ID   GYRB_HELPY              Reviewed;         773 AA.
AC   P55992;
DT   01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1997, sequence version 1.
DT   27-MAR-2024, entry version 138.
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=HP_0501;
OS   Helicobacter pylori (strain ATCC 700392 / 26695) (Campylobacter pylori).
OC   Bacteria; Campylobacterota; Epsilonproteobacteria; Campylobacterales;
OC   Helicobacteraceae; Helicobacter.
OX   NCBI_TaxID=85962;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 700392 / 26695;
RX   PubMed=9252185; DOI=10.1038/41483;
RA   Tomb J.-F., White O., Kerlavage A.R., Clayton R.A., Sutton G.G.,
RA   Fleischmann R.D., Ketchum K.A., Klenk H.-P., Gill S.R., Dougherty B.A.,
RA   Nelson K.E., Quackenbush J., Zhou L., Kirkness E.F., Peterson S.N.,
RA   Loftus B.J., Richardson D.L., Dodson R.J., Khalak H.G., Glodek A.,
RA   McKenney K., FitzGerald L.M., Lee N., Adams M.D., Hickey E.K., Berg D.E.,
RA   Gocayne J.D., Utterback T.R., Peterson J.D., Kelley J.M., Cotton M.D.,
RA   Weidman J.F., Fujii C., Bowman C., Watthey L., Wallin E., Hayes W.S.,
RA   Borodovsky M., Karp P.D., Smith H.O., Fraser C.M., Venter J.C.;
RT   "The complete genome sequence of the gastric pathogen Helicobacter
RT   pylori.";
RL   Nature 388:539-547(1997).
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; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_01898};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_01898};
CC       Name=Ca(2+); Xref=ChEBI:CHEBI:29108; Evidence={ECO:0000255|HAMAP-
CC         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; AE000511; AAD07566.1; -; Genomic_DNA.
DR   PIR; E64582; E64582.
DR   RefSeq; NP_207298.1; NC_000915.1.
DR   RefSeq; WP_001182024.1; NC_018939.1.
DR   AlphaFoldDB; P55992; -.
DR   SMR; P55992; -.
DR   DIP; DIP-3593N; -.
DR   IntAct; P55992; 3.
DR   MINT; P55992; -.
DR   STRING; 85962.HP_0501; -.
DR   PaxDb; 85962-C694_02575; -.
DR   EnsemblBacteria; AAD07566; AAD07566; HP_0501.
DR   KEGG; hpy:HP_0501; -.
DR   PATRIC; fig|85962.47.peg.539; -.
DR   eggNOG; COG0187; Bacteria.
DR   InParanoid; P55992; -.
DR   OrthoDB; 9802808at2; -.
DR   PhylomeDB; P55992; -.
DR   Proteomes; UP000000429; 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; IBA:GO_Central.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0006265; P:DNA topological change; IBA:GO_Central.
DR   GO; GO:0006261; P:DNA-templated DNA replication; IEA:UniProtKB-UniRule.
DR   CDD; cd16928; HATPase_GyrB-like; 1.
DR   CDD; cd00822; TopoII_Trans_DNA_gyrase; 1.
DR   CDD; cd03366; TOPRIM_TopoIIA_GyrB; 1.
DR   Gene3D; 3.30.230.10; -; 1.
DR   Gene3D; 3.40.50.670; -; 2.
DR   Gene3D; 3.30.565.10; Histidine kinase-like ATPase, C-terminal domain; 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_Su5_D2-typ_SF.
DR   InterPro; IPR014721; Ribsml_uS5_D2-typ_fold_subgr.
DR   InterPro; IPR001241; Topo_IIA.
DR   InterPro; IPR013760; Topo_IIA-like_dom_sf.
DR   InterPro; IPR000565; Topo_IIA_B.
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   NCBIfam; TIGR01059; gyrB; 1.
DR   PANTHER; PTHR45866:SF1; DNA GYRASE SUBUNIT B, MITOCHONDRIAL; 1.
DR   PANTHER; PTHR45866; DNA GYRASE/TOPOISOMERASE SUBUNIT B; 1.
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; PR01159; DNAGYRASEB.
DR   PRINTS; PR00418; TPI2FAMILY.
DR   SMART; SM00387; HATPase_c; 1.
DR   SMART; SM00433; TOP2c; 1.
DR   SUPFAM; SSF55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase; 1.
DR   SUPFAM; SSF54211; Ribosomal protein S5 domain 2-like; 1.
DR   SUPFAM; SSF56719; Type II DNA topoisomerase; 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..773
FT                   /note="DNA gyrase subunit B"
FT                   /id="PRO_0000145314"
FT   DOMAIN          416..530
FT                   /note="Toprim"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT   BINDING         422
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         495
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         495
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT   BINDING         497
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT   SITE            447
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT   SITE            450
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
SQ   SEQUENCE   773 AA;  87367 MW;  FDB47D3112CE8661 CRC64;
     MQNYQSHSIK VLKGLEGVRK RPGMYIGDTN VGGLHHMVYE VVDNAVDESM AGFCDTINIT
     LTDEGSCIVE DNGRGIPVDI HPTEKIPACT VVLTILHAGG KFDNDTYKVS GGLHGVGVSV
     VNALSKRLIM TIKKEGQIYR QEFEKGIPTS ELEIIGKTKS AKESGTTIEF FPDESVMEVV
     EFQAGILQKR FKEMAYLNDG LKISFKEEKT QLQETYFYED GLKQFVKDSA KKELLTPIIS
     FKSMDEETRT SIEVALAYAD DYNENTLSFV NNIKTSEGGT HEAGFKMGLS KAILQYIGNN
     IKTKESRPIS EDIKEGLIAV VSLKMSEPLF EGQTKSKLGS SYARALVSKL VYDKIHQFLE
     ENPNEAKIIA NKALLAAKAR EASKKARELT RKKDNLSVGT LPGKLADCQS KDPLESEIFL
     VEGDSAGGSA KQGRDRVFQA ILPLKGKILN VEKSHLSKIL KSEEIKNMIT AFGCGIQESF
     DIERLRYHKI IIMTDADVDG SHIQTLLMTF FYRYLRPLIE QGHVYIAQAP LYKYKKGKTE
     IYLKDSVALD HFLIEHGINS VDIEGIGKND LMNLLKVARH YRYALLELEK RYNLLEILRF
     LIETKDALSL DMKVLEKSIL EKLEGLNYQI LRSFATEESL HLHTQTPKGL VEFNLDDNLF
     KEVLFEEANY TYQKLMEYNL DFLENKDILA FLEEVENHAK KGANIQRYKG LGEMNPNDLW
     ETTMHKENRS LIKLKIEDLE KTDAVFSLCM GDEVEPRRAF IQAHAKDVKQ LDV
//