Genomes and Genes
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
- Menzel R, Gellert M. Fusions of the Escherichia coli gyrA and gyrB control regions to the galactokinase gene are inducible by coumermycin treatment. J Bacteriol. 1987;169:1272-8 pubmed..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 ..
- Pruss G, Franco R, Chevalier S, Manes S, Drlica K. Effects of DNA gyrase inhibitors in Escherichia coli topoisomerase I mutants. J Bacteriol. 1986;168:276-82 pubmed..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.
- Ullsperger C, Cozzarelli N. Contrasting enzymatic activities of topoisomerase IV and DNA gyrase from Escherichia coli. J Biol Chem. 1996;271:31549-55 pubmed..This ability of Topo IV to selectively unlink catenated molecules mirrors its key role in decatenation of replicating chromosomes in vivo. ..
- Morais Cabral J, Jackson A, Smith C, Shikotra N, Maxwell A, Liddington R. Crystal structure of the breakage-reunion domain of DNA gyrase. Nature. 1997;388:903-6 pubmed publisher..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...
- Steck T, Drlica K. Bacterial chromosome segregation: evidence for DNA gyrase involvement in decatenation. Cell. 1984;36:1081-8 pubmedNucleoids isolated from a temperature-sensitive gyrB mutant of E. coli, incubated at restrictive temperatures, exhibit increased sedimentation rates and an abnormal doublet or dumbbell-shaped morphology...
- Chatterji M, Unniraman S, Maxwell A, Nagaraja V. The additional 165 amino acids in the B protein of Escherichia coli DNA gyrase have an important role in DNA binding. J Biol Chem. 2000;275:22888-94 pubmed..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...
- Peter B, Arsuaga J, Breier A, Khodursky A, Brown P, Cozzarelli N. Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol. 2004;5:R87 pubmed..We propose that supercoiling acts as a second messenger that transmits information about the environment to many regulatory networks in the cell. ..
- Menzel R, Gellert M. Modulation of transcription by DNA supercoiling: a deletion analysis of the Escherichia coli gyrA and gyrB promoters. Proc Natl Acad Sci U S A. 1987;84:4185-9 pubmedExpression 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...
- Espeli O, Boccard F. In vivo cleavage of Escherichia coli BIME-2 repeats by DNA gyrase: genetic characterization of the target and identification of the cut site. Mol Microbiol. 1997;26:767-77 pubmed..DNA gyrase cleavage at repetitive BIME-2 elements may have consequences for DNA topology and genomic rearrangements. ..
- Zechiedrich E, Khodursky A, Bachellier S, Schneider R, Chen D, Lilley D, et al. Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli. J Biol Chem. 2000;275:8103-13 pubmed..09), greatly stimulating transcription from the supercoiling sensitive leu-500 promoter and increasing the number of supercoils trapped by lambda integrase site-specific recombination. ..
- Kampranis S, Howells A, Maxwell A. The interaction of DNA gyrase with the bacterial toxin CcdB: evidence for the existence of two gyrase-CcdB complexes. J Mol Biol. 1999;293:733-44 pubmed..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 ..
- Loris R, Dao Thi M, Bahassi E, Van Melderen L, Poortmans F, Liddington R, et al. Crystal structure of CcdB, a topoisomerase poison from E. coli. J Mol Biol. 1999;285:1667-77 pubmed publisher..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...
- DiNardo S, Voelkel K, Sternglanz R, Reynolds A, Wright A. Escherichia coli DNA topoisomerase I mutants have compensatory mutations in DNA gyrase genes. Cell. 1982;31:43-51 pubmed..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...
- Menzel R, Gellert M. Regulation of the genes for E. coli DNA gyrase: homeostatic control of DNA supercoiling. Cell. 1983;34:105-13 pubmed..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. ..
- Noble C, Maxwell A. The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a proposed two metal-ion mechanism. J Mol Biol. 2002;318:361-71 pubmed..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. ..
