ID GYRB_ECOLI STANDARD; PRT; 803 AA.
AC P06982; O08438;
DT 01-APR-1988 (Rel. 07, Created)
DT 01-AUG-1991 (Rel. 19, Last sequence update)
DT 25-OCT-2004 (Rel. 45, Last annotation update)
DE DNA gyrase subunit B (EC 5.99.1.3).
GN Name=gyrB; Synonyms=acrB, himB, hisU, nalC, parA, pcbA;
GN OrderedLocusNames=b3699, z5190, ECs4634, SF3765, S4006;
OS Escherichia coli,
OS Escherichia coli O157:H7, and
OS Shigella flexneri.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=562, 83334, 623;
RN [1]
RP NUCLEOTIDE SEQUENCE.
RC SPECIES=E.coli; STRAIN=K12;
RX MEDLINE=87014111; PubMed=3020376;
RA Yamagishi J., Yoshida H., Yamayoshi M., Nakamura S.;
RT "Nalidixic acid-resistant mutations of the gyrB gene of Escherichia
RT coli.";
RL Mol. Gen. Genet. 204:367-373(1986).
RN [2]
RP NUCLEOTIDE SEQUENCE.
RC SPECIES=E.coli; STRAIN=K12;
RX MEDLINE=87146392; PubMed=3029692;
RA Adachi T., Mizuuchi M., Robinson E.A., Appella E., O'Dea M.H.,
RA Gellert M., Mizuuchi K.;
RT "DNA sequence of the E. coli gyrB gene: application of a new
RT sequencing strategy.";
RL Nucleic Acids Res. 15:771-784(1987).
RN [3]
RP NUCLEOTIDE SEQUENCE.
RC SPECIES=E.coli; STRAIN=K12 / N2879;
RX MEDLINE=97294746; 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.
RC SPECIES=E.coli; STRAIN=K12 / MG1655;
RX MEDLINE=93315143; PubMed=7686882;
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
RT genome: organizational symmetry around the origin of replication.";
RL Genomics 16:551-561(1993).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC SPECIES=E.coli; STRAIN=K12 / MG1655;
RX MEDLINE=97426617; 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.,
RA Mau B., Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1474(1997).
RN [6]
RP SEQUENCE REVISION TO 384.
RC SPECIES=E.coli;
RA Arnaud M., Berlyn M.K.B., Blattner F.R., Galperin M.Y., Glasner J.D.,
RA Horiuchi T., Kosuge T., Mori H., Perna N.T., Plunkett G. III,
RA Riley M., Rudd K.E., Serres M.H., Thomas G.H., Wanner B.L.;
RT "Workshop on annotation of Escherichia coli K-12.";
RL Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC SPECIES=E.coli; STRAIN=O157:H7 / EDL933 / ATCC 700927 / EHEC;
RX MEDLINE=21074935; PubMed=11206551; DOI=10.1038/35054089;
RA Perna N.T., Plunkett G. III, Burland V., Mau B., Glasner J.D.,
RA Rose D.J., Mayhew G.F., Evans P.S., Gregor J., Kirkpatrick H.A.,
RA Posfai G., Hackett J., Klink S., Boutin A., Shao Y., Miller L.,
RA Grotbeck E.J., Davis N.W., Lim A., Dimalanta E.T., Potamousis K.,
RA Apodaca J., Anantharaman T.S., Lin J., Yen G., Schwartz D.C.,
RA Welch R.A., Blattner F.R.;
RT "Genome sequence of enterohaemorrhagic Escherichia coli O157:H7.";
RL Nature 409:529-533(2001).
