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Database: UniProt
Entry: A0A2I2A5D7_9GAMM
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ID   A0A2I2A5D7_9GAMM        Unreviewed;       814 AA.
AC   A0A2I2A5D7;
DT   28-FEB-2018, integrated into UniProtKB/TrEMBL.
DT   28-FEB-2018, sequence version 1.
DT   24-JAN-2024, entry version 25.
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:PLA74596.1};
GN   ORFNames=CYQ88_04600 {ECO:0000313|EMBL:PLA74596.1};
OS   Hydrogenovibrio sp. SC-1.
OC   Bacteria; Pseudomonadota; Gammaproteobacteria; Thiotrichales;
OC   Piscirickettsiaceae; Hydrogenovibrio.
OX   NCBI_TaxID=2065820 {ECO:0000313|EMBL:PLA74596.1, ECO:0000313|Proteomes:UP000234529};
RN   [1] {ECO:0000313|Proteomes:UP000234529}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=SC-1 {ECO:0000313|Proteomes:UP000234529};
RA   Barco R.A., Emerson D.;
RL   Submitted (DEC-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:PLA74596.1}.
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DR   EMBL; PKGB01000006; PLA74596.1; -; Genomic_DNA.
DR   AlphaFoldDB; A0A2I2A5D7; -.
DR   OrthoDB; 9802808at2; -.
DR   Proteomes; UP000234529; 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:UP000234529};
KW   Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW   Rule:MF_01898}.
FT   DOMAIN          426..541
FT                   /note="Toprim"
FT                   /evidence="ECO:0000259|PROSITE:PS50880"
FT   BINDING         432
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         506
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT   BINDING         506
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         508
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT   SITE            457
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT   SITE            460
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
SQ   SEQUENCE   814 AA;  91168 MW;  259CB110F82E9F7A CRC64;
     MTTEAEKTNQ PDEYNSSSIK VLKGLDAVRK RPGMYIGDTD DGTGLHHMVF EVVDNGIDEA
     LAGHCDKVVV TIHTDGSVSV TDNGRGIPVG IHEEEGVSAA EVIMTVLHAG GKFDDNSYKV
     SGGLHGVGVS VVNALSEELH LTIKREGHVW KQTYRHGVPV EPLKAVSETT ETGTEIRFLP
     SKETFTQTEF SFDYLLKRLR ELSFLNSGVH IELLDKRDDR HEVFQFEGGI KAFVDYINTN
     KTPINEKAFY FSTTREDIVV EVAMQWSEAY QESIFCFTNN IPQRDGGTHL SGFRAALTRT
     LNQYAEKEGL TKKYKMTVSG DDAREGLAAV ISVKVPDPKF SSQTKDKLVS SEVKSAVETA
     MNEKLAEYLL EHPKEAQSVF SKIVDAARAR EAARKAREMT RRKGALDIAG LPGKLADCQE
     KDPALSELYL VEGDSAGGSA KQGRDRRTQA ILPLKGKILN VEKARFDKML ASAEVGTLIT
     ALGCGIGHEE YNPDKLRYHR IIIMTDADVD GSHIRTLLLT FFYRQMPELI ERGYIYIAQP
     PLYKVKKGKQ EAYLKDDSEL ESYLLQSALD KAALWTAPEA PAIKEMALET LAKSFLQANR
     IISRLARRFS HTFLELMLDL NPIQVDTLNN YDACQQWINE ALPRLKAIGE LQKVEYQLQV
     EPALNGETQF QIRLQQREHG TLTSQIYDED FFASAEFENI AKVASQLKGL LTDQAKIQRG
     EKEQPVASFK EVMDWLLAEA KRGQSIQRYK GLGEMNPEQL WETTMNAEAR RLLQVKISDA
     VQADQVFTTL MGDEVEPRRD FIESNALKAE NIDV
//
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