantitative Biosciences, University of California, Berkeley and Fluidigm Corporation, South San Francisco, CA 94080, USA
    Nucleic Acids Res 38:7830-44. 2010
    ..a 170-amino acid insertion of unknown architecture and function in the metal- and DNA-binding TOPRIM domain of the GyrB subunit...
  69. doi Exploring the conformational changes of the ATP binding site of gyrase B from Escherichia coli complexed with different established inhibitors by using molecular dynamics simulation: protein-ligand interactions in the light of the alanine scanning and fre
    Liane Saiz-Urra
    Chemical Bioactive Center, Central University of Las Villas, Santa Clara, Villa Clara, C P 54830, Cuba
    J Mol Graph Model 29:726-39. 2011
    ..DNA gyrase is a well-established antibacterial target consisting of two subunits, GyrA and GyrB, in a heterodimer A(2)B(2). GyrA is involved in DNA breakage and reunion and GyrB catalyzes the hydrolysis of ATP...
  70. ncbi Site-specific cleavage of DNA by E. coli DNA gyrase
    A Morrison
    Cell 17:175-84. 1979
    ..This diverse recognition sequence with common elements is a pattern shared with several other specific nucleic acid-protein interactions...
  71. pmc Mutations causing aminotriazole resistance and temperature sensitivity reside in gyrB, which encodes the B subunit of DNA gyrase
    W M Toone
    Department of Genetics, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada
    J Bacteriol 174:5479-81. 1992
    Certain mutations in gyrA and gyrB, the genes encoding the two subunits of DNA gyrase, are known to influence expression of the his operon (K. E. Rudd and R. Menzel, Proc. Natl. Acad. Sci. USA 84:517-521, 1987)...
  72. ncbi Energy coupling in DNA gyrase: a thermodynamic limit to the extent of DNA supercoiling
    P M Cullis
    Department of Chemistry, The University, Leicester, U K
    Biochemistry 31:9642-6. 1992
    ..These results provide direct evidence to support the proposal that the extent of DNA supercoiling by DNA gyrase is limited by the free energy of hydrolysis of the nucleotide...
  73. pmc The peptide antibiotic microcin B17 induces double-strand cleavage of DNA mediated by E. coli DNA gyrase
    J L Vizán
    Unidad de Genetica Molecular, Hospital Ramon y Cajal, Madrid, Spain
    EMBO J 10:467-76. 1991
    ..Cloning of the mutations and Tn5 insertional analysis demonstrated that they were located inside gyrB. The approximate location of the mutations within gyrB was determined by constructing hybrid genes, as a previous ..
  74. pmc Effects of inhibition of the B subunit of DNA gyrase on conjugation in Escherichia coli
    D C Hooper
    Medical Services, Massachusetts General Hospital, Boston 02114
    J Bacteriol 171:2235-7. 1989
    ....
  75. pmc DNA sequence and transcription of the region upstream of the E. coli gyrB gene
    T Adachi
    Nucleic Acids Res 12:6389-95. 1984
    ..coli that extends from within dnaN through recF and into the gyrB gene. An open reading frame of 1071 base pairs has been identified with the recF structural gene...
  76. ncbi The hisR locus of Salmonella: nucleotide sequence and expression
    L Bossi
    Mol Gen Genet 192:163-70. 1983
    ..can be processed to 4S RNA in vitro with a wild-type Salmonella extract, but not with an extract prepared from a hisU (RNase P) mutant...
  77. ncbi Identification of DNA topoisomerases involved in immediate and transient DNA relaxation induced by heat shock in Escherichia coli
    Y Ogata
    Department of Microbiology, Faculty of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
    Mol Gen Genet 244:451-5. 1994
    ..These results are interpreted as indicating that both DNA topoisomerase I and DNA gyrase are involved in the DNA relaxation induced by heat shock...
  78. ncbi Energy coupling in Escherichia coli DNA gyrase: the relationship between nucleotide binding, strand passage, and DNA supercoiling
    A D Bates
    Department of Biochemistry, University of Liverpool, UK
    Biochemistry 35:1408-16. 1996
    ..The implications for the normal ATP-dependent supercoiling reaction of the enzyme are considered and the results discussed in terms of current mechanistic models for DNA gyrase action and the possible in vivo roles of the enzyme...
  79. ncbi Roles of DNA topoisomerases in the regulation of R-loop formation in vitro
    P Phoenix
    Departement de Microbiologie et Immunologie, Universite de Montreal, C P 6128, Succursale Centre Ville, Montreal, Quebec H3C 3J7, Canada
    J Biol Chem 272:1473-9. 1997
    ..In addition, we found that an R-looped plasmid DNA is a better substrate for relaxation by E. coli DNA topoisomerase I as compared with a non-R-looped substrate...
  80. ncbi DNA gyrase and topoisomerase IV: biochemical activities, physiological roles during chromosome replication, and drug sensitivities
    C Levine
    Graduate Program in Molecular Biology, Cornell University Graduate School of Medical Sciences, New York, NY, USA
    Biochim Biophys Acta 1400:29-43. 1998
    ..These different roles can be attributed to differences in the biochemical properties of the two enzymes. The biochemical activities, physiological roles, and drug sensitivities of the enzymes are reviewed...
  81. ncbi Locking the ATP-operated clamp of DNA gyrase: probing the mechanism of strand passage
    N L Williams
    Department of Biochemistry, University of Leicester, Leicester, LE1 7RH, UK
    J Mol Biol 306:969-84. 2001
    ....
