GYRB_ECOLI
ID GYRB_ECOLI Reviewed; 804 AA.
AC P0AES6; O08438; P06982; Q2M811;
DT 01-APR-1988, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 153.
DE RecName: Full=DNA gyrase subunit B {ECO:0000255|HAMAP-Rule:MF_01898};
DE EC=5.6.2.2 {ECO:0000255|HAMAP-Rule:MF_01898, ECO:0000269|PubMed:12051842, ECO:0000269|PubMed:12051843, ECO:0000269|PubMed:18642932, ECO:0000269|PubMed:186775, ECO:0000269|PubMed:19965760};
DE AltName: Full=Type IIA topoisomerase subunit GyrB;
GN Name=gyrB {ECO:0000255|HAMAP-Rule:MF_01898};
GN Synonyms=acrB {ECO:0000303|PubMed:9148951}, cou, himB, hisU, nalC, parA,
GN pcbA; OrderedLocusNames=b3699, JW5625;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=3020376; DOI=10.1007/bf00331012;
RA Yamagishi J., Yoshida H., Yamayoshi M., Nakamura S.;
RT "Nalidixic acid-resistant mutations of the gyrB gene of Escherichia coli.";
RL Mol. Gen. Genet. 204:367-373(1986).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=3029692; DOI=10.1093/nar/15.2.771;
RA Adachi T., Mizuuchi M., Robinson E.A., Appella E., O'Dea M.H., Gellert M.,
RA Mizuuchi K.;
RT "DNA sequence of the E. coli gyrB gene: application of a new sequencing
RT strategy.";
RL Nucleic Acids Res. 15:771-784(1987).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF VARIANT ACRB, FUNCTION, ACTIVITY
RP REGULATION, SUBUNIT, DNA-BINDING, AND ACRIDINE SENSITIVITY.
RC STRAIN=K12 / N2879;
RX PubMed=9148951; DOI=10.1074/jbc.272.20.13302;
RA Funatsuki K., Tanaka R., Inagaki S., Konno H., Katoh K., Nakamura H.;
RT "acrB mutation located at carboxyl-terminal region of gyrase B subunit
RT reduces DNA binding of DNA gyrase.";
RL J. Biol. Chem. 272:13302-13308(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=7686882; DOI=10.1006/geno.1993.1230;
RA Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.;
RT "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome:
RT organizational symmetry around the origin of replication.";
RL Genomics 16:551-561(1993).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [6]
RP SEQUENCE REVISION TO 385.
RX PubMed=16397293; DOI=10.1093/nar/gkj405;
RA Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R.,
RA Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T.,
RA Mori H., Perna N.T., Plunkett G. III, Rudd K.E., Serres M.H., Thomas G.H.,
RA Thomson N.R., Wishart D., Wanner B.L.;
RT "Escherichia coli K-12: a cooperatively developed annotation snapshot
RT -- 2005.";
RL Nucleic Acids Res. 34:1-9(2006).
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [8]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-106.
RC STRAIN=K12;
RX PubMed=6089112; DOI=10.1093/nar/12.16.6389;
RA Adachi T., Mizuuchi K., Menzel R., Gellert M.;
RT "DNA sequence and transcription of the region upstream of the E. coli gyrB
RT gene.";
RL Nucleic Acids Res. 12:6389-6395(1984).
RN [9]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-22.
RX PubMed=3029031; DOI=10.1128/jb.169.3.1272-1278.1987;
RA Menzel R., Gellert M.;
RT "Fusions of the Escherichia coli gyrA and gyrB control regions to the
RT galactokinase gene are inducible by coumermycin treatment.";
RL J. Bacteriol. 169:1272-1278(1987).
RN [10]
RP PROTEIN SEQUENCE OF 93-129, AND ATP-BINDING.
RX PubMed=2174443; DOI=10.1016/s0021-9258(17)45366-x;
RA Tamura J.K., Gellert M.;
RT "Characterization of the ATP binding site on Escherichia coli DNA gyrase.
RT Affinity labeling of Lys-103 and Lys-110 of the B subunit by pyridoxal 5'-
RT diphospho-5'-adenosine.";
RL J. Biol. Chem. 265:21342-21349(1990).
RN [11]
RP FUNCTION IN GENERATING NEGATIVELY SUPERCOILED DNA, CATALYTIC ACTIVITY, AND
RP ATP-DEPENDENCE.
RX PubMed=186775; DOI=10.1073/pnas.73.11.3872;
RA Gellert M., Mizuuchi K., O'Dea M.H., Nash H.A.;
RT "DNA gyrase: an enzyme that introduces superhelical turns into DNA.";
RL Proc. Natl. Acad. Sci. U.S.A. 73:3872-3876(1976).
RN [12]
RP FUNCTION IN RELAXING SUPERCOILED DNA, AND ACTIVITY REGULATION.
RX PubMed=337300; DOI=10.1073/pnas.74.11.4772;
RA Gellert M., Mizuuchi K., O'Dea M.H., Itoh T., Tomizawa J.I.;
RT "Nalidixic acid resistance: a second genetic character involved in DNA
RT gyrase activity.";
RL Proc. Natl. Acad. Sci. U.S.A. 74:4772-4776(1977).
RN [13]
RP REACTION MECHANISM, AND DNA-BINDING.
RX PubMed=3031051; DOI=10.1016/s0021-9258(18)61193-7;
RA Horowitz D.S., Wang J.C.;
RT "Mapping the active site tyrosine of Escherichia coli DNA gyrase.";
RL J. Biol. Chem. 262:5339-5344(1987).
RN [14]
RP MUTANTS MICROCIN B17 RESISTANT.
RX PubMed=1846808; DOI=10.1002/j.1460-2075.1991.tb07969.x;
RA Vizan J.L., Hernandez-Chico C., del Castillo I., Moreno F.;
RT "The peptide antibiotic microcin B17 induces double-strand cleavage of DNA
RT mediated by E. coli DNA gyrase.";
RL EMBO J. 10:467-476(1991).
RN [15]
RP FUNCTION, MUTAGENESIS OF ARG-136 AND GLY-164, AND ANTIBIOTIC RESISTANCE.
RX PubMed=1323022; DOI=10.1111/j.1365-2958.1992.tb00886.x;
RA Contreras A., Maxwell A.;
RT "gyrB mutations which confer coumarin resistance also affect DNA
RT supercoiling and ATP hydrolysis by Escherichia coli DNA gyrase.";
RL Mol. Microbiol. 6:1617-1624(1992).
RN [16]
RP FUNCTION, ATPASE ACTIVE SITE, AND MUTAGENESIS OF HIS-38 AND GLU-42.
RX PubMed=8248233; DOI=10.1073/pnas.90.23.11232;
RA Jackson A.P., Maxwell A.;
RT "Identifying the catalytic residue of the ATPase reaction of DNA gyrase.";
RL Proc. Natl. Acad. Sci. U.S.A. 90:11232-11236(1993).
RN [17]
RP FUNCTION, AND ACTIVITY REGULATION.
RX PubMed=7811004; DOI=10.1128/aac.38.9.1966;
RA Nakada N., Gmuender H., Hirata T., Arisawa M.;
RT "Mechanism of inhibition of DNA gyrase by cyclothialidine, a novel DNA
RT gyrase inhibitor.";
RL Antimicrob. Agents Chemother. 38:1966-1973(1994).
RN [18]
RP FUNCTION, DOMAIN, AND MUTAGENESIS OF LYS-103 AND LYS-110.
RX PubMed=8621650; DOI=10.1074/jbc.271.16.9723;
RA O'Dea M.H., Tamura J.K., Gellert M.;
RT "Mutations in the B subunit of Escherichia coli DNA gyrase that affect ATP-
RT dependent reactions.";
RL J. Biol. Chem. 271:9723-9729(1996).
RN [19]
RP FUNCTION.
