GYRB_BACAN
ID GYRB_BACAN Reviewed; 640 AA.
AC Q9X3Y6; Q6I534; Q6KYS7; Q81W31;
DT 24-OCT-2001, integrated into UniProtKB/Swiss-Prot.
DT 21-JUN-2004, sequence version 2.
DT 03-AUG-2022, entry version 150.
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};
GN Name=gyrB {ECO:0000255|HAMAP-Rule:MF_01898};
GN OrderedLocusNames=BA_0005, GBAA_0005, BAS0005;
OS Bacillus anthracis.
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus;
OC Bacillus cereus group.
OX NCBI_TaxID=1392;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Ames / isolate Porton;
RX PubMed=12721629; DOI=10.1038/nature01586;
RA Read T.D., Peterson S.N., Tourasse N.J., Baillie L.W., Paulsen I.T.,
RA Nelson K.E., Tettelin H., Fouts D.E., Eisen J.A., Gill S.R.,
RA Holtzapple E.K., Okstad O.A., Helgason E., Rilstone J., Wu M.,
RA Kolonay J.F., Beanan M.J., Dodson R.J., Brinkac L.M., Gwinn M.L.,
RA DeBoy R.T., Madpu R., Daugherty S.C., Durkin A.S., Haft D.H., Nelson W.C.,
RA Peterson J.D., Pop M., Khouri H.M., Radune D., Benton J.L., Mahamoud Y.,
RA Jiang L., Hance I.R., Weidman J.F., Berry K.J., Plaut R.D., Wolf A.M.,
RA Watkins K.L., Nierman W.C., Hazen A., Cline R.T., Redmond C., Thwaite J.E.,
RA White O., Salzberg S.L., Thomason B., Friedlander A.M., Koehler T.M.,
RA Hanna P.C., Kolstoe A.-B., Fraser C.M.;
RT "The genome sequence of Bacillus anthracis Ames and comparison to closely
RT related bacteria.";
RL Nature 423:81-86(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Ames ancestor;
RX PubMed=18952800; DOI=10.1128/jb.01347-08;
RA Ravel J., Jiang L., Stanley S.T., Wilson M.R., Decker R.S., Read T.D.,
RA Worsham P., Keim P.S., Salzberg S.L., Fraser-Liggett C.M., Rasko D.A.;
RT "The complete genome sequence of Bacillus anthracis Ames 'Ancestor'.";
RL J. Bacteriol. 191:445-446(2009).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Sterne;
RA Brettin T.S., Bruce D., Challacombe J.F., Gilna P., Han C., Hill K.,
RA Hitchcock P., Jackson P., Keim P., Longmire J., Lucas S., Okinaka R.,
RA Richardson P., Rubin E., Tice H.;
RT "Complete genome sequence of Bacillus anthracis Sterne.";
RL Submitted (JAN-2004) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 104-507.
RC STRAIN=Pasteur #2H;
RX PubMed=10103241; DOI=10.1128/aem.65.4.1483-1490.1999;
RA Yamada S., Ohashi E., Agata N., Venkateswaran K.;
RT "Cloning and nucleotide sequence analysis of gyrB of Bacillus cereus, B.
RT thuringiensis, B. mycoides, and B. anthracis and their application to the
RT detection of B. cereus in rice.";
RL Appl. Environ. Microbiol. 65:1483-1490(1999).
CC -!- FUNCTION: A type II topoisomerase that negatively supercoils closed
CC circular double-stranded (ds) DNA in an ATP-dependent manner to
CC modulate DNA topology and maintain chromosomes in an underwound state.
CC Negative supercoiling favors strand separation, and DNA replication,
CC transcription, recombination and repair, all of which involve strand
CC separation. Also able to catalyze the interconversion of other
CC topological isomers of dsDNA rings, including catenanes and knotted
CC rings. Type II topoisomerases break and join 2 DNA strands
CC simultaneously in an ATP-dependent manner. {ECO:0000255|HAMAP-
CC Rule:MF_01898}.
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-
CC Rule:MF_01898};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898};
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898};
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+). {ECO:0000255|HAMAP-Rule:MF_01898};
CC -!- SUBUNIT: Heterotetramer, composed of two GyrA and two GyrB chains. In
CC the heterotetramer, GyrA contains the active site tyrosine that forms a
CC transient covalent intermediate with DNA, while GyrB binds cofactors
CC and catalyzes ATP hydrolysis. {ECO:0000255|HAMAP-Rule:MF_01898}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01898}.