  82. pmc Active-site residues of Escherichia coli DNA gyrase required in coupling ATP hydrolysis to DNA supercoiling and amino acid substitutions leading to novobiocin resistance
    Christian H Gross
    Vertex Pharmaceuticals Incorporated, Cambridge, Massachusetts 02139, USA
    Antimicrob Agents Chemother 47:1037-46. 2003
    ..Amino acids in proximity to bound nonhydrolyzable ATP analog (AMP. PNP) or novobiocin in the gyrase B (GyrB) subunit crystal structures were examined for their roles in enzyme function and novobiocin resistance by site-..
  83. ncbi Replication restart in gyrB Escherichia coli mutants
    Gianfranco Grompone
    Laboratoire de Genetique Microbienne, Institut National de la Recherche Agronomique, 78352 Jouy en Josas, France
    Mol Microbiol 48:845-54. 2003
    ..We show that the preprimosomal protein PriA is essential for the viability of these gyrB mutants. The helicase function of PriA is not essential...
  84. ncbi Eclipse-synchrony relationship in Escherichia coli strains with mutations affecting sequestration, initiation of replication and superhelicity of the bacterial chromosome
    Jan A Olsson
    Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Box 596, SE 751 24 Uppsala, Sweden
    J Mol Biol 334:919-31. 2003
    ..An eclipse period of approximately 0.5 generation time appeared to be the critical value for the switch from synchronous to asynchronous initiation...
  85. ncbi Microbiology. Dynamic instability of a bacterial engine
    Jakob Møller-Jensen
    MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK
    Science 306:987-9. 2004
  86. ncbi A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias
    Alexander J Ruthenburg
    Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    J Biol Chem 280:26177-84. 2005
    ..We propose a model wherein the right-handed ((+) solenoidal) wrapping of DNA around the E. coli GyrA-CTD enforces unidirectional (-) DNA supercoiling...
  87. pmc Norfloxacin-induced DNA gyrase cleavage complexes block Escherichia coli replication forks, causing double-stranded breaks in vivo
    Jennifer Reineke Pohlhaus
    Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
    Mol Microbiol 56:1416-29. 2005
    ..Additionally, some branched plasmid DNA isolated under resealing conditions nonetheless contained broken DNA ends. We discuss a model for the creation of double-stranded breaks by an indirect mechanism after quinolone treatment...
  88. pmc Dynamics of the trimeric AcrB transporter protein inferred from a B-factor analysis of the crystal structure
    W C Lu
    Ames Laboratory U S DOE, Department of Physics and Astronomy, Iowa State University, Ames, Iowa 50011, USA
    Proteins 62:152-8. 2006
    The Escherichia coli AcrB multidrug transporter recognizes a wide range of toxic chemicals and actively extrudes them from cells. The molecular basis of multidrug transport in AcrB remains unknown...
  89. ncbi Growth inhibition mediated by excess negative supercoiling: the interplay between transcription elongation, R-loop formation and DNA topology
    Marc Drolet
    Departement de Microbiologie et Immunologie, Universite de Montreal, C P 6128, Succ Centre Ville, Montreal, P Quebec, Canada H3C 3J7
    Mol Microbiol 59:723-30. 2006
    ..Growth inhibition mediated by excess negative supercoiling might be related to this interplay between transcription elongation and supercoiling...
  90. ncbi The effect of promoter strength, supercoiling and secondary structure on mutation rates in Escherichia coli
    Karen H Schmidt
    Division of Biological Sciences, The University of Montana, Missoula, MT 59812, USA
    Mol Microbiol 60:1251-61. 2006
    ..higher reversion rates in a topA mutant strain with increased negative supercoiling compared with wild-type levels, and the cat reversion rates were lower in a topA gyrB mutant strain with decreased negative supercoiling, as predicted.
  91. pmc A strand-passage conformation of DNA gyrase is required to allow the bacterial toxin, CcdB, to access its binding site
    Andrew B Smith
    Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
    Nucleic Acids Res 34:4667-76. 2006
    ..of gyrase by stabilization of the cleavage complex and that the GyrA C-terminal DNA-wrapping domain and the GyrB N-terminal ATPase domain are dispensable for CcdB's action...
  92. pmc Effect of anaerobic growth on quinolone lethality with Escherichia coli
    Muhammad Malik
    Public Health Research Institute, 225 Warren Street, Newark, NJ 07103, USA
    Antimicrob Agents Chemother 51:28-34. 2007
    ....
  93. pmc The phytotoxin albicidin is a novel inhibitor of DNA gyrase
    Saeed M Hashimi
    Botany Department SIB, The University of Queensland, Brisbane 4072, Australia
    Antimicrob Agents Chemother 51:181-7. 2007
    ..albilineans encodes a gyrase-interacting protein for self-protection. The novel features of the gyrase-albicidin interaction indicate the potential for the development of new antibacterial drugs...
  94. pmc Dual targeting of GyrB and ParE by a novel aminobenzimidazole class of antibacterial compounds
    Trudy H Grossman
    Vertex Pharmaceuticals Incorporated, 130 Waverly Street, Cambridge, MA 02139, USA
    Antimicrob Agents Chemother 51:657-66. 2007
    ..Sequencing of DNA corresponding to the GyrB and ParE ATP-binding regions in VRT-125853- and VRT-752586-resistant mutants revealed that their primary target in ..
  95. ncbi Green tea catechins inhibit bacterial DNA gyrase by interaction with its ATP binding site
    Helena Gradisar
    Laboratory of Biotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
    J Med Chem 50:264-71. 2007
    ....
  96. ncbi Ribonucleotide reductase and the regulation of DNA replication: an old story and an ancient heritage
    John Herrick
    3, rue des Jeûneurs, Paris 75002, France
    Mol Microbiol 63:22-34. 2007
    ..In this review we examine the role RNR plays in regulating the total rate of DNA synthesis in E. coli and, hence, in maintaining constant DNA/cell mass ratios during normal growth and under conditions of DNA stress...