RX PubMed=8962066; DOI=10.1073/pnas.93.25.14416;
RA Kampranis S.C., Maxwell A.;
RT "Conversion of DNA gyrase into a conventional type II topoisomerase.";
RL Proc. Natl. Acad. Sci. U.S.A. 93:14416-14421(1996).
RN [20]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [21]
RP FUNCTION.
RX PubMed=9334322; DOI=10.1101/gad.11.19.2580;
RA Zechiedrich E.L., Khodursky A.B., Cozzarelli N.R.;
RT "Topoisomerase IV, not gyrase, decatenates products of site-specific
RT recombination in Escherichia coli.";
RL Genes Dev. 11:2580-2592(1997).
RN [22]
RP FUNCTION, DOMAIN, AND MUTAGENESIS OF GLN-335 AND LYS-337.
RX PubMed=9657678; DOI=10.1021/bi9801309;
RA Smith C.V., Maxwell A.;
RT "Identification of a residue involved in transition-state stabilization in
RT the ATPase reaction of DNA gyrase.";
RL Biochemistry 37:9658-9667(1998).
RN [23]
RP FUNCTION, CATALYTIC ACTIVITY, AND SUBUNIT.
RX PubMed=12051842; DOI=10.1016/s0022-2836(02)00048-7;
RA Hockings S.C., Maxwell A.;
RT "Identification of four GyrA residues involved in the DNA breakage-reunion
RT reaction of DNA gyrase.";
RL J. Mol. Biol. 318:351-359(2002).
RN [24]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, SUBUNIT, AND MUTAGENESIS OF
RP GLU-424; ASP-498; ASP-500 AND ASP-502.
RX PubMed=12051843; DOI=10.1016/s0022-2836(02)00049-9;
RA Noble C.G., Maxwell A.;
RT "The role of GyrB in the DNA cleavage-religation reaction of DNA gyrase: a
RT proposed two metal-ion mechanism.";
RL J. Mol. Biol. 318:361-371(2002).
RN [25]
RP FUNCTION.
RX PubMed=16332690; DOI=10.1074/jbc.m511160200;
RA Kramlinger V.M., Hiasa H.;
RT "The 'GyrA-box' is required for the ability of DNA gyrase to wrap DNA and
RT catalyze the supercoiling reaction.";
RL J. Biol. Chem. 281:3738-3742(2006).
RN [26]
RP FUNCTION, AND MUTAGENESIS OF ARG-436.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=17400739; DOI=10.1128/jb.00083-07;
RA Champion K., Higgins N.P.;
RT "Growth rate toxicity phenotypes and homeostatic supercoil control
RT differentiate Escherichia coli from Salmonella enterica serovar
RT Typhimurium.";
RL J. Bacteriol. 189:5839-5849(2007).
RN [27]
RP FUNCTION, CATALYTIC ACTIVITY, COFACTOR, AND SUBUNIT.
RX PubMed=18642932; DOI=10.1021/bi800480j;
RA Sissi C., Chemello A., Vazquez E., Mitchenall L.A., Maxwell A., Palumbo M.;
RT "DNA gyrase requires DNA for effective two-site coordination of divalent
RT metal ions: further insight into the mechanism of enzyme action.";
RL Biochemistry 47:8538-8545(2008).
RN [28]
RP FUNCTION, AND ACTIVITY REGULATION.
RX PubMed=19060136; DOI=10.1128/jb.01205-08;
RA Merens A., Matrat S., Aubry A., Lascols C., Jarlier V., Soussy C.J.,
RA Cavallo J.D., Cambau E.;
RT "The pentapeptide repeat proteins MfpAMt and QnrB4 exhibit opposite effects
RT on DNA gyrase catalytic reactions and on the ternary gyrase-DNA-quinolone
RT complex.";
RL J. Bacteriol. 191:1587-1594(2009).
RN [29]
RP FUNCTION, CATALYTIC ACTIVITY, AND SUBUNIT.
RX PubMed=19965760; DOI=10.1126/science.1179123;
RA Edwards M.J., Flatman R.H., Mitchenall L.A., Stevenson C.E., Le T.B.,
RA Clarke T.A., McKay A.R., Fiedler H.P., Buttner M.J., Lawson D.M.,
RA Maxwell A.;
RT "A crystal structure of the bifunctional antibiotic simocyclinone D8, bound
RT to DNA gyrase.";
RL Science 326:1415-1418(2009).
RN [30]
RP FUNCTION, AND DNA-BINDING.
RX PubMed=22457353; DOI=10.1074/jbc.m112.345678;
RA Tretter E.M., Berger J.M.;
RT "Mechanisms for defining supercoiling set point of DNA gyrase orthologs: I.
RT A nonconserved acidic C-terminal tail modulates Escherichia coli gyrase
RT activity.";
RL J. Biol. Chem. 287:18636-18644(2012).
RN [31]
RP FUNCTION, AND DNA-BINDING.
RX PubMed=22457352; DOI=10.1074/jbc.m112.345736;
RA Tretter E.M., Berger J.M.;
RT "Mechanisms for defining supercoiling set point of DNA gyrase orthologs:
RT II. The shape of the GyrA subunit C-terminal domain (CTD) is not a sole
RT determinant for controlling supercoiling efficiency.";
RL J. Biol. Chem. 287:18645-18654(2012).
RN [32]
RP VARIANTS QUINOLONE-RESISTANT ASN-426 AND GLU-447.
RC STRAIN=K16;
RX PubMed=1656869; DOI=10.1128/aac.35.8.1647;
RA Yoshida H., Bogaki M., Nakamura M., Yamanaka L.M., Nakamura S.;
RT "Quinolone resistance-determining region in the DNA gyrase gyrB gene of
RT Escherichia coli.";
RL Antimicrob. Agents Chemother. 35:1647-1650(1991).
RN [33]
RP FUNCTION, AND ACTIVITY REGULATION.
RX PubMed=23294697; DOI=10.1016/j.bmcl.2012.11.073;
RA Trzoss M., Bensen D.C., Li X., Chen Z., Lam T., Zhang J., Creighton C.J.,
RA Cunningham M.L., Kwan B., Stidham M., Nelson K., Brown-Driver V.,
RA Castellano A., Shaw K.J., Lightstone F.C., Wong S.E., Nguyen T.B., Finn J.,
RA Tari L.W.;
RT "Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV
RT (ParE), Part II: development of inhibitors with broad spectrum, Gram-
RT negative antibacterial activity.";
RL Bioorg. Med. Chem. Lett. 23:1537-1543(2013).
RN [34]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1-393 IN COMPLEX WITH ATP ANALOG,
RP AND DOMAIN.
RX PubMed=1646964; DOI=10.1038/351624a0;
RA Wigley D.B., Davies G.J., Dodson E.J., Maxwell A., Dodson G.;
RT "Crystal structure of an N-terminal fragment of the DNA gyrase B protein.";
RL Nature 351:624-629(1991).
RN [35]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 1-220 IN COMPLEX WITH COUMARIN AND
RP CYCLOTHIALIDINE ANTIBIOTICS, AND ACTIVITY REGULATION.
RX PubMed=8635474; DOI=10.1002/j.1460-2075.1996.tb00483.x;
RA Lewis R.J., Singh O.M., Smith C.V., Skarzynski T., Maxwell A.,
RA Wonacott A.J., Wigley D.B.;
RT "The nature of inhibition of DNA gyrase by the coumarins and the
RT cyclothialidines revealed by X-ray crystallography.";
RL EMBO J. 15:1412-1420(1996).
RN [36]
RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 1-220 IN COMPLEX WITH
RP CHLOROBIOCIN.
RX PubMed=9144789;
RX DOI=10.1002/(sici)1097-0134(199705)28:1<41::aid-prot4>3.0.co;2-m;
RA Tsai F.T., Singh O.M., Skarzynski T., Wonacott A.J., Weston S., Tucker A.,
RA Pauptit R.A., Breeze A.L., Poyser J.P., O'Brien R., Ladbury J.E.,
RA Wigley D.B.;
RT "The high-resolution crystal structure of a 24-kDa gyrase B fragment from
RT E. coli complexed with one of the most potent coumarin inhibitors,
RT clorobiocin.";
RL Proteins 28:41-52(1997).