CC -!- MISCELLANEOUS: Few gyrases are as efficient as E.coli at forming
CC negative supercoils. Not all organisms have 2 type II topoisomerases;
CC in organisms with a single type II topoisomerase this enzyme also has
CC to decatenate newly replicated chromosomes. {ECO:0000255|HAMAP-
CC Rule:MF_01898}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase GyrB family.
CC {ECO:0000255|HAMAP-Rule:MF_01898}.
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DR EMBL; AE016879; AAP24063.1; -; Genomic_DNA.
DR EMBL; AE017334; AAT29083.1; -; Genomic_DNA.
DR EMBL; AE017225; AAT52347.1; -; Genomic_DNA.
DR EMBL; AF090333; AAD25958.1; -; Genomic_DNA.
DR RefSeq; NP_842577.1; NC_003997.3.
DR RefSeq; WP_000435993.1; NZ_WXXJ01000028.1.
DR RefSeq; YP_026296.1; NC_005945.1.
DR AlphaFoldDB; Q9X3Y6; -.
DR SMR; Q9X3Y6; -.
DR STRING; 261594.GBAA_0005; -.
DR DNASU; 1083919; -.
DR EnsemblBacteria; AAP24063; AAP24063; BA_0005.
DR EnsemblBacteria; AAT29083; AAT29083; GBAA_0005.
DR GeneID; 45020039; -.
DR KEGG; ban:BA_0005; -.
DR KEGG; bar:GBAA_0005; -.
DR KEGG; bat:BAS0005; -.
DR PATRIC; fig|198094.11.peg.5; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_1_2_9; -.
DR OMA; LWETTMH; -.
DR Proteomes; UP000000427; Chromosome.
DR Proteomes; UP000000594; Chromosome.
DR GO; GO:0005694; C:chromosome; IEA:InterPro.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003918; F:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006265; P:DNA topological change; IEA:UniProtKB-UniRule.
DR GO; GO:0006261; P:DNA-templated DNA replication; IEA:UniProtKB-UniRule.
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; -; 1.
DR HAMAP; MF_01898; GyrB; 1.
DR InterPro; IPR002288; DNA_gyrase_B_C.
DR InterPro; IPR011557; GyrB.
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; 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 3: Inferred from homology;
KW ATP-binding; Cytoplasm; DNA-binding; Isomerase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Topoisomerase.
FT CHAIN 1..640
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000145290"
FT DOMAIN 424..538
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 430
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 BINDING 503
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 BINDING 503
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 505
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 455
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 458
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT CONFLICT 110
FT /note="G -> D (in Ref. 4; AAD25958)"
FT /evidence="ECO:0000305"
FT CONFLICT 224
FT /note="Y -> C (in Ref. 4; AAD25958)"
FT /evidence="ECO:0000305"
FT CONFLICT 335
FT /note="N -> D (in Ref. 4; AAD25958)"
FT /evidence="ECO:0000305"
FT CONFLICT 412
FT /note="K -> R (in Ref. 4; AAD25958)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 640 AA; 71896 MW; 3F745302E2CD4FDE CRC64;
MEQKQMQENS YDESQIQVLE GLEAVRKRPG MYIGSTSGKG LHHLVWEIVD NSIDEALAGY
CDEINVSIEE DNSIRVTDNG RGIPVGIQEK MGRPAVEVIM TVLHAGGKFG GGGYKVSGGL
HGVGASVVNA LSTELEVFVH REGKIHYQKY ERGIPVADLK VIGDTDQTGT ITRFKPDPEI
FQETTVYEFD TLATRMRELA FLNRNIKLTI EDKREHKQKK EFHYEGGIKS YVEHLNRSKQ
PIHEEPVYVE GSKDGIQVEV SLQYNEGYTN NIYSFTNNIH TYEGGTHEVG FKTALTRVIN
DYGRKNSILK DADSNLTGED VREGLTAIVS IKHPNPQFEG QTKTKLGNSE ARTITESVFS
EAFEKFLLEN PNVARKIVEK GTMAARARVA AKKARELTRR KSALEVSSLP GKLADCSSKD
PAISEIYIVE GDSAGGSAKQ GRDRHFQAIL PLKGKIINVE KARLDKILSN DEVRTIITAI
GTNIGGDFDI EKARYHKVII MTDADVDGAH IRTLLLTFFY RYMRQIIEHG YIYIAQPPLF
KVQQGKKIQY AYNEKELEKI LAELPAQPKP GIQRYKGLGE MNPTQLWETT MDPEVRSLLQ
VSLQDAIEAD ETFEILMGDK VEPRRNFIQE NAKYVKNLDI