- Valjavec Gratian M, Henderson T, Hill T. Tus-mediated arrest of DNA replication in Escherichia coli is modulated by DNA supercoiling. Mol Microbiol. 2005;58:758-73 pubmed..Introduction of gyrB mutations in combination with the topA869 mutation restored supercoiling density to normal values and also restored ..
- Thornton M, Armitage M, Maxwell A, Dosanjh B, Howells A, Norris V, et al. Immunogold localization of GyrA and GyrB proteins in Escherichia coli. Microbiology. 1994;140 ( Pt 9):2371-82 pubmedImmunogold 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...
- Travers A, Muskhelishvili G. DNA supercoiling - a global transcriptional regulator for enterobacterial growth?. Nat Rev Microbiol. 2005;3:157-69 pubmed
- Costenaro L, Grossmann J, Ebel C, Maxwell A. Small-angle X-ray scattering reveals the solution structure of the full-length DNA gyrase a subunit. Structure. 2005;13:287-96 pubmed..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. ..
- Steck T, Pruss G, Manes S, Burg L, Drlica K. DNA supercoiling in gyrase mutants. J Bacteriol. 1984;158:397-403 pubmedNucleoids isolated from Escherichia coli strains carrying temperature-sensitive gyrA or gyrB mutations were examined by sedimentation in ethidium bromide-containing sucrose density gradients...
- Gellert M, Mizuuchi K, O Dea M, Nash H. DNA gyrase: an enzyme that introduces superhelical turns into DNA. Proc Natl Acad Sci U S A. 1976;73:3872-6 pubmed..The enzyme acts equally well on relaxed closed-circular colicin E1, phage lambda, and simian virus 40 DNA. The final superhelix density of the DNA can be considerably greater than that found in intracellularly supercoiled DNA. ..
- Khodursky A, Peter B, Schmid M, DeRisi J, Botstein D, Brown P, et al. Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays. Proc Natl Acad Sci U S A. 2000;97:9419-24 pubmed..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. ..
- Ebersbach G, Gerdes K. Bacterial mitosis: partitioning protein ParA oscillates in spiral-shaped structures and positions plasmids at mid-cell. Mol Microbiol. 2004;52:385-98 pubmedThe 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)...
- Heddle J, Mitelheiser S, Maxwell A, Thomson N. Nucleotide binding to DNA gyrase causes loss of DNA wrap. J Mol Biol. 2004;337:597-610 pubmed
- Zechiedrich E, Cozzarelli N. Roles of topoisomerase IV and DNA gyrase in DNA unlinking during replication in Escherichia coli. Genes Dev. 1995;9:2859-69 pubmed..We conclude that catenanes are kinetic intermediates in DNA replication and that the essential role of topo IV is to unlink daughter replicons. ..
- Gellert M, Fisher L, O Dea M. DNA gyrase: purification and catalytic properties of a fragment of gyrase B protein. Proc Natl Acad Sci U S A. 1979;76:6289-93 pubmed..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 ..
- Maxwell A, Howells A. Overexpression and purification of bacterial DNA gyrase. Methods Mol Biol. 1999;94:135-44 pubmed
- Pierrat O, Maxwell A. The action of the bacterial toxin microcin B17. Insight into the cleavage-religation reaction of DNA gyrase. J Biol Chem. 2003;278:35016-23 pubmed..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. ..
- Ashiuchi M, Kuwana E, Yamamoto T, Komatsu K, Soda K, Misono H. Glutamate racemase is an endogenous DNA gyrase inhibitor. J Biol Chem. 2002;277:39070-3 pubmed..This is the first finding of the enzyme protein participating in both d-amino acid metabolism and DNA processing. ..
- Williams N, Maxwell A. Probing the two-gate mechanism of DNA gyrase using cysteine cross-linking. Biochemistry. 1999;38:13502-11 pubmed..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. ..