RN [37]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 2-220 OF MUTANT HIS-136 IN COMPLEX
RP WITH NOVOBIOCIN.
RX PubMed=9245398; DOI=10.1021/bi970294+;
RA Holdgate G.A., Tunnicliffe A., Ward W.H., Weston S.A., Rosenbrock G.,
RA Barth P.T., Taylor I.W., Pauptit R.A., Timms D.;
RT "The entropic penalty of ordered water accounts for weaker binding of the
RT antibiotic novobiocin to a resistant mutant of DNA gyrase: a thermodynamic
RT and crystallographic study.";
RL Biochemistry 36:9663-9673(1997).
RN [38]
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 2-392 OF MUTANT SER-5 IN COMPLEX
RP WITH ATP ANALOG, ACTIVE SITE, DOMAIN, MUTAGENESIS OF 1-MET--LYS-14; TYR-5
RP AND ILE-10, AND ATP-BINDING.
RX PubMed=10734094; DOI=10.1074/jbc.275.13.9468;
RA Brino L., Urzhumtsev A., Mousli M., Bronner C., Mitschler A., Oudet P.,
RA Moras D.;
RT "Dimerization of Escherichia coli DNA-gyrase B provides a structural
RT mechanism for activating the ATPase catalytic center.";
RL J. Biol. Chem. 275:9468-9475(2000).
RN [39]
RP X-RAY CRYSTALLOGRAPHY (2.30 ANGSTROMS) OF 15-219 IN COMPLEX WITH
RP CLOROBIOCIN.
RX PubMed=12044152; DOI=10.1021/bi0159837;
RA Lafitte D., Lamour V., Tsvetkov P.O., Makarov A.A., Klich M., Deprez P.,
RA Moras D., Briand C., Gilli R.;
RT "DNA gyrase interaction with coumarin-based inhibitors: the role of the
RT hydroxybenzoate isopentenyl moiety and the 5'-methyl group of the
RT noviose.";
RL Biochemistry 41:7217-7223(2002).
RN [40]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS) OF 15-217 IN COMPLEX WITH
RP PYRAZOLTHIAZOLE INHIBITOR, FUNCTION, AND ACTIVITY REGULATION.
RX PubMed=20356737; DOI=10.1016/j.bmcl.2010.03.052;
RA Ronkin S.M., Badia M., Bellon S., Grillot A.L., Gross C.H., Grossman T.H.,
RA Mani N., Parsons J.D., Stamos D., Trudeau M., Wei Y., Charifson P.S.;
RT "Discovery of pyrazolthiazoles as novel and potent inhibitors of bacterial
RT gyrase.";
RL Bioorg. Med. Chem. Lett. 20:2828-2831(2010).
RN [41]
RP X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) OF 388-804, FUNCTION, CATALYTIC
RP ACTIVITY, AND SUBUNIT.
RX PubMed=20675723; DOI=10.1093/nar/gkq665;
RA Schoeffler A.J., May A.P., Berger J.M.;
RT "A domain insertion in Escherichia coli GyrB adopts a novel fold that plays
RT a critical role in gyrase function.";
RL Nucleic Acids Res. 38:7830-7844(2010).
RN [42]
RP X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 1-220, AND CATALYTIC ACTIVITY.
RX PubMed=22731783; DOI=10.1021/jm300395d;
RA Brvar M., Perdih A., Renko M., Anderluh G., Turk D., Solmajer T.;
RT "Structure-based discovery of substituted 4,5'-bithiazoles as novel DNA
RT gyrase inhibitors.";
RL J. Med. Chem. 55:6413-6426(2012).
RN [43]
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 15-220 IN COMPLEX WITH INHIBITOR,
RP FUNCTION, AND ACTIVITY REGULATION.
RX PubMed=23352267; DOI=10.1016/j.bmcl.2012.11.032;
RA Tari L.W., Trzoss M., Bensen D.C., Li X., Chen Z., Lam T., Zhang J.,
RA Creighton C.J., Cunningham M.L., Kwan B., Stidham M., Shaw K.J.,
RA Lightstone F.C., Wong S.E., Nguyen T.B., Nix J., Finn J.;
RT "Pyrrolopyrimidine inhibitors of DNA gyrase B (GyrB) and topoisomerase IV
RT (ParE). Part I: Structure guided discovery and optimization of dual
RT targeting agents with potent, broad-spectrum enzymatic activity.";
RL Bioorg. Med. Chem. Lett. 23:1529-1536(2013).
RN [44]
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS) OF 15-220 IN COMPLEX WITH INHIBITOR,
RP FUNCTION, AND ACTIVITY REGULATION.
RX PubMed=24386374; DOI=10.1371/journal.pone.0084409;
RA Tari L.W., Li X., Trzoss M., Bensen D.C., Chen Z., Lam T., Zhang J.,
RA Lee S.J., Hough G., Phillipson D., Akers-Rodriguez S., Cunningham M.L.,
RA Kwan B.P., Nelson K.J., Castellano A., Locke J.B., Brown-Driver V.,
RA Murphy T.M., Ong V.S., Pillar C.M., Shinabarger D.L., Nix J.,
RA Lightstone F.C., Wong S.E., Nguyen T.B., Shaw K.J., Finn J.;
RT "Tricyclic GyrB/ParE (TriBE) inhibitors: a new class of broad-spectrum
RT dual-targeting antibacterial agents.";
RL PLoS ONE 8:E84409-E84409(2013).
RN [45]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) OF 2-392 IN OPEN; SEMI-OPEN AND
RP CLOSED STATES IN COMPLEX WITH ADP AND ATP ANALOGS, ATPASE ACTIVITY,
RP PROBABLE MECHANISM, DOMAIN, AND ATP-BINDING.
RX PubMed=25202966; DOI=10.1371/journal.pone.0107289;
RA Stanger F.V., Dehio C., Schirmer T.;
RT "Structure of the N-terminal Gyrase B fragment in complex with ADPPi
RT reveals rigid-body motion induced by ATP hydrolysis.";
RL PLoS ONE 9:E107289-E107289(2014).
RN [46]
RP X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) OF 2-393 IN COMPLEX WITH ATP ANALOG
RP AND MONOVALENT CATIONS, AND ATPASE ACTIVITY.
RX PubMed=25849408; DOI=10.1107/s1399004715002916;
RA Hearnshaw S.J., Chung T.T., Stevenson C.E., Maxwell A., Lawson D.M.;
RT "The role of monovalent cations in the ATPase reaction of DNA gyrase.";
RL Acta Crystallogr. D 71:996-1005(2015).
CC -!- FUNCTION: DNA gyrase negatively supercoils closed circular double-
CC stranded DNA in an ATP-dependent manner to maintain chromosomes in an
CC underwound state (PubMed:186775, PubMed:3031051, PubMed:1323022,
CC PubMed:8248233, PubMed:7811004, PubMed:8621650, PubMed:9657678,
CC PubMed:12051842, PubMed:12051843, PubMed:18642932, PubMed:19060136,
CC PubMed:19965760, PubMed:22457353, PubMed:23294697, PubMed:20356737,
CC PubMed:20675723, PubMed:23352267, PubMed:24386374, PubMed:25202966,
CC PubMed:25849408). This makes better substrates for topoisomerase 4
CC (ParC and ParE) which is the main enzyme that unlinks newly replicated
CC chromosomes in E.coli (PubMed:9334322). Gyrase catalyzes the
CC interconversion of other topological isomers of double-stranded DNA
CC rings, including catenanes (PubMed:22457352). Relaxes negatively
CC supercoiled DNA in an ATP-independent manner (PubMed:337300). E.coli
CC gyrase has higher supercoiling activity than other characterized
CC bacterial gyrases; at comparable concentrations E.coli gyrase
CC introduces more supercoils faster than M.tuberculosis gyrase, while
CC M.tuberculosis gyrase has higher decatenation than supercoiling
CC activity compared to E.coli (PubMed:22457352). E.coli makes 15% more
CC negative supercoils in pBR322 plasmid DNA than S.typhimurium; the
CC S.typhimurium GyrB subunit is toxic in E.coli, while the E.coli copy
CC can be expressed in S.typhimurium even though the 2 subunits have
CC 777/804 residues identical (PubMed:17400739). The enzymatic differences
CC between E.coli gyrase and topoisomerase IV are largely due to the GyrA
CC C-terminal domain (approximately residues 524-841) and specifically the
CC GyrA-box (PubMed:8962066, PubMed:16332690).
