ID GYRB_VIBPA Reviewed; 805 AA.
AC O51859;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 04-APR-2003, sequence version 2.
DT 27-MAR-2024, entry version 148.
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=VP0014;
OS Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633).
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=223926;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=RIMD 2210633;
RX PubMed=12620739; DOI=10.1016/s0140-6736(03)12659-1;
RA Makino K., Oshima K., Kurokawa K., Yokoyama K., Uda T., Tagomori K.,
RA Iijima Y., Najima M., Nakano M., Yamashita A., Kubota Y., Kimura S.,
RA Yasunaga T., Honda T., Shinagawa H., Hattori M., Iida T.;
RT "Genome sequence of Vibrio parahaemolyticus: a pathogenic mechanism
RT distinct from that of V. cholerae.";
RL Lancet 361:743-749(2003).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 92-510.
RC STRAIN=ATCC 17802 / DSM 10027 / NBRC 12711 / NCIMB 1902 / LMG 2850 / NCTC
RC 10903;
RX PubMed=9464408; DOI=10.1128/aem.64.2.681-687.1998;
RA Venkateswaran K., Dohmoto N., Harayama S.;
RT "Cloning and nucleotide sequence of the gyrB gene of Vibrio
RT parahaemolyticus and its application in detection of this pathogen in
RT shrimp.";
RL Appl. Environ. Microbiol. 64:681-687(1998).
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; BA000031; BAC58277.1; -; Genomic_DNA.
DR EMBL; AF007287; AAC38147.1; -; Genomic_DNA.
DR RefSeq; NP_796393.1; NC_004603.1.
DR RefSeq; WP_005458663.1; NC_004603.1.
DR AlphaFoldDB; O51859; -.
DR SMR; O51859; -.
DR GeneID; 1187470; -.
DR KEGG; vpa:VP0014; -.
DR PATRIC; fig|223926.6.peg.14; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_4_1_6; -.
DR Proteomes; UP000002493; Chromosome 1.
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; cd16928; HATPase_GyrB-like; 1.
DR CDD; cd00822; TopoII_Trans_DNA_gyrase; 1.
DR CDD; cd03366; TOPRIM_TopoIIA_GyrB; 1.
DR Gene3D; 3.10.20.690; -; 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; IPR049353; GyrB_hook.
DR InterPro; IPR041423; GyrB_insert.
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; PF21249; GyrB_hook; 1.
DR Pfam; PF18053; GyrB_insert; 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..805
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000145359"
FT DOMAIN 419..534
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 425
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 499
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 499
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 501
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 450
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 453
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT CONFLICT 152
FT /note="A -> T (in Ref. 2; AAC38147)"
FT /evidence="ECO:0000305"
FT CONFLICT 160
FT /note="T -> A (in Ref. 2; AAC38147)"
FT /evidence="ECO:0000305"
FT CONFLICT 290
FT /note="L -> I (in Ref. 2; AAC38147)"
FT /evidence="ECO:0000305"
FT CONFLICT 484
FT /note="Y -> H (in Ref. 2; AAC38147)"
FT /evidence="ECO:0000305"
FT CONFLICT 503..510
FT /note="DGSHIRTL -> EARTSVPC (in Ref. 2; AAC38147)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 805 AA; 89442 MW; 135962F21D351E1C CRC64;
MSENYDSSSI KVLKGLDAVR KRPGMYIGDT DDGTGLHHMV FEVVDNSIDE ALAGHCKDIV
VTIHEDNSVS VSDDGRGIPT EMHPEEKVSA AEVIMTVLHA GGKFDDNSYK VSGGLHGVGV
SVVNALSEKV VLTIHRGGHI HTQTYRHGEP EAPLAVVGDT DKTGTQIRFW PSAETFSNTE
FHYDILAKRL RELSFLNSGV SIKLIDEREA DKQDHFMYEG GIQAFVQHLN TNKTPIIEKI
FHFDLEREDG ISVEVAMQWN DGFQENIFCF TNNIPQRDGG THLAGFRAAL TRTLNSFMDK
EGFSKKAKTA TSGDDAREGL TAVVSVKVPD PKFSSQTKDK LVSSEVKSAV ESAMGEKLSE
FLVENPSEAK MVCSKIIDAA RAREAARKAR EMTRRKGALD LAGLPGKLAD CQEKDPALSE
LYIVEGDSAG GSAKQGRNRK NQAILPLKGK ILNVEKARFD KMLSSQEVAT LITALGCGIG
RDEYNPDKLR YHNIIIMTDA DVDGSHIRTL LLTFFYRQMP ELIERGYVYI AQPPLYKVKK
GKQEQYIKDE EAMNQYQVSL ALDNASLHVN AEAPALAGEA LEKLVQQYNA GIKLADRMSR
RYPRALVHEL IYTSRLTAEQ CHDAAAVEAW TKQLVEQLNA KEVGASQYSY EVELHAELGL
SLPKIIVRTH GVTHEHALSV DFLNSKEYGK LADLSEVLDG LLEEGAYIKR GERTLPVSSF
AEALEWLVKE SMRGLSRQRY KGLGEMNPDQ LWETTMDPET RRMMQVTIED AVGADQLFTT
LMGDQVEPRR HFIEENALKV ANLDV
//