- Fisher L, Mizuuchi K, O Dea M, Ohmori H, Gellert M. Site-specific interaction of DNA gyrase with DNA. Proc Natl Acad Sci U S A. 1981;78:4165-9 pubmed..This result supports the view that, in the DNA gyrase--DNA complex, the DNA is largely wrapped on the outside of the enzyme. ..
- Sugino A, Higgins N, Cozzarelli N. DNA gyrase subunit stoichiometry and the covalent attachment of subunit A to DNA during DNA cleavage. Nucleic Acids Res. 1980;8:3865-74 pubmedEscherichia 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...
- Snoep J, van der Weijden C, Andersen H, Westerhoff H, Jensen P. 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. Eur J Biochem. 2002;269:1662-9 pubmed..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). ..
- Nollmann M, Crisona N, Arimondo P. Thirty years of Escherichia coli DNA gyrase: from in vivo function to single-molecule mechanism. Biochimie. 2007;89:490-9 pubmed..Here, we review the biological roles of gyrase in vivo and its mechanism in vitro. ..
- Maxwell A, Gellert M. The DNA dependence of the ATPase activity of DNA gyrase. J Biol Chem. 1984;259:14472-80 pubmed..To account for these data we propose a model for the interaction of gyrase with ATP and DNA in which ATP hydrolysis requires the binding of DNA to two sites on the enzyme. ..
- Brino L, Bronner C, Oudet P, Mousli M. Isoleucine 10 is essential for DNA gyrase B function in Escherichia coli. Biochimie. 1999;81:973-80 pubmed..work was to study the contribution of I10, one of the most important residues responsible for the stabilization of GyrB dimer and involved in the ATP-binding step, in the ATP-hydrolysis reaction and in the DNA supercoiling mechanism...
- Anderle C, Stieger M, Burrell M, Reinelt S, Maxwell A, Page M, et al. Biological activities of novel gyrase inhibitors of the aminocoumarin class. Antimicrob Agents Chemother. 2008;52:1982-90 pubmed publisher..Several compounds showed high levels of activity against staphylococci, including a methicillin-resistant Staphylococcus aureus strain. However, they showed only poor activities against gram-negative strains. ..
- Grompone G, Ehrlich S, Michel B. Replication restart in gyrB Escherichia coli mutants. Mol Microbiol. 2003;48:845-54 pubmed..We show that the preprimosomal protein PriA is essential for the viability of these gyrB mutants. The helicase function of PriA is not essential...
- Nakamura S, Nakamura M, Kojima T, Yoshida H. gyrA and gyrB mutations in quinolone-resistant strains of Escherichia coli. Antimicrob Agents Chemother. 1989;33:254-5 pubmedThe proportion of gyrA and gyrB mutations in quinolone-resistant Escherichia coli strains was examined by introducing cloned wild-type gyrA and gyrB genes. In 25 spontaneous mutants of strain KL16, 13 had gyrA and 12 had gyrB mutations...
- Ohniwa R, Morikawa K, Kim J, Ohta T, Ishihama A, Wada C, et al. Dynamic state of DNA topology is essential for genome condensation in bacteria. EMBO J. 2006;25:5591-602 pubmed..These results indicate that the topology of DNA is dynamically transmutable and that the topology control is important for Dps-induced nucleoid condensation. ..
- Mustaev A, Malik M, Zhao X, Kurepina N, Luan G, Oppegard L, et al. Fluoroquinolone-gyrase-DNA complexes: two modes of drug binding. J Biol Chem. 2014;289:12300-12 pubmed publisher..the presence of DNA breaks, have been crystallized and found to have the fluoroquinolone C-7 ring system facing the GyrB/ParE subunits...
- Hashimi S, Wall M, Smith A, Maxwell A, Birch R. The phytotoxin albicidin is a novel inhibitor of DNA gyrase. Antimicrob Agents Chemother. 2007;51:181-7 pubmed..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. ..