CC {ECO:0000269|PubMed:12051842, ECO:0000269|PubMed:12051843,
CC ECO:0000269|PubMed:1323022, ECO:0000269|PubMed:16332690,
CC ECO:0000269|PubMed:17400739, ECO:0000269|PubMed:18642932,
CC ECO:0000269|PubMed:186775, ECO:0000269|PubMed:19060136,
CC ECO:0000269|PubMed:19965760, ECO:0000269|PubMed:20356737,
CC ECO:0000269|PubMed:20675723, ECO:0000269|PubMed:22457352,
CC ECO:0000269|PubMed:22457353, ECO:0000269|PubMed:23294697,
CC ECO:0000269|PubMed:23352267, ECO:0000269|PubMed:24386374,
CC ECO:0000269|PubMed:25202966, ECO:0000269|PubMed:25849408,
CC ECO:0000269|PubMed:3031051, ECO:0000269|PubMed:337300,
CC ECO:0000269|PubMed:7811004, ECO:0000269|PubMed:8248233,
CC ECO:0000269|PubMed:8621650, ECO:0000269|PubMed:8962066,
CC ECO:0000269|PubMed:9148951, ECO:0000269|PubMed:9334322,
CC ECO:0000269|PubMed:9657678}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP-dependent breakage, passage and rejoining of double-
CC stranded DNA.; EC=5.6.2.2; Evidence={ECO:0000255|HAMAP-Rule:MF_01898,
CC ECO:0000269|PubMed:12051842, ECO:0000269|PubMed:12051843,
CC ECO:0000269|PubMed:18642932, ECO:0000269|PubMed:186775,
CC ECO:0000269|PubMed:19965760, ECO:0000269|PubMed:20675723,
CC ECO:0000269|PubMed:22731783};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898,
CC ECO:0000269|PubMed:12051843, ECO:0000269|PubMed:18642932};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898,
CC ECO:0000269|PubMed:12051843, ECO:0000269|PubMed:18642932};
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898,
CC ECO:0000269|PubMed:12051843, ECO:0000269|PubMed:18642932};
CC Note=Binds two Mg(2+) per subunit. The magnesium ions form salt bridges
CC with both the protein and the DNA. Can also accept other divalent metal
CC cations, such as Mn(2+) or Ca(2+) (PubMed:12051843, PubMed:18642932).
CC {ECO:0000255|HAMAP-Rule:MF_01898, ECO:0000269|PubMed:12051843,
CC ECO:0000269|PubMed:18642932};
CC -!- COFACTOR:
CC Name=K(+); Xref=ChEBI:CHEBI:29103;
CC Evidence={ECO:0000269|PubMed:25849408};
CC Note=Binds one K(+) per subunit which interacts with the alpha-
CC phosphate of ATP analog and stimulates ATPase activity of the N-
CC terminal fragment; Na(+) or water bind less well (PubMed:25849408).
CC {ECO:0000269|PubMed:25849408};
CC -!- COFACTOR:
CC Name=Na(+); Xref=ChEBI:CHEBI:29101;
CC Evidence={ECO:0000269|PubMed:25849408};
CC Note=Binds one Na(+) per subunit, with 4 ligands provided by water; may
CC be able to bind K(+), the functional significance of this ion is
CC unclear (PubMed:25849408). {ECO:0000269|PubMed:25849408};
CC -!- ACTIVITY REGULATION: Gyrase is the target of many classes of
CC inhibitors, including coumarins, cyclothialidines, pyrrolopyrimidines,
CC pyrazolthiazoles and (fluoro)quinolones. Coumarins bind to GyrB and are
CC competitive inhibitors of its ATPase activity (PubMed:7811004).
CC Cyclothialidines also bind GyrB and are ATPase competitive inhibitors;
CC they seem to act differently from coumarins (PubMed:7811004,
CC PubMed:8635474). Pyrrolopyrimidines inhibit both GyrB and its paralog
CC in topoisomerase 4 (parE) (PubMed:23294697, PubMed:23352267,
CC PubMed:24386374). Pyrazolthiazoles also inhibit the ATPase activity of
CC GyrB (PubMed:20356737). Quinolones bind GyrA when the enzyme is
CC complexed with DNA and trap the enzyme in a covalent reaction
CC intermediate with DNA (PubMed:3031051, PubMed:12051842, PubMed:337300).
CC Acriflavine inhibits DNA supercoiling and DNA-stimulated ATPase
CC activity (PubMed:9148951). DNA supercoiling activity is protected from
CC fluoroquinolone inhibition by QnrB4; QnrB4 has no effect on
CC supercoiling activity alone (PubMed:19060136).
CC {ECO:0000269|PubMed:19060136, ECO:0000269|PubMed:20356737,
CC ECO:0000269|PubMed:23294697, ECO:0000269|PubMed:23352267,
CC ECO:0000269|PubMed:24386374, ECO:0000269|PubMed:3031051,
CC ECO:0000269|PubMed:337300, ECO:0000269|PubMed:7811004,
CC ECO:0000269|PubMed:8635474, ECO:0000269|PubMed:9148951,
CC ECO:0000305|PubMed:12051842}.
CC -!- SUBUNIT: Heterotetramer, composed of two GyrA and two GyrB chains
CC (PubMed:9148951, PubMed:12051842). In the heterotetramer, GyrA contains
CC the active site tyrosine that forms a transient covalent intermediate
CC with the DNA, while GyrB binds cofactors and catalyzes ATP hydrolysis
CC (PubMed:12051843, PubMed:18642932, PubMed:20675723, PubMed:19965760).
CC {ECO:0000255|HAMAP-Rule:MF_01898, ECO:0000269|PubMed:12051842,
CC ECO:0000269|PubMed:12051843, ECO:0000269|PubMed:18642932,
CC ECO:0000269|PubMed:19965760, ECO:0000269|PubMed:20675723,
CC ECO:0000269|PubMed:9148951}.
CC -!- INTERACTION:
CC P0AES6; P0AES4: gyrA; NbExp=7; IntAct=EBI-541911, EBI-547129;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01898}.
CC -!- DOMAIN: Consists of 3 domains; the ATPase domain (residues 1-220), the
CC transducer domain (221-392) and the toprim domain (393-804)
CC (PubMed:1646964, PubMed:10734094). ATP-binding is cooperative, and both
CC subunits must be wild-type at residue 103 for supercoiling to occur
CC (PubMed:8621650). Non-hydrolyzable ATP analogs (and ATP-binding) induce
CC dimerization and enhance ATPase activity (PubMed:10734094,
CC PubMed:9657678). ATP hydrolysis induces domain shifts that are probably
CC part of the mechanism of DNA cleavage and rejoining (PubMed:25202966).
CC {ECO:0000269|PubMed:10734094, ECO:0000269|PubMed:1646964,
CC ECO:0000269|PubMed:8621650, ECO:0000305|PubMed:25202966,
CC ECO:0000305|PubMed:9657678}.
CC -!- MISCELLANEOUS: When the enzyme transiently cleaves DNA a
CC phosphotyrosine bond is formed between GyrA and DNA in an ATP-
CC independent manner (PubMed:3031051). In the presence of quinolones this
CC intermediate can be trapped and is used as an indicator of drug
CC toxicity (PubMed:12051842). {ECO:0000269|PubMed:3031051,
CC ECO:0000305|PubMed:12051842}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase family.
