ID A0A0G9MKZ9_9SPHN Unreviewed; 840 AA.
AC A0A0G9MKZ9;
DT 16-SEP-2015, integrated into UniProtKB/TrEMBL.
DT 16-SEP-2015, sequence version 1.
DT 24-JAN-2024, entry version 48.
DE RecName: Full=DNA gyrase subunit B {ECO:0000256|HAMAP-Rule:MF_01898};
DE EC=5.6.2.2 {ECO:0000256|HAMAP-Rule:MF_01898};
GN Name=gyrB {ECO:0000256|HAMAP-Rule:MF_01898};
GN ORFNames=AAW01_07095 {ECO:0000313|EMBL:KLE31365.1}, BMF35_a0416
GN {ECO:0000313|EMBL:APE27245.1};
OS Aurantiacibacter gangjinensis.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Erythrobacteraceae; Aurantiacibacter.
OX NCBI_TaxID=502682 {ECO:0000313|EMBL:KLE31365.1, ECO:0000313|Proteomes:UP000053070};
RN [1] {ECO:0000313|EMBL:KLE31365.1, ECO:0000313|Proteomes:UP000053070}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K7-2 {ECO:0000313|EMBL:KLE31365.1,
RC ECO:0000313|Proteomes:UP000053070};
RA Zhuang L., Liu Y., Shao Z.;
RT "The draft genome sequence of Erythrobacr gangjinensis K7-2.";
RL Submitted (APR-2015) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:APE27245.1, ECO:0000313|Proteomes:UP000183202}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CGMCC1.15024 {ECO:0000313|EMBL:APE27245.1,
RC ECO:0000313|Proteomes:UP000183202};
RA Xu L., Wu Y.-H., Cheng H., Zhou Y.-G., Wu M., Cheng L., Xu X.-W.;
RT "Complete genome sequence of two-chromosomal Erythrobacter gangjinensis
RT CGMCC 1.15024T, isolated from seawater.";
RL Submitted (NOV-2016) 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}.
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DR EMBL; CP018097; APE27245.1; -; Genomic_DNA.
DR EMBL; LBHC01000002; KLE31365.1; -; Genomic_DNA.
DR RefSeq; WP_047006717.1; NZ_LBHC01000002.1.
DR AlphaFoldDB; A0A0G9MKZ9; -.
DR STRING; 502682.BMF35_a0416; -.
DR KEGG; egn:BMF35_a0416; -.
DR PATRIC; fig|502682.8.peg.1446; -.
DR OrthoDB; 9802808at2; -.
DR Proteomes; UP000053070; Unassembled WGS sequence.
DR Proteomes; UP000183202; Chromosome i.
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; 3.30.230.10; -; 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; 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; 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:UP000053070};
KW Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW Rule:MF_01898}.
FT DOMAIN 443..553
FT /note="Toprim"
FT /evidence="ECO:0000259|PROSITE:PS50880"
FT REGION 715..750
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 449
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 522
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT BINDING 522
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 524
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 474
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 477
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
SQ SEQUENCE 840 AA; 91850 MW; 208744F5B7D95860 CRC64;
MSDTPEKARQ NGEYSSDSIK VLKGLDAVRK RPGMYIGDTD DGSGLHHMVF EVSDNAIDEA
LAGHCDLVLI ELNPDGSVSV EDNGRGIPVD IHKEEGVSAA EVIMTQLHAG GKFENTSDDN
AYKVSGGLHG VGVSVVNALS EWLELEVWRN GKSHTMRFEH GDAVNSLTIT GDAPPVESNG
DDNGLKKGTR VTFMPSTDTF KNVTEFDFEK LEHRYRELAF LNSGVRILLR DNRPEEPIEH
DLFYEGGIAA FVKWLDRNKQ PLVPEPISVS AEKDGIGIDV ALEWNDSYYE NVLTFTNNIP
QRDGGTHLAA FRAALTRTLN NYATSSGLLK GGKISLSGED MREGLTAIVS VKLPDPKFSS
QTKDKLVSSE VRSPLESLIG EKMTEWLEEN PNDAKTIIQK IIDAAAAREA ARKAREMSRK
GAMSVASLPG KLSDCRERDP AKSEIFLVEG DSAGGSAKSG RDSKYQAILP LKGKILNVER
ARFDRIISSK EVGTLIQAMG TGLRDEFNLE KLRYHKIVIM TDADVDGAHI RTLLLTFFHR
QMPDIIKAGH LFIAQPPLFK VAKGKSEVYL KDQGALDRYL VTAGLNDRVL ETAGGARSGA
DLADLVDKAL LLKNLLAFAP KKYDPAVIES MAMAGALGPD MSVADRNTAL SQAAAQLQLG
DGEAEWSARV TDDGDVRFDR VWRGVADVHL IDAKFLDSAE ARKLHKRGIE QADTYASPTR
LVKSGSEQAA PVGDNPDETD ADTPAFDPDT AITRPTQLLE AVMAAGRRGL SVSRYKGLGE
MNAEQLWETT LDPDNRELLQ VKVEDADVTD EIFTRLMGDV VEPRREFIQD NALNVANLDV
//
