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Database: UniProt
Entry: E1VFE4_9GAMM
LinkDB: E1VFE4_9GAMM
Original site: E1VFE4_9GAMM 
ID   E1VFE4_9GAMM            Unreviewed;       807 AA.
AC   E1VFE4;
DT   30-NOV-2010, integrated into UniProtKB/TrEMBL.
DT   30-NOV-2010, sequence version 1.
DT   24-JAN-2024, entry version 79.
DE   RecName: Full=DNA gyrase subunit B {ECO:0000256|ARBA:ARBA00019166, ECO:0000256|HAMAP-Rule:MF_01898};
DE            EC=5.6.2.2 {ECO:0000256|ARBA:ARBA00012895, ECO:0000256|HAMAP-Rule:MF_01898};
GN   Name=gyrB {ECO:0000256|HAMAP-Rule:MF_01898,
GN   ECO:0000313|EMBL:CBL43587.1};
GN   ORFNames=HDN1F_00040 {ECO:0000313|EMBL:CBL43587.1};
OS   gamma proteobacterium HdN1.
OC   Bacteria; Pseudomonadota; Gammaproteobacteria.
OX   NCBI_TaxID=83406 {ECO:0000313|EMBL:CBL43587.1, ECO:0000313|Proteomes:UP000002677};
RN   [1] {ECO:0000313|EMBL:CBL43587.1, ECO:0000313|Proteomes:UP000002677}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=HdN1 {ECO:0000313|Proteomes:UP000002677};
RA   Widdel F., Rabus R., Grundmann O., Werner I., Schreiber F., Ehrenreich P.,
RA   Behrends A., Wilkes H., Kube M., Reinhardt R., Zedelius J.;
RT   "Alkane degradation by a new type of denitrifying bacterium with possible
RT   involvement of the electron acceptor in substrate activation.";
RL   Environ. Microbiol. 0:0-0(2010).
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:0000256|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:0000256|ARBA:ARBA00000185,
CC         ECO:0000256|HAMAP-Rule:MF_01898};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_01898};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_01898};
CC       Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC         Evidence={ECO:0000256|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:0000256|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:0000256|HAMAP-Rule:MF_01898}.
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|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:0000256|HAMAP-
CC       Rule:MF_01898}.
CC   -!- SIMILARITY: Belongs to the type II topoisomerase GyrB family.
CC       {ECO:0000256|ARBA:ARBA00010708, ECO:0000256|HAMAP-Rule:MF_01898}.
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DR   EMBL; FP929140; CBL43587.1; -; Genomic_DNA.
DR   AlphaFoldDB; E1VFE4; -.
DR   STRING; 83406.HDN1F_00040; -.
DR   KEGG; gpb:HDN1F_00040; -.
DR   eggNOG; COG0187; Bacteria.
DR   HOGENOM; CLU_006146_4_1_6; -.
DR   OrthoDB; 9802808at2; -.
DR   Proteomes; UP000002677; 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; 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 {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW   Rule:MF_01898};
KW   Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_01898};
KW   DNA-binding {ECO:0000256|ARBA:ARBA00023125};
KW   Isomerase {ECO:0000256|ARBA:ARBA00023235, ECO:0000256|HAMAP-Rule:MF_01898};
KW   Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_01898};
KW   Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW   Rule:MF_01898};
KW   Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW   Rule:MF_01898}; Reference proteome {ECO:0000313|Proteomes:UP000002677};
KW   Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW   Rule:MF_01898}.
FT   DOMAIN          421..536
FT                   /note="Toprim"
FT                   /evidence="ECO:0000259|PROSITE:PS50880"
FT   BINDING         427
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT   BINDING         501
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT   BINDING         501
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /ligand_note="catalytic"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT   BINDING         503
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT   SITE            452
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT   SITE            455
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
SQ   SEQUENCE   807 AA;  89818 MW;  3F87C5E5C51CEE4A CRC64;
     MSQEEDTKGY DSSSIKVLRG LDAVRKRPGM YIGDTDDGTG LHHMVFEVVD NSIDEALAGF
     CKEITVTIHQ DETITVCDDG RGIPVDIHPE EGVSAAEVIM TVLHAGGKFD DNTYKVSGGL
     HGVGVSVVNA LSEELVLTIR RKGKVWQQIY RHGVPQEPLA PIGESSTTGT QVHFKPSSET
     FSNIEFSHEI LARRLRELSF LNSGVKILLK DERTDATDVF CYEGGLEQFV KFLNLNKTPL
     NKVFYFSSEK DGVSVEVALQ WNDGYQENVR CYTNNIPQRD GGTHLAGFRS AMTRAINQYL
     DQEGITKKHK ISASGDDARE GLVAIVSVKV GDPKFSSQTK DKLVSSEVKP AVETLMFEKL
     SEYLAEQPNE AKIVCQKIID AARAREAARK AREMTRRKGA LDIAGLPGKL ADCQEKDPAL
     SELYLVEGDS AGGSAKQGRN RKTQAILPLK GKILNVEKAR FDKMLSSAEV GTLITALGCG
     IGREEYDPDK TRYHNIIIMT DADVDGSHIR TLLLTFFFRQ MPELIERGYI YIAQPPLYKI
     KKGKQEQYLK DDEALSHYLT AAAIDDASLN PGGDLAPILG TELAALLEEY KRATNRVARL
     SRLYPGLLLN ELIYRPALDT DDLNSVDVVR NWCSGIETHL NAICPPSEHY EVSAVEVPEK
     GIFVPKIILT AHGVPHHYTL GRDFFISNDY RMFTTLGAKV RNLIQEGAFV KKGEKVKTVS
     SFPEVVEWLM DESRRGHQIQ RYKGLGEMNP EQLWETTMDP EMRRMLRVTV EDAIAADQIF
     TTLMGDAVEP RRDFIETNAL NVANLDI
//
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