CC {ECO:0000255|HAMAP-Rule:MF_01898}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; X04341; CAA27871.1; -; Genomic_DNA.
DR EMBL; D87842; BAA20341.1; -; Genomic_DNA.
DR EMBL; L10328; AAA62050.1; -; Genomic_DNA.
DR EMBL; U00096; AAT48201.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77595.1; -; Genomic_DNA.
DR EMBL; M15548; AAA23949.1; -; Genomic_DNA.
DR PIR; D65172; ISECTB.
DR RefSeq; WP_000072067.1; NZ_STEB01000015.1.
DR RefSeq; YP_026241.1; NC_000913.3.
DR PDB; 1AJ6; X-ray; 2.30 A; A=2-220.
DR PDB; 1EI1; X-ray; 2.30 A; A/B=2-392.
DR PDB; 1KZN; X-ray; 2.30 A; A=15-219.
DR PDB; 3G7E; X-ray; 2.20 A; A=15-217.
DR PDB; 3NUH; X-ray; 3.10 A; B=389-804.
DR PDB; 4DUH; X-ray; 1.50 A; A/B=1-220.
DR PDB; 4HYP; X-ray; 2.60 A; A/B/C/D=15-220.
DR PDB; 4KFG; X-ray; 1.60 A; A/B=15-220.
DR PDB; 4PRV; X-ray; 2.00 A; A=2-392.
DR PDB; 4PRX; X-ray; 1.80 A; A=2-392.
DR PDB; 4PU9; X-ray; 2.40 A; A=2-392.
DR PDB; 4WUB; X-ray; 1.75 A; A=2-393.
DR PDB; 4WUC; X-ray; 1.90 A; A=2-393.
DR PDB; 4WUD; X-ray; 1.95 A; A=2-393.
DR PDB; 4XTJ; X-ray; 1.92 A; A=2-392.
DR PDB; 4ZVI; X-ray; 2.20 A; A=16-392.
DR PDB; 5L3J; X-ray; 2.83 A; A=15-392.
DR PDB; 5MMN; X-ray; 1.90 A; A=1-220.
DR PDB; 5MMO; X-ray; 1.81 A; A=1-220.
DR PDB; 5MMP; X-ray; 2.05 A; A=1-220.
DR PDB; 5Z4H; X-ray; 2.00 A; A/B=15-221.
DR PDB; 5Z4O; X-ray; 1.73 A; A/B=15-221.
DR PDB; 5Z9B; X-ray; 2.10 A; A/B=15-221.
DR PDB; 5Z9E; X-ray; 1.80 A; A/B=15-221.
DR PDB; 5Z9F; X-ray; 1.76 A; A/B=15-221.
DR PDB; 5Z9L; X-ray; 1.60 A; A/B=15-221.
DR PDB; 5Z9M; X-ray; 2.74 A; A/B=15-221.
DR PDB; 5Z9N; X-ray; 2.54 A; A=15-221.
DR PDB; 5Z9Q; X-ray; 1.80 A; A/B=15-221.
DR PDB; 6ENG; X-ray; 2.30 A; A/B=1-393.
DR PDB; 6F86; X-ray; 1.90 A; A=15-220.
DR PDB; 6F8J; X-ray; 1.95 A; A=1-220.
DR PDB; 6F94; X-ray; 2.35 A; A=1-220.
DR PDB; 6KZV; X-ray; 2.40 A; A=1-220.
DR PDB; 6KZX; X-ray; 2.10 A; A=1-220.
DR PDB; 6KZZ; X-ray; 2.00 A; A=1-220.
DR PDB; 6L01; X-ray; 2.60 A; A=1-220.
DR PDB; 6RKS; EM; 4.00 A; B/D=1-804.
DR PDB; 6RKU; EM; 4.00 A; B/D=1-804.
DR PDB; 6RKV; EM; 4.60 A; B/D=1-804.
DR PDB; 6RKW; EM; 6.60 A; B/D=1-804.
DR PDB; 6YD9; X-ray; 1.60 A; A=1-220.
DR PDB; 7C7N; X-ray; 2.30 A; A=1-220.
DR PDB; 7C7O; X-ray; 1.80 A; A=1-220.
DR PDB; 7DOR; X-ray; 1.89 A; A/B=16-221.
DR PDB; 7DPR; X-ray; 1.75 A; A/B=16-221.
DR PDB; 7DPS; X-ray; 2.26 A; A/B=16-221.
DR PDB; 7DQF; X-ray; 1.80 A; A/B=16-221.
DR PDB; 7DQH; X-ray; 1.91 A; A/B=16-221.
DR PDB; 7DQI; X-ray; 1.91 A; A/B=16-221.
DR PDB; 7DQJ; X-ray; 1.92 A; A/B=16-221.
DR PDB; 7DQL; X-ray; 1.93 A; A/B=16-221.
DR PDB; 7DQM; X-ray; 1.78 A; A/B=16-221.
DR PDB; 7DQS; X-ray; 1.85 A; A/B=16-221.
DR PDB; 7DQU; X-ray; 1.88 A; A/B=16-221.
DR PDB; 7DQW; X-ray; 1.88 A; A/B=16-221.
DR PDBsum; 1AJ6; -.
DR PDBsum; 1EI1; -.
DR PDBsum; 1KZN; -.
DR PDBsum; 3G7E; -.
DR PDBsum; 3NUH; -.
DR PDBsum; 4DUH; -.
DR PDBsum; 4HYP; -.
DR PDBsum; 4KFG; -.
DR PDBsum; 4PRV; -.
DR PDBsum; 4PRX; -.
DR PDBsum; 4PU9; -.
DR PDBsum; 4WUB; -.
DR PDBsum; 4WUC; -.
DR PDBsum; 4WUD; -.
DR PDBsum; 4XTJ; -.
DR PDBsum; 4ZVI; -.
DR PDBsum; 5L3J; -.
DR PDBsum; 5MMN; -.
DR PDBsum; 5MMO; -.
DR PDBsum; 5MMP; -.
DR PDBsum; 5Z4H; -.
DR PDBsum; 5Z4O; -.
DR PDBsum; 5Z9B; -.
DR PDBsum; 5Z9E; -.
DR PDBsum; 5Z9F; -.
DR PDBsum; 5Z9L; -.
DR PDBsum; 5Z9M; -.
DR PDBsum; 5Z9N; -.
DR PDBsum; 5Z9Q; -.
DR PDBsum; 6ENG; -.
DR PDBsum; 6F86; -.
DR PDBsum; 6F8J; -.
DR PDBsum; 6F94; -.
DR PDBsum; 6KZV; -.
DR PDBsum; 6KZX; -.
DR PDBsum; 6KZZ; -.
DR PDBsum; 6L01; -.
DR PDBsum; 6RKS; -.
DR PDBsum; 6RKU; -.
DR PDBsum; 6RKV; -.
DR PDBsum; 6RKW; -.
DR PDBsum; 6YD9; -.
DR PDBsum; 7C7N; -.
DR PDBsum; 7C7O; -.
DR PDBsum; 7DOR; -.
DR PDBsum; 7DPR; -.
DR PDBsum; 7DPS; -.
DR PDBsum; 7DQF; -.
DR PDBsum; 7DQH; -.
DR PDBsum; 7DQI; -.
DR PDBsum; 7DQJ; -.
DR PDBsum; 7DQL; -.
DR PDBsum; 7DQM; -.
DR PDBsum; 7DQS; -.
DR PDBsum; 7DQU; -.
DR PDBsum; 7DQW; -.
DR AlphaFoldDB; P0AES6; -.
DR BMRB; P0AES6; -.
DR SMR; P0AES6; -.
DR BioGRID; 4259537; 175.
DR ComplexPortal; CPX-2177; GyrA-GyrB DNA Gyrase complex.
