GenomeNet

Database: UniProt
Entry: A0A1X1MW09_9VIBR
LinkDB: A0A1X1MW09_9VIBR
Original site: A0A1X1MW09_9VIBR 
ID   A0A1X1MW09_9VIBR        Unreviewed;       805 AA.
AC   A0A1X1MW09;
DT   05-JUL-2017, integrated into UniProtKB/TrEMBL.
DT   05-JUL-2017, sequence version 1.
DT   24-JAN-2024, entry version 30.
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:ORT51395.1};
GN   ORFNames=ST37_05420 {ECO:0000313|EMBL:ORT51395.1};
OS   Vibrio sp. qd031.
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC   Vibrio.
OX   NCBI_TaxID=1603038 {ECO:0000313|EMBL:ORT51395.1, ECO:0000313|Proteomes:UP000193432};
RN   [1] {ECO:0000313|EMBL:ORT51395.1, ECO:0000313|Proteomes:UP000193432}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=qd031 {ECO:0000313|Proteomes:UP000193432};
RA   Xiang T., Song Y., Huang L., Wang B., Wu P.;
RL   Submitted (JAN-2015) to the EMBL/GenBank/DDBJ databases.
RN   [2] {ECO:0000313|EMBL:ORT51395.1, ECO:0000313|Proteomes:UP000193432}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=qd031 {ECO:0000313|Proteomes:UP000193432};
RA   Chen G.;
RT   "Denovo assembling a bacteria genome.";
RL   Submitted (MAY-2017) to the EMBL/GenBank/DDBJ databases.
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}.
CC   -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC       whole genome shotgun (WGS) entry which is preliminary data.
CC       {ECO:0000313|EMBL:ORT51395.1}.
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; JXQD01000009; ORT51395.1; -; Genomic_DNA.
DR   AlphaFoldDB; A0A1X1MW09; -.
DR   STRING; 1603038.ST37_05420; -.
DR   OrthoDB; 9802808at2; -.
DR   Proteomes; UP000193432; Unassembled WGS sequence.
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:UP000193432};
KW   Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW   Rule:MF_01898}.
FT   DOMAIN          419..534
FT                   /note="Toprim"
FT                   /evidence="ECO:0000259|PROSITE:PS50880"
FT   BINDING         425
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         499
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         499
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="2"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT   SITE            450
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT   SITE            453
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
SQ   SEQUENCE   805 AA;  89634 MW;  769B3902DA9F41CC CRC64;
     MAENYDSSSI KVLKGLDAVR KRPGMYIGDT DDGTGLHHMV FEVVDNSIDE ALAGHCNDII
     VTIHEDNSVS VKDDGRGIPT ELHEEENVSA AEVIMTVLHA GGKFDDNSYK VSGGLHGVGV
     SVVNALSKQV TLTIQRGGEI HSQTYRHGEP QAPLAVTGQT DQTGTEIRFW PSEETFTNIE
     FHYDILAKRL RELSFLNSGV SIKLVDEREE DKSDHFMFEG GIRAFVDHLN TNKTPIIQKI
     FHFDTEREDG ITVEVAMQWN DGFQENIYCF TNNIPQRDGG THLAGFRSAL TRTLNTFMDK
     EGFSKKAKAA TSGDDAREGL TAVISVKVPD PKFSSQTKDK LVSSEVKSAV ESAMGEKLSE
     FLVENPGEAK IVCSKIIDAA RAREAARKAR EMTRRKGALD LAGLPGKLAD CQEKDPALSE
     LYIVEGDSAG GSAKQGRNRK NQAILPLKGK ILNVEKARFD KMLSSQEVAT LITALGCGIG
     RDEYNPDKLR YHNIIIMTDA DVDGSHIRTL LLTFFYRQMP ELIERGYIYI AQPPLYKVKK
     GKQEQYIKDE DAMEQYQTSL ALDNASLHVN ADAPGISGEG LEQLVTQYKN AIAAANKLKR
     RFPEAIMHEL VYVPRLTAED CQSDDKVQAW GEQLIKQLNA KEIGASQYTL EVEKHEELNI
     SLPKVIVRTH GVTHEHVLSV ELFGTKEYLK LADLSETLDG LLEEGAFIKR GERVQVIADF
     VSALEWLQKE SRRGLSLQRY KGLGEMNPDQ LWETTMDPDT RRMMQVTIED AVGADQLFTT
     LMGDQVEPRR NFIEENALKV ANLDV
//
DBGET integrated database retrieval system