RN [8]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC SPECIES=E.coli; STRAIN=O157:H7 / Sakai / RIMD 0509952 / EHEC;
RX MEDLINE=21156231; PubMed=11258796;
RA Hayashi T., Makino K., Ohnishi M., Kurokawa K., Ishii K., Yokoyama K.,
RA Han C.-G., Ohtsubo E., Nakayama K., Murata T., Tanaka M., Tobe T.,
RA Iida T., Takami H., Honda T., Sasakawa C., Ogasawara N., Yasunaga T.,
RA Kuhara S., Shiba T., Hattori M., Shinagawa H.;
RT "Complete genome sequence of enterohemorrhagic Escherichia coli
RT O157:H7 and genomic comparison with a laboratory strain K-12.";
RL DNA Res. 8:11-22(2001).
RN [9]
RP NUCLEOTIDE SEQUENCE OF 1-105.
RC SPECIES=E.coli; STRAIN=K12;
RX MEDLINE=84297235; PubMed=6089112;
RA Adachi T., Mizuuchi K., Menzel R., Gellert M.;
RT "DNA sequence and transcription of the region upstream of the E. coli
RT gyrB gene.";
RL Nucleic Acids Res. 12:6389-6395(1984).
RN [10]
RP NUCLEOTIDE SEQUENCE OF 1-21.
RC SPECIES=E.coli;
RX MEDLINE=87137287; PubMed=3029031;
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 [11]
RP PROTEIN SEQUENCE OF 92-128.
RC SPECIES=E.coli;
RX PubMed=2174443;
RA Tamura J.K., Gellert M.;
RT "Characterization of the ATP binding site on Escherichia coli DNA
RT gyrase. Affinity labeling of Lys-103 and Lys-110 of the B subunit by
RT pyridoxal 5'-diphospho-5'-adenosine.";
RL J. Biol. Chem. 265:21342-21349(1990).
RN [12]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC SPECIES=S.flexneri; STRAIN=301 / Serotype 2a;
RX MEDLINE=22272406; PubMed=12384590; DOI=10.1093/nar/gkf566;
RA Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H.,
RA Yang J., Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J.,
RA Sun L., Xue Y., Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S.,
RA Cheng H., Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y.,
RA Yu J.;
RT "Genome sequence of Shigella flexneri 2a: insights into pathogenicity
RT through comparison with genomes of Escherichia coli K12 and O157.";
RL Nucleic Acids Res. 30:4432-4441(2002).
RN [13]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC SPECIES=S.flexneri; STRAIN=2457T / ATCC 700930 / Serotype 2a;
RX MEDLINE=22590274; PubMed=12704152;
RX DOI=10.1128/IAI.71.5.2775-2786.2003;
RA Wei J., Goldberg M.B., Burland V., Venkatesan M.M., Deng W.,
RA Fournier G., Mayhew G.F., Plunkett G. III, Rose D.J., Darling A.,
RA Mau B., Perna N.T., Payne S.M., Runyen-Janecky L.J., Zhou S.,
RA Schwartz D.C., Blattner F.R.;
RT "Complete genome sequence and comparative genomics of Shigella
RT flexneri serotype 2a strain 2457T.";
RL Infect. Immun. 71:2775-2786(2003).
RN [14]
RP MUTANTS B17 RESISTANT.
RC SPECIES=E.coli;
RX MEDLINE=91122055; PubMed=1846808;
RA Vizan J.L., Hernandez-Chico C., del Castillo I., Moreno F.;
RT "The peptide antibiotic microcin B17 induces double-strand cleavage of
RT DNA mediated by E. coli DNA gyrase.";
RL EMBO J. 10:467-476(1991).
RN [15]
RP VARIANTS QUINOLONE-RESISTANT.
RC SPECIES=E.coli; STRAIN=K16;
RX MEDLINE=92027669; PubMed=1656869;
RA Yoshida H., Bogaki M., Nakamura M., Yamanaka L.M., Nakamura S.;
RT "Quinolone resistance-determining region in the DNA gyrase gyrB gene
RT of Escherichia coli.";
RL Antimicrob. Agents Chemother. 35:1647-1650(1991).
RN [16]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 1-392.
RC SPECIES=E.coli;
RX MEDLINE=91270367; 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
RT protein.";
RL Nature 351:624-629(1991).
RN [17]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 1-220 OF MUTANT HIS-135.