DR DIP; DIP-48005N; -.
DR IntAct; P0AES6; 20.
DR STRING; 511145.b3699; -.
DR BindingDB; P0AES6; -.
DR ChEMBL; CHEMBL1826; -.
DR DrugBank; DB03966; Clorobiocin.
DR DrugBank; DB04395; Phosphoaminophosphonic Acid-Adenylate Ester.
DR DrugBank; DB00817; Rosoxacin.
DR DrugBank; DB05488; Technetium Tc-99m ciprofloxacin.
DR DrugCentral; P0AES6; -.
DR jPOST; P0AES6; -.
DR PaxDb; P0AES6; -.
DR PRIDE; P0AES6; -.
DR EnsemblBacteria; AAT48201; AAT48201; b3699.
DR EnsemblBacteria; BAE77595; BAE77595; BAE77595.
DR GeneID; 66672403; -.
DR GeneID; 948211; -.
DR KEGG; ecj:JW5625; -.
DR KEGG; eco:b3699; -.
DR PATRIC; fig|511145.12.peg.3823; -.
DR EchoBASE; EB0419; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_4_1_6; -.
DR InParanoid; P0AES6; -.
DR OMA; LWETTMH; -.
DR PhylomeDB; P0AES6; -.
DR BioCyc; EcoCyc:EG10424-MON; -.
DR BioCyc; MetaCyc:EG10424-MON; -.
DR BRENDA; 5.6.2.2; 2026.
DR EvolutionaryTrace; P0AES6; -.
DR PRO; PR:P0AES6; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005694; C:chromosome; IEA:InterPro.
DR GO; GO:0005737; C:cytoplasm; IDA:EcoliWiki.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0120217; C:DNA gyrase complex; IPI:ComplexPortal.
DR GO; GO:0009330; C:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex; IDA:EcoliWiki.
DR GO; GO:0005524; F:ATP binding; IDA:EcoliWiki.
DR GO; GO:0008094; F:ATP-dependent activity, acting on DNA; IDA:EcoliWiki.
DR GO; GO:0003677; F:DNA binding; IDA:EcoliWiki.
DR GO; GO:0034335; F:DNA negative supercoiling activity; IDA:UniProtKB.
DR GO; GO:0003918; F:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity; IDA:EcoliWiki.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006265; P:DNA topological change; IDA:ComplexPortal.
DR GO; GO:0006261; P:DNA-templated DNA replication; IEA:UniProtKB-UniRule.
DR GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
DR GO; GO:0009410; P:response to xenobiotic stimulus; IDA:EcoliWiki.
DR GO; GO:0006351; P:transcription, DNA-templated; IMP:EcoliWiki.
DR CDD; cd03366; TOPRIM_TopoIIA_GyrB; 1.
DR Gene3D; 3.30.230.10; -; 1.
DR Gene3D; 3.30.565.10; -; 1.
DR Gene3D; 3.40.50.670; -; 2.
DR HAMAP; MF_01898; GyrB; 1.
DR InterPro; IPR002288; DNA_gyrase_B_C.
DR InterPro; IPR011557; GyrB.
DR InterPro; IPR041423; GyrB_insert.
DR InterPro; IPR003594; HATPase_C.
DR InterPro; IPR036890; HATPase_C_sf.
DR InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR InterPro; IPR014721; Ribosomal_S5_D2-typ_fold_subgr.
DR InterPro; IPR001241; Topo_IIA.
DR InterPro; IPR013760; Topo_IIA-like_dom_sf.
DR InterPro; IPR013759; Topo_IIA_B_C.
DR InterPro; IPR013506; Topo_IIA_bsu_dom2.
DR InterPro; IPR018522; TopoIIA_CS.
DR InterPro; IPR006171; TOPRIM_domain.
DR InterPro; IPR034160; TOPRIM_GyrB.
DR Pfam; PF00204; DNA_gyraseB; 1.
DR Pfam; PF00986; DNA_gyraseB_C; 1.
DR Pfam; PF18053; GyrB_insert; 1.
DR Pfam; PF02518; HATPase_c; 1.
DR Pfam; PF01751; Toprim; 1.
DR SMART; SM00387; HATPase_c; 1.
DR SMART; SM00433; TOP2c; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR SUPFAM; SSF55874; SSF55874; 1.
DR SUPFAM; SSF56719; SSF56719; 1.
DR TIGRFAMs; TIGR01059; gyrB; 1.
DR PROSITE; PS00177; TOPOISOMERASE_II; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Antibiotic resistance; ATP-binding; Cytoplasm;
KW Direct protein sequencing; DNA-binding; Isomerase; Magnesium;
KW Metal-binding; Nucleotide-binding; Potassium; Reference proteome; Sodium;
KW Topoisomerase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000305|PubMed:1646964"
FT CHAIN 2..804
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000145309"
FT DOMAIN 418..533
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT REGION 2..220
FT /note="ATPase domain"
FT /evidence="ECO:0000305|PubMed:10734094,
FT ECO:0000305|PubMed:1646964"
FT REGION 221..392
FT /note="Transducer domain"
FT /evidence="ECO:0000305|PubMed:10734094,
FT ECO:0000305|PubMed:1646964"
FT ACT_SITE 42
FT /note="Proton acceptor (ATPase activity)"
FT /evidence="ECO:0000305|PubMed:10734094,
FT ECO:0000305|PubMed:8248233"
FT BINDING 5
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:25202966,
FT ECO:0000269|PubMed:25849408, ECO:0000305|PubMed:10734094"
FT BINDING 46
FT /ligand="ADP"
FT /ligand_id="ChEBI:CHEBI:456216"
FT /evidence="ECO:0000269|PubMed:10734094,
FT ECO:0000269|PubMed:25202966, ECO:0000269|PubMed:25849408"
FT BINDING 73
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:10734094,
FT ECO:0000269|PubMed:25202966, ECO:0000269|PubMed:25849408"
FT BINDING 94
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000269|PubMed:25849408"
FT BINDING 97
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000269|PubMed:25849408"
FT BINDING 100
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000269|PubMed:25849408"
FT BINDING 102..103
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:10734094,
FT ECO:0000269|PubMed:25202966, ECO:0000269|PubMed:25849408"
FT BINDING 103
FT /ligand="Na(+)"
FT /ligand_id="ChEBI:CHEBI:29101"
FT /evidence="ECO:0000269|PubMed:25849408"
FT BINDING 105
FT /ligand="Na(+)"
FT /ligand_id="ChEBI:CHEBI:29101"
FT /evidence="ECO:0000269|PubMed:25849408"
FT BINDING 109
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:10734094,
FT ECO:0000269|PubMed:25202966, ECO:0000269|PubMed:25849408"
FT BINDING 115..120
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:10734094,
FT ECO:0000269|PubMed:25202966, ECO:0000269|PubMed:25849408"
FT BINDING 117
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000269|PubMed:25849408"
FT BINDING 121
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000269|PubMed:25849408"
FT BINDING 335..337
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000269|PubMed:10734094,
FT ECO:0000269|PubMed:25849408"
FT BINDING 424
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898,
FT ECO:0000305|PubMed:12051843, ECO:0000305|PubMed:18642932"
FT BINDING 498
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898,
FT ECO:0000305|PubMed:12051843, ECO:0000305|PubMed:18642932"
FT BINDING 498
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898,
FT ECO:0000305|PubMed:12051843, ECO:0000305|PubMed:18642932"
FT BINDING 500
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898,
FT ECO:0000305|PubMed:12051843, ECO:0000305|PubMed:18642932"
FT SITE 337
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000305|PubMed:9657678"
FT SITE 449
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 452
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT VARIANT 426
FT /note="D -> N (in nal-24, nal-102, nal-103, nal-107, nal-
FT 108, nal-111, nal-114, en-2 and en-5 mutants; resistant to
FT nalidixic acid and to enoxacin)"
FT /evidence="ECO:0000269|PubMed:1656869"
FT VARIANT 447
FT /note="K -> E (in nal-31, nal-109, nal-115 and nal-120
FT mutants; resistant to nalidixic acid)"
FT /evidence="ECO:0000269|PubMed:1656869"
FT VARIANT 751
FT /note="W -> R (in microcin B17 resistant mutant)"
FT /evidence="ECO:0000269|PubMed:1846808"
FT VARIANT 759..760
FT /note="SR -> RC (in acriflavine susceptible mutant acrB,
FT decreased supercoiling activity, ATPase activity no longer
FT stimulated by DNA, decreased DNA-binding, bind GyrA
FT normally)"
FT /evidence="ECO:0000269|PubMed:9148951"
FT MUTAGEN 1..14
FT /note="Missing: No dimerization of residues 15-393,
FT fragment has no ATPase activity."
