GYRB_STAAU
ID GYRB_STAAU Reviewed; 644 AA.
AC P0A0K8; P20832;
DT 15-FEB-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 116.
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};
OS Staphylococcus aureus.
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=1280;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND PROTEIN SEQUENCE OF 2-27 AND
RP 314-335.
RC STRAIN=601055;
RX PubMed=8388872; DOI=10.1128/jb.175.11.3269-3277.1993;
RA Brockbank S.M.V., Barth P.T.;
RT "Cloning, sequencing, and expression of the DNA gyrase genes from
RT Staphylococcus aureus.";
RL J. Bacteriol. 175:3269-3277(1993).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 12600 / DSM 20231 / IAM 12544 / NCDO 949 / NCTC 8532;
RX PubMed=7811012; DOI=10.1128/aac.38.9.2014;
RA Ito H., Yoshida H., Bogaki-Shonai M., Niga T., Hattori H., Nakamura S.;
RT "Quinolone resistance mutations in the DNA gyrase gyrA and gyrB genes of
RT Staphylococcus aureus.";
RL Antimicrob. Agents Chemother. 38:2014-2023(1994).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=1311298; DOI=10.1128/jb.174.5.1596-1603.1992;
RA Margerrison E.E.C., Hopewell R., Fisher L.M.;
RT "Nucleotide sequence of the Staphylococcus aureus gyrB-gyrA locus encoding
RT the DNA gyrase A and B proteins.";
RL J. Bacteriol. 174:1596-1603(1992).
RN [4]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-30.
RC STRAIN=YB886;
RX PubMed=7898435; DOI=10.1007/bf00290713;
RA Alonso J.C., Fisher L.M.;
RT "Nucleotide sequence of the recF gene cluster from Staphylococcus aureus
RT and complementation analysis in Bacillus subtilis recF mutants.";
RL Mol. Gen. Genet. 246:680-686(1995).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 593-644.
RX PubMed=2160946; DOI=10.1128/jb.172.6.3481-3484.1990;
RA Hopewell R., Oram M., Briesewitz R., Fisher L.M.;
RT "DNA cloning and organization of the Staphylococcus aureus gyrA and gyrB
RT genes: close homology among gyrase proteins and implications for 4-
RT quinolone action and resistance.";
RL J. Bacteriol. 172:3481-3484(1990).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 24-230 IN COMPLEX WITH
RP PYRAZOLTHIAZOLE INHIBITOR, 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).
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 -!- ACTIVITY REGULATION: Pyrazolthiazoles inhibit the ATPase activity of
CC GyrB (PubMed:20356737). {ECO:0000269|PubMed:20356737}.
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; X71437; CAA50570.1; -; Genomic_DNA.
DR EMBL; D10489; BAA01369.1; -; Genomic_DNA.
DR EMBL; M86227; AAA73951.1; -; Genomic_DNA.
DR EMBL; M37915; AAA26635.1; -; Genomic_DNA.
DR PIR; A40585; A40585.
DR RefSeq; WP_000255586.1; NZ_WTUM01000002.1.
DR PDB; 3G75; X-ray; 2.30 A; A/B=24-230.
DR PDB; 3G7B; X-ray; 2.30 A; A/B=24-230.
DR PDB; 3TTZ; X-ray; 1.63 A; A/B=14-233.
DR PDB; 3U2D; X-ray; 1.85 A; A/B=14-233.
DR PDB; 3U2K; X-ray; 1.64 A; A/B=14-233.
DR PDB; 4PLB; X-ray; 2.69 A; B/D=410-543, B/D=580-644.
DR PDB; 4URM; X-ray; 2.94 A; A/B/C/D=1-231.
DR PDB; 4URO; X-ray; 2.59 A; A/B/C/D=1-231.
DR PDB; 5BS3; X-ray; 2.65 A; B/D=410-543, B/D=580-644.
DR PDB; 5CPH; X-ray; 1.20 A; A/B=2-234.
DR PDB; 5CTU; X-ray; 1.45 A; A/B=2-234.
DR PDB; 5CTW; X-ray; 1.48 A; A/B=2-234.
DR PDB; 5CTX; X-ray; 1.60 A; A/B=2-234.
DR PDB; 5CTY; X-ray; 1.60 A; A/B=2-234.
DR PDB; 5D6P; X-ray; 2.05 A; A/B=2-234.
DR PDB; 5D6Q; X-ray; 1.50 A; A/B=2-234.
DR PDB; 5D7C; X-ray; 1.55 A; A/B=2-234.
DR PDB; 5D7D; X-ray; 1.60 A; A/B=2-234.
DR PDB; 5D7R; X-ray; 1.55 A; A/B=2-234.