RC SPECIES=E.coli;
RX MEDLINE=97392632; 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
RT the antibiotic novobiocin to a resistant mutant of DNA gyrase: a
RT thermodynamic and crystallographic study.";
RL Biochemistry 36:9663-9673(1997).
CC -!- FUNCTION: DNA gyrase negatively supercoils closed circular double-
CC stranded DNA in an ATP-dependent manner and also catalyzes the
CC interconversion of other topological isomers of double-stranded
CC DNA rings, including catenanes and knotted rings.
CC -!- CATALYTIC ACTIVITY: ATP-dependent breakage, passage and rejoining
CC of double-stranded DNA.
CC -!- ENZYME REGULATION: Target of two classes of inhibitors, coumarins
CC and quinolones. Coumarins bind to gyrB and are competitive
CC inhibitors with respect to ATP. Quinolones bind DNA gyrase when
CC the enzyme is complexed with DNA and trap the enzyme in an
CC abortive ternary complex.
CC -!- SUBUNIT: Made up of two chains. The A chain is responsible for DNA
CC breakage and rejoining; the B chain catalyzes ATP hydrolysis. The
CC enzyme forms an A2B2 tetramer.
CC -!- SIMILARITY: Belongs to the type II topoisomerase family.
CC --------------------------------------------------------------------------
CC This Swiss-Prot entry is copyright. It is produced through a collaboration
CC between the Swiss Institute of Bioinformatics and the EMBL outstation -
CC the European Bioinformatics Institute. There are no restrictions on its
CC use as long as its content is in no way modified and this statement is not
CC removed.
CC --------------------------------------------------------------------------
DR EMBL; X04341; CAA27871.1; -.
DR EMBL; D87842; BAA20341.1; -.
DR EMBL; L10328; AAA62050.1; -.
DR EMBL; U00096; AAT48201.1; -.
DR EMBL; AE005601; AAG58896.1; -.
DR EMBL; AP002566; BAB38057.1; -.
DR EMBL; M15548; AAA23949.1; -.
DR EMBL; AE015383; AAN45208.1; ALT_INIT.
DR EMBL; AE016991; AAP18989.1; -.
DR PIR; B91208; B91208.
DR PIR; D65172; ISECTB.
DR PDB; 1AJ6; X-ray; @=1-219.
DR PDB; 1EI1; X-ray; A/B=1-391.
DR PDB; 1KZN; X-ray; A=14-218.
DR ECO2DBASE; G094.0; 6TH EDITION.
DR EchoBASE; EB0419; -.
DR EcoGene; EG10424; gyrB.
DR InterPro; IPR003594; ATPbind_ATPase.
DR InterPro; IPR002288; DNA_gyraseB_C.
DR InterPro; IPR000565; DNA_gyrB.
DR InterPro; IPR001241; DNA_topoisoII.
DR InterPro; IPR006171; Toprim_dom.
DR Pfam; PF00204; DNA_gyraseB; 1.
DR Pfam; PF00986; DNA_gyraseB_C; 1.
DR Pfam; PF02518; HATPase_c; 1.
DR Pfam; PF01751; Toprim; 1.
DR PRINTS; PR00418; TPI2FAMILY.
DR ProDom; PD149633; DNA_gyrase_B; 1.
DR SMART; SM00387; HATPase_c; 1.
DR SMART; SM00433; TOP2c; 1.
DR TIGRFAMs; TIGR01059; gyrB; 1.
DR PROSITE; PS00177; TOPOISOMERASE_II; 1.
KW 3D-structure; Antibiotic resistance; ATP-binding; Complete proteome;
KW Direct protein sequencing; Isomerase; Topoisomerase.
FT INIT_MET 0 0
FT VARIANT 425 425 D -> N (in nal-24, nal-102, nal-103, nal-
FT 107, nal-108, nal-111, nal-114, en-2 and
FT en-5 mutants resistant to nalidixic acid
FT and to enoxacin).