FT /evidence="ECO:0000269|PubMed:10734094"
FT MUTAGEN 5
FT /note="Y->F,S: 5- to 10-fold reduced dimerization of
FT residues 2-393, fragment has 3- to 5-fold reduced ATPase
FT activity. Fragment dimerizes upon crystallization."
FT /evidence="ECO:0000269|PubMed:10734094"
FT MUTAGEN 10
FT /note="I->G: No dimerization of residues 2-393, fragment
FT has significantly decreased ATPase activity."
FT /evidence="ECO:0000269|PubMed:10734094"
FT MUTAGEN 38
FT /note="H->A: 0.2% supercoiling activity, 7% DNA-dependent
FT ATPase activity, binds ATP normally, complements the N4177
FT ts mutant."
FT /evidence="ECO:0000269|PubMed:8248233"
FT MUTAGEN 42
FT /note="E->A: No supercoiling or DNA-dependent ATPase
FT activity, 25% fluoroquinolone-induced DNA cleavage, 50%
FT ATP-independent DNA relaxation, binds ATP normally, does
FT not complement the N4177 ts mutant."
FT /evidence="ECO:0000269|PubMed:8248233"
FT MUTAGEN 42
FT /note="E->D: 7% supercoiling activity, 16% DNA-dependent
FT ATPase activity, fluoroquinolone-induced DNA cleavage
FT normal, 40% ATP-independent DNA relaxation, binds ATP
FT normally, complements the N4177 ts mutant."
FT /evidence="ECO:0000269|PubMed:8248233"
FT MUTAGEN 42
FT /note="E->Q: No supercoiling or DNA-dependent ATPase
FT activity, binds ATP normally, does not complement the N4177
FT ts mutant."
FT /evidence="ECO:0000269|PubMed:8248233"
FT MUTAGEN 103
FT /note="K->E,I,T: Retains ATP-independent DNA relaxation and
FT quinolone-induced DNA cleavage; loss of supercoiling
FT activity, loss of ATPase, does not bind ATP analogs."
FT /evidence="ECO:0000269|PubMed:8621650"
FT MUTAGEN 110
FT /note="K->E,V: Binds about 50% ATP analog, 2- to 3-fold
FT decreased ATPase, retains ATP-independent DNA relaxation,
FT quinolone-induced DNA cleavage and negative supercoiling
FT activity."
FT /evidence="ECO:0000269|PubMed:8621650"
FT MUTAGEN 136
FT /note="R->C,H,S: Resistance to coumarin antibiotics,
FT decreased ATPase and DNA supercoiling."
FT /evidence="ECO:0000269|PubMed:1323022"
FT MUTAGEN 164
FT /note="G->V: Resistance to coumarin antibiotics, decreased
FT ATPase and DNA supercoiling."
FT /evidence="ECO:0000269|PubMed:1323022"
FT MUTAGEN 335
FT /note="Q->A: Wild-type ATP analog-binding and ATPase
FT activity in N-terminal fragment GyrB43 (residues 2-393), in
FT whole protein wild-type DNA supercoiling and ATP-
FT independent DNA relaxation, 50% ATPase activity which is
FT not stimulated by DNA, complements the N4177 ts mutant."
FT /evidence="ECO:0000269|PubMed:9657678"
FT MUTAGEN 337
FT /note="K->Q: Binds about 60% ATP analog but strongly
FT decreased enzyme turnover for ATPase activity in N-terminal
FT fragment GyrB43 (residues 2-393), in whole protein <1% DNA
FT supercoiling and ATPase activity not stimulated by DNA,
FT wild-type ATP-independent DNA relaxation and quinolone-
FT induced DNA cleavage, does not complement the N4177 ts
FT mutant."
FT /evidence="ECO:0000269|PubMed:9657678"
FT MUTAGEN 424
FT /note="E->A,Q: Strongly reduced DNA supercoiling and
FT relaxation activity. Reduces ATP hydrolysis in response to
FT DNA binding, but has only minor effect on the basal rate of
FT ATP hydrolysis."
FT /evidence="ECO:0000269|PubMed:12051843"
FT MUTAGEN 436
FT /note="R->S: Cannot be made, suggesting it is lethal. This
FT is temperature-sensitive in S.typhimurium, but not lethal."
FT /evidence="ECO:0000269|PubMed:17400739"
FT MUTAGEN 498
FT /note="D->A,N: Strongly reduced DNA supercoiling and
FT relaxation activity. Reduces ATP hydrolysis in response to
FT DNA binding, but has only minor effect on the basal rate of
FT ATP hydrolysis."
FT /evidence="ECO:0000269|PubMed:12051843"
FT MUTAGEN 500
FT /note="D->A: Strongly reduced DNA supercoiling and
FT relaxation activity. Reduces ATP hydrolysis in response to
FT DNA binding, but has only minor effect on the basal rate of
FT ATP hydrolysis."
FT /evidence="ECO:0000269|PubMed:12051843"
FT MUTAGEN 500
FT /note="D->C,H: Alters metal-dependency of ATP-independent
FT DNA relaxation, prefers Mn(2+) and Co(2+) over wild-type
FT Mg(2+)."
FT /evidence="ECO:0000269|PubMed:12051843"
FT MUTAGEN 502
FT /note="D->A: Strongly reduced DNA supercoiling and
FT relaxation activity. Reduces ATP hydrolysis in response to
FT DNA binding, but has only minor effect on the basal rate of
FT ATP hydrolysis."
FT /evidence="ECO:0000269|PubMed:12051843"
FT MUTAGEN 502
FT /note="D->C,H: Alters metal-dependency of ATP-independent
FT DNA relaxation, prefers Mn(2+) and Co(2+) over wild-type
FT Mg(2+)."
