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Database: UniProt/TrEMBL
Entry: Q5E8Y9_VIBF1
LinkDB: Q5E8Y9_VIBF1
Original site: Q5E8Y9_VIBF1 
ID   Q5E8Y9_VIBF1            Unreviewed;       805 AA.
AC   Q5E8Y9;
DT   15-MAR-2005, integrated into UniProtKB/TrEMBL.
DT   15-MAR-2005, sequence version 1.
DT   26-NOV-2014, entry version 86.
DE   RecName: Full=DNA gyrase subunit B {ECO:0000256|HAMAP-Rule:MF_01898, ECO:0000256|RuleBase:RU003363};
DE            EC=5.99.1.3 {ECO:0000256|HAMAP-Rule:MF_01898, ECO:0000256|RuleBase:RU003363};
GN   Name=gyrB {ECO:0000256|HAMAP-Rule:MF_01898,
GN   ECO:0000313|EMBL:AAW84507.1};
GN   OrderedLocusNames=VF_0012 {ECO:0000313|EMBL:AAW84507.1};
OS   Vibrio fischeri (strain ATCC 700601 / ES114).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales;
OC   Vibrionaceae; Aliivibrio.
OX   NCBI_TaxID=312309 {ECO:0000313|EMBL:AAW84507.1, ECO:0000313|Proteomes:UP000000537};
RN   [1] {ECO:0000313|EMBL:AAW84507.1, ECO:0000313|Proteomes:UP000000537}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 700601 / ES114 {ECO:0000313|Proteomes:UP000000537};
RX   PubMed=15703294; DOI=10.1073/pnas.0409900102;
RA   Ruby E.G., Urbanowski M., Campbell J., Dunn A., Faini M., Gunsalus R.,
RA   Lostroh P., Lupp C., McCann J., Millikan D., Schaefer A., Stabb E.,
RA   Stevens A., Visick K., Whistler C., Greenberg E.P.;
RT   "Complete genome sequence of Vibrio fischeri: a symbiotic bacterium
RT   with pathogenic congeners.";
RL   Proc. Natl. Acad. Sci. U.S.A. 102:3004-3009(2005).
CC   -!- FUNCTION: DNA gyrase negatively supercoils closed circular double-
CC       stranded DNA in an ATP-dependent manner and also catalyzes the
CC       interconversion of other topological isomers of double-stranded
CC       DNA rings, including catenanes and knotted rings.
CC       {ECO:0000256|HAMAP-Rule:MF_01898, ECO:0000256|RuleBase:RU003363}.
CC   -!- CATALYTIC ACTIVITY: ATP-dependent breakage, passage and rejoining
CC       of double-stranded DNA. {ECO:0000256|HAMAP-Rule:MF_01898,
CC       ECO:0000256|RuleBase:RU003363, ECO:0000256|SAAS:SAAS00030552}.
CC   -!- COFACTOR:
CC       Note=Magnesium. Binds two Mg(2+) per subunit. The magnesium ions
CC       form salt bridges with both the protein and the DNA. Can also
CC       accept other divalent metal cations, such as Mn(2+) and Ca(2+).
CC       {ECO:0000256|HAMAP-Rule:MF_01898};
CC   -!- SUBUNIT: Heterotetramer, composed of two GyrA and two GyrB chains.
CC       Within the heterotetramer, GyrA contains the active site tyrosine
CC       that forms a covalent intermediate with the DNA, while GyrB
CC       contributes the cofactor binding sites and catalyzes ATP
CC       hydrolysis. {ECO:0000256|HAMAP-Rule:MF_01898}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01898}.
CC   -!- SIMILARITY: Belongs to the type II topoisomerase family.
CC       {ECO:0000256|HAMAP-Rule:MF_01898}.
CC   -!- SIMILARITY: Contains 1 Toprim domain. {ECO:0000256|HAMAP-
CC       Rule:MF_01898}.
CC   -!- SIMILARITY: Contains Toprim domain.
CC       {ECO:0000256|SAAS:SAAS00106838}.
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DR   EMBL; CP000020; AAW84507.1; -; Genomic_DNA.
DR   RefSeq; YP_203395.1; NC_006840.2.
DR   ProteinModelPortal; Q5E8Y9; -.
DR   SMR; Q5E8Y9; 10-393.
DR   STRING; 312309.VF_0012; -.
DR   EnsemblBacteria; AAW84507; AAW84507; VF_0012.
DR   GeneID; 3279826; -.
DR   KEGG; vfi:VF_0012; -.
DR   PATRIC; 20110509; VBIVibFis127983_0013.
DR   eggNOG; COG0187; -.
DR   HOGENOM; HOG000075155; -.
DR   KO; K02470; -.
DR   OMA; IRFWPST; -.
DR   OrthoDB; EOG6P334W; -.
DR   BioCyc; AFIS312309:GIWP-12-MONOMER; -.
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-HAMAP.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-HAMAP.
DR   GO; GO:0003918; F:DNA topoisomerase type II (ATP-hydrolyzing) activity; IEA:UniProtKB-HAMAP.
DR   GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-HAMAP.
DR   GO; GO:0006265; P:DNA topological change; IEA:InterPro.
DR   GO; GO:0006261; P:DNA-dependent DNA replication; IEA:UniProtKB-HAMAP.