DR PDB; 5IWI; X-ray; 1.98 A; B/D=410-543, B/D=580-644.
DR PDB; 5IWM; X-ray; 2.50 A; B/D=410-543, B/D=580-644.
DR PDB; 5Z9P; X-ray; 1.45 A; A/B=14-233.
DR PDB; 6QTK; X-ray; 2.31 A; B/D=409-644.
DR PDB; 6QTP; X-ray; 2.37 A; B/D=409-543, B/D=580-644.
DR PDB; 6QX1; X-ray; 2.65 A; B/D=409-543.
DR PDB; 6QX2; X-ray; 3.40 A; B/S/b/s=416-638.
DR PDB; 6TCK; X-ray; 1.60 A; A/B=2-234.
DR PDB; 6TTG; X-ray; 1.70 A; A/B=2-234.
DR PDB; 6Z1A; X-ray; 2.30 A; B/D=409-644.
DR PDB; 7MVS; X-ray; 2.60 A; A/B=410-543, A/B=580-644.
DR PDBsum; 3G75; -.
DR PDBsum; 3G7B; -.
DR PDBsum; 3TTZ; -.
DR PDBsum; 3U2D; -.
DR PDBsum; 3U2K; -.
DR PDBsum; 4PLB; -.
DR PDBsum; 4URM; -.
DR PDBsum; 4URO; -.
DR PDBsum; 5BS3; -.
DR PDBsum; 5CPH; -.
DR PDBsum; 5CTU; -.
DR PDBsum; 5CTW; -.
DR PDBsum; 5CTX; -.
DR PDBsum; 5CTY; -.
DR PDBsum; 5D6P; -.
DR PDBsum; 5D6Q; -.
DR PDBsum; 5D7C; -.
DR PDBsum; 5D7D; -.
DR PDBsum; 5D7R; -.
DR PDBsum; 5IWI; -.
DR PDBsum; 5IWM; -.
DR PDBsum; 5Z9P; -.
DR PDBsum; 6QTK; -.
DR PDBsum; 6QTP; -.
DR PDBsum; 6QX1; -.
DR PDBsum; 6QX2; -.
DR PDBsum; 6TCK; -.
DR PDBsum; 6TTG; -.
DR PDBsum; 6Z1A; -.
DR PDBsum; 7MVS; -.
DR AlphaFoldDB; P0A0K8; -.
DR BMRB; P0A0K8; -.
DR SMR; P0A0K8; -.
DR BindingDB; P0A0K8; -.
DR ChEMBL; CHEMBL1921666; -.
DR DrugBank; DB01051; Novobiocin.
DR DrugCentral; P0A0K8; -.
DR OMA; LWETTMH; -.
DR BRENDA; 5.6.2.2; 3352.
DR EvolutionaryTrace; P0A0K8; -.
DR PRO; PR:P0A0K8; -.
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 GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
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 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; Topoisomerase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:8388872"
FT CHAIN 2..644
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000145342"
FT DOMAIN 429..543
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 435
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 508
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 508
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 510
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 460
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 463
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT CONFLICT 40..49
FT /note="SERGLHHLVW -> QRELHISV (in Ref. 3; AAA73951)"
FT /evidence="ECO:0000305"
FT CONFLICT 66
FT /note="Q -> K (in Ref. 3; AAA73951)"
FT /evidence="ECO:0000305"
FT CONFLICT 312..321
FT /note="KIMKEEKDRL -> RYEEEKIA (in Ref. 3; AAA73951)"
FT /evidence="ECO:0000305"
FT CONFLICT 424
FT /note="K -> Q (in Ref. 3; AAA73951)"
FT /evidence="ECO:0000305"
FT CONFLICT 522
FT /note="T -> I (in Ref. 3; AAA73951)"
FT /evidence="ECO:0000305"
FT CONFLICT 579
FT /note="R -> L (in Ref. 3; AAA73951)"
FT /evidence="ECO:0000305"
FT TURN 2..4
FT /evidence="ECO:0007829|PDB:5CTU"
FT HELIX 17..30
FT /evidence="ECO:0007829|PDB:5CPH"
FT HELIX 32..36
FT /evidence="ECO:0007829|PDB:5CPH"
FT HELIX 41..60