FT /evidence="ECO:0000269|PubMed:12051843"
FT CONFLICT 385
FT /note="A -> P (in Ref. 4; AAA62050)"
FT /evidence="ECO:0000305"
FT CONFLICT 436
FT /note="R -> G (in Ref. 3; BAA20341)"
FT /evidence="ECO:0000305"
FT HELIX 7..9
FT /evidence="ECO:0007829|PDB:4WUB"
FT HELIX 16..21
FT /evidence="ECO:0007829|PDB:4DUH"
FT HELIX 24..27
FT /evidence="ECO:0007829|PDB:4DUH"
FT STRAND 30..33
FT /evidence="ECO:0007829|PDB:4DUH"
FT HELIX 34..53
FT /evidence="ECO:0007829|PDB:4DUH"
FT STRAND 54..56
FT /evidence="ECO:0007829|PDB:5Z9L"
FT STRAND 58..63
FT /evidence="ECO:0007829|PDB:4DUH"
FT TURN 65..67
FT /evidence="ECO:0007829|PDB:1AJ6"
FT STRAND 69..73
FT /evidence="ECO:0007829|PDB:4DUH"
FT STRAND 81..83
FT /evidence="ECO:0007829|PDB:4DUH"
FT TURN 84..87
FT /evidence="ECO:0007829|PDB:4DUH"
FT HELIX 90..96
FT /evidence="ECO:0007829|PDB:4DUH"
FT TURN 98..101
FT /evidence="ECO:0007829|PDB:1AJ6"
FT STRAND 104..108
FT /evidence="ECO:0007829|PDB:4WUB"
FT STRAND 114..117
FT /evidence="ECO:0007829|PDB:6ENG"
FT HELIX 120..125
FT /evidence="ECO:0007829|PDB:4DUH"
FT STRAND 127..136
FT /evidence="ECO:0007829|PDB:4DUH"
FT STRAND 139..146
FT /evidence="ECO:0007829|PDB:4DUH"
FT STRAND 149..153
FT /evidence="ECO:0007829|PDB:4DUH"
FT STRAND 155..159
FT /evidence="ECO:0007829|PDB:4DUH"
FT STRAND 164..171
FT /evidence="ECO:0007829|PDB:4DUH"
FT TURN 173..175
FT /evidence="ECO:0007829|PDB:4DUH"
FT HELIX 184..197
FT /evidence="ECO:0007829|PDB:4DUH"
FT TURN 198..200
FT /evidence="ECO:0007829|PDB:4KFG"
FT STRAND 201..207
FT /evidence="ECO:0007829|PDB:4DUH"
FT TURN 208..210
FT /evidence="ECO:0007829|PDB:4DUH"
FT STRAND 213..216
FT /evidence="ECO:0007829|PDB:4DUH"
FT HELIX 221..230
FT /evidence="ECO:0007829|PDB:4WUB"
FT STRAND 231..233
FT /evidence="ECO:0007829|PDB:4PU9"
FT STRAND 235..238
FT /evidence="ECO:0007829|PDB:4WUB"
FT STRAND 241..247
FT /evidence="ECO:0007829|PDB:4WUB"
FT STRAND 250..262
FT /evidence="ECO:0007829|PDB:4WUB"
FT STRAND 265..270
FT /evidence="ECO:0007829|PDB:4WUB"
FT STRAND 273..279
FT /evidence="ECO:0007829|PDB:5L3J"
FT HELIX 280..299
FT /evidence="ECO:0007829|PDB:4WUB"
FT HELIX 302..306
FT /evidence="ECO:0007829|PDB:1EI1"
FT TURN 309..311
FT /evidence="ECO:0007829|PDB:6ENG"
FT HELIX 312..316
FT /evidence="ECO:0007829|PDB:4WUB"
FT STRAND 319..326
FT /evidence="ECO:0007829|PDB:4WUB"
FT STRAND 332..334
FT /evidence="ECO:0007829|PDB:4WUB"
FT HELIX 343..363
FT /evidence="ECO:0007829|PDB:4WUB"
FT HELIX 365..391
FT /evidence="ECO:0007829|PDB:4WUB"
FT STRAND 419..424
FT /evidence="ECO:0007829|PDB:3NUH"
FT HELIX 425..435
FT /evidence="ECO:0007829|PDB:3NUH"
FT TURN 438..440
FT /evidence="ECO:0007829|PDB:3NUH"
FT STRAND 441..446
FT /evidence="ECO:0007829|PDB:3NUH"
FT HELIX 465..474
FT /evidence="ECO:0007829|PDB:3NUH"
FT STRAND 491..495
FT /evidence="ECO:0007829|PDB:3NUH"
FT TURN 501..504
FT /evidence="ECO:0007829|PDB:3NUH"
FT HELIX 505..517
FT /evidence="ECO:0007829|PDB:3NUH"
FT HELIX 519..523
FT /evidence="ECO:0007829|PDB:3NUH"
FT STRAND 527..530
FT /evidence="ECO:0007829|PDB:3NUH"
FT STRAND 534..539
FT /evidence="ECO:0007829|PDB:3NUH"
FT STRAND 542..546
FT /evidence="ECO:0007829|PDB:3NUH"
FT HELIX 549..561
FT /evidence="ECO:0007829|PDB:3NUH"
FT STRAND 564..571
FT /evidence="ECO:0007829|PDB:3NUH"
FT STRAND 573..576
FT /evidence="ECO:0007829|PDB:3NUH"
FT HELIX 577..596
FT /evidence="ECO:0007829|PDB:3NUH"
FT TURN 597..600
FT /evidence="ECO:0007829|PDB:3NUH"
FT HELIX 603..611
FT /evidence="ECO:0007829|PDB:3NUH"
FT HELIX 617..621
FT /evidence="ECO:0007829|PDB:3NUH"
FT HELIX 623..640
FT /evidence="ECO:0007829|PDB:3NUH"
FT STRAND 646..653
FT /evidence="ECO:0007829|PDB:3NUH"
FT STRAND 660..667
FT /evidence="ECO:0007829|PDB:3NUH"
FT STRAND 669..676
FT /evidence="ECO:0007829|PDB:3NUH"
FT HELIX 679..683
FT /evidence="ECO:0007829|PDB:3NUH"
FT HELIX 685..699
FT /evidence="ECO:0007829|PDB:3NUH"
FT TURN 700..703
FT /evidence="ECO:0007829|PDB:3NUH"
FT STRAND 704..711
FT /evidence="ECO:0007829|PDB:3NUH"
FT STRAND 713..718
FT /evidence="ECO:0007829|PDB:3NUH"
FT HELIX 719..730
FT /evidence="ECO:0007829|PDB:3NUH"
FT TURN 731..733
FT /evidence="ECO:0007829|PDB:3NUH"
FT STRAND 735..738
FT /evidence="ECO:0007829|PDB:3NUH"
FT HELIX 742..744
FT /evidence="ECO:0007829|PDB:3NUH"
FT HELIX 747..754
FT /evidence="ECO:0007829|PDB:3NUH"
FT TURN 757..759
FT /evidence="ECO:0007829|PDB:3NUH"
FT STRAND 762..764
FT /evidence="ECO:0007829|PDB:3NUH"
FT HELIX 767..780
FT /evidence="ECO:0007829|PDB:3NUH"
SQ SEQUENCE 804 AA; 89950 MW; D831B95FFB3A7EE3 CRC64;
MSNSYDSSSI KVLKGLDAVR KRPGMYIGDT DDGTGLHHMV FEVVDNAIDE ALAGHCKEII
VTIHADNSVS VQDDGRGIPT GIHPEEGVSA AEVIMTVLHA GGKFDDNSYK VSGGLHGVGV
SVVNALSQKL ELVIQREGKI HRQIYEHGVP QAPLAVTGET EKTGTMVRFW PSLETFTNVT
EFEYEILAKR LRELSFLNSG VSIRLRDKRD GKEDHFHYEG GIKAFVEYLN KNKTPIHPNI
FYFSTEKDGI GVEVALQWND GFQENIYCFT NNIPQRDGGT HLAGFRAAMT RTLNAYMDKE
GYSKKAKVSA TGDDAREGLI AVVSVKVPDP KFSSQTKDKL VSSEVKSAVE QQMNELLAEY
LLENPTDAKI VVGKIIDAAR AREAARRARE MTRRKGALDL AGLPGKLADC QERDPALSEL
YLVEGDSAGG SAKQGRNRKN QAILPLKGKI LNVEKARFDK MLSSQEVATL ITALGCGIGR
DEYNPDKLRY HSIIIMTDAD VDGSHIRTLL LTFFYRQMPE IVERGHVYIA QPPLYKVKKG
KQEQYIKDDE AMDQYQISIA LDGATLHTNA SAPALAGEAL EKLVSEYNAT QKMINRMERR
YPKAMLKELI YQPTLTEADL SDEQTVTRWV NALVSELNDK EQHGSQWKFD VHTNAEQNLF
EPIVRVRTHG VDTDYPLDHE FITGGEYRRI CTLGEKLRGL LEEDAFIERG ERRQPVASFE
QALDWLVKES RRGLSIQRYK GLGEMNPEQL WETTMDPESR RMLRVTVKDA IAADQLFTTL
MGDAVEPRRA FIEENALKAA NIDI