- Pohlhaus J, Kreuzer K. Norfloxacin-induced DNA gyrase cleavage complexes block Escherichia coli replication forks, causing double-stranded breaks in vivo. Mol Microbiol. 2005;56:1416-29 pubmed..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. ..
- Tamura J, Bates A, Gellert M. Slow interaction of 5'-adenylyl-beta,gamma-imidodiphosphate with Escherichia coli DNA gyrase. Evidence for cooperativity in nucleotide binding. J Biol Chem. 1992;267:9214-22 pubmed..To account for these data, a model is proposed for the interaction of nucleotides at the two ATP binding sites on DNA gyrase. ..
- Smith A, Maxwell A. A strand-passage conformation of DNA gyrase is required to allow the bacterial toxin, CcdB, to access its binding site. Nucleic Acids Res. 2006;34:4667-76 pubmed..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...
- Dorman C, Corcoran C. Bacterial DNA topology and infectious disease. Nucleic Acids Res. 2009;37:672-8 pubmed publisher..Knowledge of the molecular connections between physiology, DNA topology and gene expression offers new opportunities to fight infection. ..
- Saing K, Orii H, Tanaka Y, Yanagisawa K, Miura A, Ikeda H. Formation of deletion in Escherichia coli between direct repeats located in the long inverted repeats of a cellular slime mold plasmid: participation of DNA gyrase. Mol Gen Genet. 1988;214:1-5 pubmed..These sequences consist of local short inverted repeats, where cutting and rejoining occur at one of the two regions. ..
- Filutowicz M, Jonczyk P. The gyrB gene product functions in both initiation and chain polymerization of Escherichia coli chromosome replication: suppression of the initiation deficiency in gyrB-ts mutants by a class of rpoB mutations. Mol Gen Genet. 1983;191:282-7 pubmedA class of rpoB mutations is described which suppresses replication and transcription deficiency in gyrB-ts mutants shifted to a nonpermissive temperature...
- Higgins N, Cozzarelli N. The binding of gyrase to DNA: analysis by retention by nitrocellulose filters. Nucleic Acids Res. 1982;10:6833-47 pubmed..The first and second complexes require Mg++ for optimal formation. The third form has been shown previously to contain denatured A protomers covalently linked to DNA that is broken at the site of attachment. ..
- Toone W, Rudd K, Friesen J. Mutations causing aminotriazole resistance and temperature sensitivity reside in gyrB, which encodes the B subunit of DNA gyrase. J Bacteriol. 1992;174:5479-81 pubmedCertain 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)...
- Staudenbauer W, Orr E. DNA gyrase: affinity chromatography on novobiocin-Sepharose and catalytic properties. Nucleic Acids Res. 1981;9:3589-603 pubmed..The two larger proteins were identified as the A subunit (gyrA protein) and the B subunit (gyrB protein) of DNA gyrase topoisomerase II)...
- Ruberti I, Crescenzi F, Paolozzi L, Ghelardini P. A class of gyrB mutants, substantially unaffected in DNA topology, suppresses the Escherichia coli K12 ftsZ84 mutation. Mol Microbiol. 1991;5:1065-72 pubmed..To settle this question, we have selected and characterized mutants in the gyrB gene able to phenotypically suppress the defects of the ftsZ84 mutation...
- Heddle J, Lu T, Zhao X, Drlica K, Maxwell A. gyrB-225, a mutation of DNA gyrase that compensates for topoisomerase I deficiency: investigation of its low activity and quinolone hypersensitivity. J Mol Biol. 2001;309:1219-31 pubmedThe 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...
- Blance S, Williams N, Preston Z, Bishara J, Smyth M, Maxwell A. Temperature-sensitive suppressor mutations of the Escherichia coli DNA gyrase B protein. Protein Sci. 2000;9:1035-7 pubmedEscherichia 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...
