GYRB_STAAN
ID GYRB_STAAN Reviewed; 644 AA.
AC P66937; Q99XG6;
DT 11-OCT-2004, 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}; OrderedLocusNames=SA0005;
OS Staphylococcus aureus (strain N315).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=158879;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=N315;
RX PubMed=11418146; DOI=10.1016/s0140-6736(00)04403-2;
RA Kuroda M., Ohta T., Uchiyama I., Baba T., Yuzawa H., Kobayashi I., Cui L.,
RA Oguchi A., Aoki K., Nagai Y., Lian J.-Q., Ito T., Kanamori M.,
RA Matsumaru H., Maruyama A., Murakami H., Hosoyama A., Mizutani-Ui Y.,
RA Takahashi N.K., Sawano T., Inoue R., Kaito C., Sekimizu K., Hirakawa H.,
RA Kuhara S., Goto S., Yabuzaki J., Kanehisa M., Yamashita A., Oshima K.,
RA Furuya K., Yoshino C., Shiba T., Hattori M., Ogasawara N., Hayashi H.,
RA Hiramatsu K.;
RT "Whole genome sequencing of meticillin-resistant Staphylococcus aureus.";
RL Lancet 357:1225-1240(2001).
RN [2]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=N315;
RA Vaezzadeh A.R., Deshusses J., Lescuyer P., Hochstrasser D.F.;
RT "Shotgun proteomic analysis of total and membrane protein extracts of S.
RT aureus strain N315.";
RL Submitted (OCT-2007) to UniProtKB.
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; BA000018; BAB41221.1; -; Genomic_DNA.
DR PIR; E89758; E89758.
DR RefSeq; WP_000255578.1; NC_002745.2.
DR PDB; 2XCO; X-ray; 3.10 A; A=410-644.
DR PDB; 2XCQ; X-ray; 2.98 A; A=410-644.
DR PDB; 2XCR; X-ray; 3.50 A; B/D/S/U=410-644.
DR PDB; 2XCS; X-ray; 2.10 A; B/D=410-543, B/D=580-644.
DR PDB; 2XCT; X-ray; 3.35 A; B/D/S/U=410-543, B/D/S/U=580-644.
DR PDB; 4BUL; X-ray; 2.60 A; A/C=410-543, A/C=580-644.
DR PDB; 5CDM; X-ray; 2.50 A; B/D=416-543, B/D=580-639.
DR PDB; 5CDN; X-ray; 2.79 A; B/D/S/U=417-543, B/D/S/U=580-639.
DR PDB; 5CDO; X-ray; 3.15 A; B/D/S/U=417-543.
DR PDB; 5CDP; X-ray; 2.45 A; B/D=417-543, B/D=580-640.
DR PDB; 5CDQ; X-ray; 2.95 A; B/D/S/U=414-543.
DR PDB; 5CDR; X-ray; 2.65 A; B/D=417-543, B/D=580-640.
DR PDB; 5NPK; X-ray; 1.98 A; B/D/b/d=409-543, B/D/b/d=580-642.
DR PDB; 5NPP; X-ray; 2.22 A; B/D=409-543, B/D=580-642.
DR PDB; 6FM4; X-ray; 2.70 A; B/D=409-543, B/D=580-644.
DR PDB; 6FQS; X-ray; 3.11 A; B/D=409-543, B/D=580-644.
DR PDB; 6FQV; X-ray; 2.60 A; B/D/S/U=409-543, B/D/S/U=580-644.
DR PDBsum; 2XCO; -.
DR PDBsum; 2XCQ; -.
DR PDBsum; 2XCR; -.
DR PDBsum; 2XCS; -.
DR PDBsum; 2XCT; -.
DR PDBsum; 4BUL; -.
DR PDBsum; 5CDM; -.
DR PDBsum; 5CDN; -.
DR PDBsum; 5CDO; -.
DR PDBsum; 5CDP; -.
DR PDBsum; 5CDQ; -.
DR PDBsum; 5CDR; -.
DR PDBsum; 5NPK; -.
DR PDBsum; 5NPP; -.
DR PDBsum; 6FM4; -.
DR PDBsum; 6FQS; -.
DR PDBsum; 6FQV; -.
DR AlphaFoldDB; P66937; -.
DR BMRB; P66937; -.
DR SMR; P66937; -.
DR EnsemblBacteria; BAB41221; BAB41221; BAB41221.
DR KEGG; sau:SA0005; -.
DR HOGENOM; CLU_006146_1_2_9; -.
DR OMA; LWETTMH; -.
DR BRENDA; 5.6.2.2; 3352.
DR EvolutionaryTrace; P66937; -.
DR Proteomes; UP000000751; 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_0000145339"
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 STRAND 415..419
FT /evidence="ECO:0007829|PDB:2XCO"
FT HELIX 426..428
FT /evidence="ECO:0007829|PDB:5NPK"
FT STRAND 430..436
FT /evidence="ECO:0007829|PDB:5NPK"
FT HELIX 437..446
FT /evidence="ECO:0007829|PDB:5NPK"
FT TURN 449..451
FT /evidence="ECO:0007829|PDB:5NPK"
FT STRAND 452..457
FT /evidence="ECO:0007829|PDB:5NPK"
FT TURN 459..461
FT /evidence="ECO:0007829|PDB:2XCQ"
FT TURN 464..466
FT /evidence="ECO:0007829|PDB:5NPK"
FT HELIX 469..473
FT /evidence="ECO:0007829|PDB:5NPK"
FT HELIX 476..485
FT /evidence="ECO:0007829|PDB:5NPK"
FT HELIX 490..492
FT /evidence="ECO:0007829|PDB:5NPK"
FT HELIX 495..497
FT /evidence="ECO:0007829|PDB:5NPK"
FT STRAND 501..506
FT /evidence="ECO:0007829|PDB:5NPK"
FT HELIX 511..527
FT /evidence="ECO:0007829|PDB:5NPK"
FT HELIX 529..533
FT /evidence="ECO:0007829|PDB:5NPK"
FT STRAND 537..539
FT /evidence="ECO:0007829|PDB:5NPK"
FT STRAND 545..547
FT /evidence="ECO:0007829|PDB:2XCQ"
FT STRAND 549..551
FT /evidence="ECO:0007829|PDB:2XCQ"
FT STRAND 554..556
FT /evidence="ECO:0007829|PDB:2XCQ"
FT HELIX 559..566
FT /evidence="ECO:0007829|PDB:2XCQ"
FT STRAND 577..579
FT /evidence="ECO:0007829|PDB:2XCQ"
FT HELIX 583..585
FT /evidence="ECO:0007829|PDB:5NPK"
FT HELIX 588..595
FT /evidence="ECO:0007829|PDB:5NPK"
FT TURN 598..600
FT /evidence="ECO:0007829|PDB:5NPK"
FT STRAND 604..607
FT /evidence="ECO:0007829|PDB:5NPK"
FT HELIX 611..622
FT /evidence="ECO:0007829|PDB:5NPK"
FT HELIX 626..636
FT /evidence="ECO:0007829|PDB:5NPK"
FT HELIX 637..639
FT /evidence="ECO:0007829|PDB:5NPK"
SQ SEQUENCE 644 AA; 72540 MW; D4E02886B97DFBC5 CRC64;
MVTALSDVNN TDNYGAGQIQ VLEGLEAVRK RPGMYIGSTS ERGLHHLVWE IVDNSIDEAL
AGYANKIEVV 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