FT VARIANT 446 446 K -> E (in nal-31, nal-109, nal-115 and
FT nal-120 mutants, resistant to nalidixic
FT acid).
FT VARIANT 750 750 W -> R (in B17 resistant mutant).
FT VARIANT 758 759 SR -> RC (in acriflavine susceptible
FT mutant).
FT CONFLICT 384 384 A -> P (in Ref. 4).
FT CONFLICT 435 435 R -> G (in Ref. 3).
FT HELIX 6 8
FT STRAND 10 11
FT TURN 14 15
FT HELIX 16 20
FT TURN 22 22
FT HELIX 23 26
FT HELIX 33 51
FT TURN 52 53
FT STRAND 57 62
FT TURN 64 65
FT STRAND 68 72
FT STRAND 81 81
FT TURN 83 85
FT STRAND 88 88
FT HELIX 89 95
FT TURN 97 98
FT STRAND 99 100
FT HELIX 118 124
FT TURN 125 125
FT STRAND 126 135
FT TURN 136 137
FT STRAND 138 145
FT TURN 146 147
FT STRAND 148 149
FT STRAND 154 158
FT STRAND 163 170
FT TURN 172 174
FT HELIX 183 196
FT TURN 198 199
FT STRAND 201 206
FT TURN 207 209
FT STRAND 212 215
FT HELIX 220 230
FT TURN 231 231
FT STRAND 234 234
FT STRAND 240 246
FT TURN 247 248
FT STRAND 249 258
FT STRAND 263 269
FT TURN 270 271
FT STRAND 272 273
FT TURN 275 276
FT STRAND 278 278
FT HELIX 279 298
FT TURN 299 300
FT HELIX 301 305
FT HELIX 311 314
FT TURN 315 317
FT STRAND 318 325
FT STRAND 331 331
FT TURN 334 335
FT STRAND 339 339
FT HELIX 342 362
FT HELIX 364 388
FT TURN 389 390
SQ SEQUENCE 803 AA; 89819 MW; 32D1754FBEC1F2E7 CRC64;
SNSYDSSSIK VLKGLDAVRK RPGMYIGDTD DGTGLHHMVF EVVDNAIDEA LAGHCKEIIV
TIHADNSVSV QDDGRGIPTG IHPEEGVSAA EVIMTVLHAG GKFDDNSYKV SGGLHGVGVS
VVNALSQKLE LVIQREGKIH RQIYEHGVPQ APLAVTGETE KTGTMVRFWP SLETFTNVTE
FEYEILAKRL RELSFLNSGV SIRLRDKRDG KEDHFHYEGG IKAFVEYLNK NKTPIHPNIF
YFSTEKDGIG VEVALQWNDG FQENIYCFTN NIPQRDGGTH LAGFRAAMTR TLNAYMDKEG
YSKKAKVSAT GDDAREGLIA VVSVKVPDPK FSSQTKDKLV SSEVKSAVEQ QMNELLAEYL
LENPTDAKIV VGKIIDAARA REAARRAREM TRRKGALDLA GLPGKLADCQ ERDPALSELY
LVEGDSAGGS AKQGRNRKNQ AILPLKGKIL NVEKARFDKM LSSQEVATLI TALGCGIGRD
EYNPDKLRYH SIIIMTDADV DGSHIRTLLL TFFYRQMPEI VERGHVYIAQ PPLYKVKKGK
QEQYIKDDEA MDQYQISIAL DGATLHTNAS APALAGEALE KLVSEYNATQ KMINRMERRY
PKAMLKELIY QPTLTEADLS DEQTVTRWVN ALVSELNDKE QHGSQWKFDV HTNAEQNLFE
PIVRVRTHGV DTDYPLDHEF ITGGEYRRIC TLGEKLRGLL EEDAFIERGE RRQPVASFEQ
ALDWLVKESR RGLSIQRYKG LGEMNPEQLW ETTMDPESRR MLRVTVKDAI AADQLFTTLM
GDAVEPRRAF IEENALKAAN IDI
//