DR   Gene3D; 3.30.230.10; -; 1.
DR   Gene3D; 3.30.565.10; -; 1.
DR   Gene3D; 3.40.50.670; -; 2.
DR   HAMAP; MF_01898; GyrB; 1.
DR   InterPro; IPR002288; DNA_gyrase_B_C.
DR   InterPro; IPR011557; GyrB.
DR   InterPro; IPR003594; HATPase_C.
DR   InterPro; IPR020568; Ribosomal_S5_D2-typ_fold.
DR   InterPro; IPR014721; Ribosomal_S5_D2-typ_fold_subgr.
DR   InterPro; IPR001241; Topo_IIA.
DR   InterPro; IPR013506; Topo_IIA_bsu_dom2.
DR   InterPro; IPR013759; Topo_IIA_cen_dom.
DR   InterPro; IPR013760; Topo_IIA_like_dom.
DR   InterPro; IPR018522; TopoIIA_CS.
DR   InterPro; IPR006171; Toprim_domain.
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; PR00418; TPI2FAMILY.
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; 2.
DR   TIGRFAMs; TIGR01059; gyrB; 1.
DR   PROSITE; PS00177; TOPOISOMERASE_II; 1.
DR   PROSITE; PS50880; TOPRIM; 1.
PE   3: Inferred from homology;
KW   ATP-binding {ECO:0000256|HAMAP-Rule:MF_01898,
KW   ECO:0000256|RuleBase:RU000380};
KW   Complete proteome {ECO:0000313|Proteomes:UP000000537};
KW   Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01898};
KW   DNA-binding {ECO:0000256|HAMAP-Rule:MF_01898};
KW   Isomerase {ECO:0000256|HAMAP-Rule:MF_01898,
KW   ECO:0000256|RuleBase:RU000380};
KW   Magnesium {ECO:0000256|HAMAP-Rule:MF_01898};
KW   Metal-binding {ECO:0000256|HAMAP-Rule:MF_01898};
KW   Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_01898,
KW   ECO:0000256|RuleBase:RU000380};
KW   Reference proteome {ECO:0000313|Proteomes:UP000000537};
KW   Topoisomerase {ECO:0000256|HAMAP-Rule:MF_01898,
KW   ECO:0000256|RuleBase:RU000380}.
FT   DOMAIN      419    534       Toprim. {ECO:0000256|HAMAP-Rule:
FT                                MF_01898}.
FT   METAL       425    425       Magnesium 1; catalytic.
FT                                {ECO:0000256|HAMAP-Rule:MF_01898}.
FT   METAL       499    499       Magnesium 1; catalytic.
FT                                {ECO:0000256|HAMAP-Rule:MF_01898}.
FT   METAL       499    499       Magnesium 2. {ECO:0000256|HAMAP-Rule:
FT                                MF_01898}.
FT   METAL       501    501       Magnesium 2. {ECO:0000256|HAMAP-Rule:
FT                                MF_01898}.
FT   SITE        450    450       Interaction with DNA. {ECO:0000256|HAMAP-
FT                                Rule:MF_01898}.
FT   SITE        453    453       Interaction with DNA. {ECO:0000256|HAMAP-
FT                                Rule:MF_01898}.
SQ   SEQUENCE   805 AA;  89404 MW;  99E2F8CE31269448 CRC64;
     MSENYDSSSI KVLKGLDAVR KRPGMYIGDT DDGTGLHHMV FEVVDNSIDE ALAGHCKDII
     VTIHEDNSVS VSDDGRGIPT AIHPEEGVSA AEVIMTVLHA GGKFDDNSYK VSGGLHGVGV
     SVVNALSEKV ELTIHRAGEI HQQVYHHGEP EAPLAVIGKT DTTGTKIRFW PSEETFTNVV
     FVYEILAKRL RELSFLNSGV SIKLQDMREE DKADHFMYEG GIQAFVQHLN RNKTPIHQKV
     FHFDSEREDG ISVEVSMQWN DGFQENIYCF TNNIPQRDGG THLAGFRSAL TRTLNTFMDK
     EGFSKKAKAA TSGDDAREGL TAVVSVKVPD PKFSSQTKDK LVSSEVKSAV ESAMGEKLSE
     FLAENPSEAK MVCSKIIDAA RAREAARKAR EMTRRKGALD IAGLPGKLAD CQEKDPGLSE
     LYIVEGDSAG GSAKQGRNRK NQAILPLKGK ILNVEKARFD KMLSSQEVGT LITALGCGIG
     RDEYNPDKLR YHNIIIMTDA DVDGSHIRTL LLTFFYRQMP ELIERGYIYI AQPPLYKVKK
     GKQEQYIKDE DAMAEYQIAL ALDNASLFTN ADAPAIAGQA LEDLVVQYNS VMKLIDRMSR
     RYPVSVLNRL VYTGRLTQEM CADEASAQAW TEAFVAELNA TEVGASQYNA ALLFDEEANA
     YQPKLVVRTH GVEHEYVLSI DLLNSKEYAR IADLAEALDG LLEESAYAQR GERKQPVSSF
     EDALAWLTKE SRRGFSLQRY KGLGEMNPEQ LWETTMDPES RRMMQVTIND AVAADELFTT
     LMGDQVEPRR NFIEENALRV SNLDI
//
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