- Ruthenburg A, Graybosch D, Huetsch J, Verdine G. A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias. J Biol Chem. 2005;280:26177-84 pubmed..We propose a model wherein the right-handed ((+) solenoidal) wrapping of DNA around the E. coli GyrA-CTD enforces unidirectional (-) DNA supercoiling. ..
- Kampranis S, Bates A, Maxwell A. A model for the mechanism of strand passage by DNA gyrase. Proc Natl Acad Sci U S A. 1999;96:8414-9 pubmed..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. ..
- Lu W, Wang C, Yu E, Ho K. Dynamics of the trimeric AcrB transporter protein inferred from a B-factor analysis of the crystal structure. Proteins. 2006;62:152-8 pubmedThe 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...
- Ostrov D, Hernandez Prada J, Corsino P, Finton K, Le N, Rowe T. Discovery of novel DNA gyrase inhibitors by high-throughput virtual screening. Antimicrob Agents Chemother. 2007;51:3688-98 pubmed..coli DNA gyrase. These compounds are structurally unrelated to previously identified gyrase inhibitors and represent potential scaffolds for the optimization of novel antibacterial agents that act on fluoroquinolone-resistant strains. ..
- Scherzinger E, Haring V, Lurz R, Otto S. Plasmid RSF1010 DNA replication in vitro promoted by purified RSF1010 RepA, RepB and RepC proteins. Nucleic Acids Res. 1991;19:1203-11 pubmed
- Younas M, Siddiqui F, Noreen Z, Bokhari S, Gomez Duarte O, Wren B, et al. Characterization of enteropathogenic Escherichia coli of clinical origin from the pediatric population in Pakistan. Trans R Soc Trop Med Hyg. 2016;110:414-20 pubmed publisher..13 (28%) showed presence of single nucleotide polymorphism (SNP) in parC (C330-T330) whereas 1 (2%) isolate showed gyrB (A660-T660) SNP. Furthermore, 27 (59%) isolates were ESBL producers...
- Orr E, Fairweather N, Holland I, Pritchard R. Isolation and characterisation of a strain carrying a conditional lethal mutation in the cou gene of Escherichia coli K12. Mol Gen Genet. 1979;177:103-12 pubmed..Genetic mapping and the molecular weight of the gene product suggest that the mutation is in the cou gene, specifying a sub-unit of DNA gyrase...
- Sissi C, Marangon E, Chemello A, Noble C, Maxwell A, Palumbo M. The effects of metal ions on the structure and stability of the DNA gyrase B protein. J Mol Biol. 2005;353:1152-60 pubmed
- Phoenix P, Raymond M, Masse E, Drolet M. Roles of DNA topoisomerases in the regulation of R-loop formation in vitro. J Biol Chem. 1997;272:1473-9 pubmed..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. ..
- Møller Jensen J, Gerdes K. Microbiology. Dynamic instability of a bacterial engine. Science. 2004;306:987-9 pubmed
- Gross C, Parsons J, Grossman T, Charifson P, Bellon S, Jernee J, et al. Active-site residues of Escherichia coli DNA gyrase required in coupling ATP hydrolysis to DNA supercoiling and amino acid substitutions leading to novobiocin resistance. Antimicrob Agents Chemother. 2003;47:1037-46 pubmed..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-..
- Ali J, Jackson A, Howells A, Maxwell A. The 43-kilodalton N-terminal fragment of the DNA gyrase B protein hydrolyzes ATP and binds coumarin drugs. Biochemistry. 1993;32:2717-24 pubmed..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. ..
- Johnson E, Yao S, Helinski D. Gyrase inhibitors and thymine starvation disrupt the normal pattern of plasmid RK2 localization in Escherichia coli. J Bacteriol. 2005;187:3538-47 pubmed..Under these conditions the RK2 plasmid clusters were not disassembled, suggesting that a completely intact replication complex is not required for plasmid clustering. ..