GYRB_STAAR
ID GYRB_STAAR Reviewed; 644 AA.
AC Q6GKU0;
DT 15-FEB-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 102.
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}; OrderedLocusNames=SAR0005;
OS Staphylococcus aureus (strain MRSA252).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=282458;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MRSA252;
RX PubMed=15213324; DOI=10.1073/pnas.0402521101;
RA Holden M.T.G., Feil E.J., Lindsay J.A., Peacock S.J., Day N.P.J.,
RA Enright M.C., Foster T.J., Moore C.E., Hurst L., Atkin R., Barron A.,
RA Bason N., Bentley S.D., Chillingworth C., Chillingworth T., Churcher C.,
RA Clark L., Corton C., Cronin A., Doggett J., Dowd L., Feltwell T., Hance Z.,
RA Harris B., Hauser H., Holroyd S., Jagels K., James K.D., Lennard N.,
RA Line A., Mayes R., Moule S., Mungall K., Ormond D., Quail M.A.,
RA Rabbinowitsch E., Rutherford K.M., Sanders M., Sharp S., Simmonds M.,
RA Stevens K., Whitehead S., Barrell B.G., Spratt B.G., Parkhill J.;
RT "Complete genomes of two clinical Staphylococcus aureus strains: evidence
RT for the rapid evolution of virulence and drug resistance.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:9786-9791(2004).
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAG39033.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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; BX571856; CAG39033.1; ALT_INIT; Genomic_DNA.
DR RefSeq; WP_000255583.1; NC_002952.2.
DR PDB; 4P8O; X-ray; 2.40 A; A/B=23-231.
DR PDBsum; 4P8O; -.
DR AlphaFoldDB; Q6GKU0; -.
DR SMR; Q6GKU0; -.
DR KEGG; sar:SAR0005; -.
DR HOGENOM; CLU_006146_1_2_9; -.
DR OrthoDB; 205481at2; -.
DR Proteomes; UP000000596; 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 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cytoplasm; DNA-binding; Isomerase; Magnesium;
KW Metal-binding; Nucleotide-binding; Topoisomerase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000250"
FT CHAIN 2..644
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000145340"
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 HELIX 26..30
FT /evidence="ECO:0007829|PDB:4P8O"
FT HELIX 32..36
FT /evidence="ECO:0007829|PDB:4P8O"
FT HELIX 41..60
FT /evidence="ECO:0007829|PDB:4P8O"
FT STRAND 66..72
FT /evidence="ECO:0007829|PDB:4P8O"
FT HELIX 73..75
FT /evidence="ECO:0007829|PDB:4P8O"
FT STRAND 76..81
FT /evidence="ECO:0007829|PDB:4P8O"
FT STRAND 92..97
FT /evidence="ECO:0007829|PDB:4P8O"
FT HELIX 98..103
FT /evidence="ECO:0007829|PDB:4P8O"
FT HELIX 130..133
FT /evidence="ECO:0007829|PDB:4P8O"
FT STRAND 135..144
FT /evidence="ECO:0007829|PDB:4P8O"
FT STRAND 147..154
FT /evidence="ECO:0007829|PDB:4P8O"
FT STRAND 157..160
FT /evidence="ECO:0007829|PDB:4P8O"
FT STRAND 163..167
FT /evidence="ECO:0007829|PDB:4P8O"
FT STRAND 172..179
FT /evidence="ECO:0007829|PDB:4P8O"
FT TURN 181..183
FT /evidence="ECO:0007829|PDB:4P8O"
FT HELIX 192..205
FT /evidence="ECO:0007829|PDB:4P8O"
FT STRAND 210..215
FT /evidence="ECO:0007829|PDB:4P8O"
FT STRAND 221..227
FT /evidence="ECO:0007829|PDB:4P8O"
SQ SEQUENCE 644 AA; 72526 MW; 11F73FD99E9561A6 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 SKIMKEDKDR 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