FT /evidence="ECO:0007829|PDB:5CPH"
FT STRAND 66..72
FT /evidence="ECO:0007829|PDB:5CPH"
FT HELIX 73..75
FT /evidence="ECO:0007829|PDB:5CPH"
FT STRAND 76..81
FT /evidence="ECO:0007829|PDB:5CPH"
FT STRAND 89..91
FT /evidence="ECO:0007829|PDB:5D7D"
FT TURN 92..94
FT /evidence="ECO:0007829|PDB:5CPH"
FT STRAND 95..97
FT /evidence="ECO:0007829|PDB:5CPH"
FT HELIX 98..104
FT /evidence="ECO:0007829|PDB:5CPH"
FT HELIX 130..133
FT /evidence="ECO:0007829|PDB:5CPH"
FT STRAND 135..144
FT /evidence="ECO:0007829|PDB:5CPH"
FT STRAND 147..154
FT /evidence="ECO:0007829|PDB:5CPH"
FT STRAND 157..160
FT /evidence="ECO:0007829|PDB:5CPH"
FT STRAND 163..167
FT /evidence="ECO:0007829|PDB:5CPH"
FT STRAND 172..179
FT /evidence="ECO:0007829|PDB:5CPH"
FT TURN 181..183
FT /evidence="ECO:0007829|PDB:5CPH"
FT HELIX 192..205
FT /evidence="ECO:0007829|PDB:5CPH"
FT TURN 206..208
FT /evidence="ECO:0007829|PDB:3G7B"
FT STRAND 210..215
FT /evidence="ECO:0007829|PDB:5CPH"
FT STRAND 223..227
FT /evidence="ECO:0007829|PDB:5CPH"
FT HELIX 426..428
FT /evidence="ECO:0007829|PDB:6Z1A"
FT STRAND 430..435
FT /evidence="ECO:0007829|PDB:6Z1A"
FT HELIX 437..446
FT /evidence="ECO:0007829|PDB:6Z1A"
FT TURN 449..451
FT /evidence="ECO:0007829|PDB:6Z1A"
FT STRAND 452..457
FT /evidence="ECO:0007829|PDB:6Z1A"
FT TURN 464..466
FT /evidence="ECO:0007829|PDB:6Z1A"
FT HELIX 469..473
FT /evidence="ECO:0007829|PDB:6Z1A"
FT HELIX 476..485
FT /evidence="ECO:0007829|PDB:6Z1A"
FT HELIX 490..492
FT /evidence="ECO:0007829|PDB:6Z1A"
FT HELIX 495..497
FT /evidence="ECO:0007829|PDB:6Z1A"
FT STRAND 501..506
FT /evidence="ECO:0007829|PDB:6Z1A"
FT HELIX 511..527
FT /evidence="ECO:0007829|PDB:6Z1A"
FT HELIX 529..533
FT /evidence="ECO:0007829|PDB:6Z1A"
FT STRAND 537..539
FT /evidence="ECO:0007829|PDB:6Z1A"
FT STRAND 578..582
FT /evidence="ECO:0007829|PDB:6Z1A"
FT HELIX 583..585
FT /evidence="ECO:0007829|PDB:6Z1A"
FT HELIX 588..595
FT /evidence="ECO:0007829|PDB:6Z1A"
FT TURN 598..600
FT /evidence="ECO:0007829|PDB:6Z1A"
FT STRAND 604..607
FT /evidence="ECO:0007829|PDB:6Z1A"
FT HELIX 611..622
FT /evidence="ECO:0007829|PDB:6Z1A"
FT HELIX 626..636
FT /evidence="ECO:0007829|PDB:6Z1A"
SQ SEQUENCE 644 AA; 72540 MW; CED22E8C446A1138 CRC64;
MVTALSDVNN TDNYGAGQIQ VLEGLEAVRK RPGMYIGSTS ERGLHHLVWE IVDNSIDEAL
AGYANQIEVV IEKDNWIKVT DNGRGIPVDI QEKMGRPAVE VILTVLHAGG KFGGGGYKVS
GGLHGVGSSV VNALSQDLEV YVHRNETIYH QAYKKGVPQF DLKEVGTTDK TGTVIRFKAD
GEIFTETTVY NYETLQQRIR ELAFLNKGIQ ITLRDERDEE NVREDSYHYE GGIKSYVELL
NENKEPIHDE PIYIHQSKDD IEVEIAIQYN SGYATNLLTY ANNIHTYEGG THEDGFKRAL
TRVLNSYGLS SKIMKEEKDR LSGEDTREGM TAIISIKHGD PQFEGQTKTK LGNSEVRQVV
DKLFSEHFER FLYENPQVAR TVVEKGIMAA RARVAAKKAR EVTRRKSALD VASLPGKLAD
CSSKSPEECE IFLVEGDSAG GSTKSGRDSR TQAILPLRGK ILNVEKARLD RILNNNEIRQ
MITAFGTGIG GDFDLAKARY HKIVIMTDAD VDGAHIRTLL LTFFYRFMRP LIEAGYVYIA
QPPLYKLTQG KQKYYVYNDR ELDKLKSELN PTPKWSIARY KGLGEMNADQ LWETTMNPEH
RALLQVKLED AIEADQTFEM LMGDVVENRR QFIEDNAVYA NLDF
