ID A0A0P0GBI7_9BACE Unreviewed; 653 AA.
AC A0A0P0GBI7;
DT 20-JAN-2016, integrated into UniProtKB/TrEMBL.
DT 20-JAN-2016, sequence version 1.
DT 24-JAN-2024, entry version 47.
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_1 {ECO:0000313|EMBL:ALJ59631.1};
GN Synonyms=gyrB {ECO:0000256|HAMAP-Rule:MF_01898,
GN ECO:0000313|EMBL:KAA5409906.1};
GN ORFNames=BcellWH2_02392 {ECO:0000313|EMBL:ALJ59631.1}, DWW88_06410
GN {ECO:0000313|EMBL:RGU28713.1}, DWX97_05680
GN {ECO:0000313|EMBL:RGS38482.1}, F2Y70_12670
GN {ECO:0000313|EMBL:KAA5425750.1}, F2Y81_09535
GN {ECO:0000313|EMBL:KAA5419628.1}, F2Y86_06880
GN {ECO:0000313|EMBL:KAA5409906.1}, F2Y87_08770
GN {ECO:0000313|EMBL:KAA5420030.1};
OS Bacteroides cellulosilyticus.
OC Bacteria; Bacteroidota; Bacteroidia; Bacteroidales; Bacteroidaceae;
OC Bacteroides.
OX NCBI_TaxID=246787 {ECO:0000313|EMBL:ALJ59631.1, ECO:0000313|Proteomes:UP000061809};
RN [1] {ECO:0000313|EMBL:ALJ59631.1, ECO:0000313|Proteomes:UP000061809}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=WH2 {ECO:0000313|EMBL:ALJ59631.1,
RC ECO:0000313|Proteomes:UP000061809};
RX PubMed=26430127;
RA Wu M., McNulty N.P., Rodionov D.A., Khoroshkin M.S., Griffin N.W.,
RA Cheng J., Latreille P., Kerstetter R.A., Terrapon N., Henrissat B.,
RA Osterman A.L., Gordon J.I.;
RT "Genetic determinants of in vivo fitness and diet responsiveness in
RT multiple human gut Bacteroides.";
RL Science 350:AAC5992-AAC5992(2015).
RN [2] {ECO:0000313|Proteomes:UP000283341, ECO:0000313|Proteomes:UP000285677}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AF17-25 {ECO:0000313|EMBL:RGU28713.1,
RC ECO:0000313|Proteomes:UP000285677}, and AF22-3AC
RC {ECO:0000313|EMBL:RGS38482.1, ECO:0000313|Proteomes:UP000283341};
RA Zou Y., Xue W., Luo G.;
RT "A genome reference for cultivated species of the human gut microbiota.";
RL Submitted (AUG-2018) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000313|Proteomes:UP000325055, ECO:0000313|Proteomes:UP000448877}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=BIOML-A3 {ECO:0000313|EMBL:KAA5425750.1,
RC ECO:0000313|Proteomes:UP000475645}, BIOML-A6
RC {ECO:0000313|EMBL:KAA5419628.1, ECO:0000313|Proteomes:UP000448877},
RC BIOML-A7 {ECO:0000313|EMBL:KAA5409906.1,
RC ECO:0000313|Proteomes:UP000325055}, and BIOML-A8
RC {ECO:0000313|EMBL:KAA5420030.1, ECO:0000313|Proteomes:UP000482653};
RX PubMed=31477907; DOI=.1038/s41591-019-0559-3;
RA Poyet M., Groussin M., Gibbons S.M., Avila-Pacheco J., Jiang X.,
RA Kearney S.M., Perrotta A.R., Berdy B., Zhao S., Lieberman T.D.,
RA Swanson P.K., Smith M., Roesemann S., Alexander J.E., Rich S.A., Livny J.,
RA Vlamakis H., Clish C., Bullock K., Deik A., Scott J., Pierce K.A.,
RA Xavier R.J., Alm E.J.;
RT "A library of human gut bacterial isolates paired with longitudinal
RT multiomics data enables mechanistic microbiome research.";
RL Nat. Med. 25:1442-1452(2019).
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; CP012801; ALJ59631.1; -; Genomic_DNA.
DR EMBL; VVYW01000005; KAA5409906.1; -; Genomic_DNA.
DR EMBL; VVYV01000013; KAA5419628.1; -; Genomic_DNA.
DR EMBL; VVYX01000009; KAA5420030.1; -; Genomic_DNA.
DR EMBL; VVYT01000034; KAA5425750.1; -; Genomic_DNA.
DR EMBL; QRVJ01000003; RGS38482.1; -; Genomic_DNA.
DR EMBL; QRXS01000003; RGU28713.1; -; Genomic_DNA.
DR RefSeq; WP_007210875.1; NZ_VVYX01000009.1.
DR AlphaFoldDB; A0A0P0GBI7; -.
DR STRING; 246787.BcellWH2_02392; -.
DR GeneID; 66306250; -.
DR KEGG; bcel:BcellWH2_02392; -.
DR PATRIC; fig|246787.4.peg.2456; -.
DR eggNOG; COG0187; Bacteria.
DR Proteomes; UP000061809; Chromosome.
DR Proteomes; UP000283341; Unassembled WGS sequence.
DR Proteomes; UP000285677; Unassembled WGS sequence.
DR Proteomes; UP000325055; Unassembled WGS sequence.
DR Proteomes; UP000448877; Unassembled WGS sequence.
DR Proteomes; UP000475645; Unassembled WGS sequence.
DR Proteomes; UP000482653; 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 Gene3D; 3.30.230.10; -; 1.
DR Gene3D; 3.40.50.670; -; 1.
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; 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 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; 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}; Cytoplasm {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};
KW Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW Rule:MF_01898}.
FT DOMAIN 430..550
FT /note="Toprim"
FT /evidence="ECO:0000259|PROSITE:PS50880"
FT REGION 400..421
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 436
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 515
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 515
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT BINDING 517
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 461
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 464
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
SQ SEQUENCE 653 AA; 73346 MW; CB8E9AC350CB4735 CRC64;
MTEEQINSNN GSYSAENIQV LEGLEAVRKR PAMYIGDIST KGLHHLVYEV VDNSIDEALA
GYCDHIEVTI NEDNSITVQD NGRGIPVDFH EKEKKSALEV VMTVLHAGGK FDKGSYKVSG
GLHGVGVSCV NALSTHMTTQ VFRNGKIYQQ EYECGHPLYP VKEIGTSDIT GTRQQFWPDN
TIFTETVYNY EILATRMREL AYLNAGIKIT LTDLRVKDEE NNAKMEVFYS EEGLKEFVRY
IDSSREHLVN DVIYINTEKQ GTPVEVAIMY NTSYNENIHS YVNNINTIEG GTHLAGFRRA
LTRTLKKYAE DNKMLEKAKV EIAGDDFREG LTAVISIKVA EPQFEGQTKT KLGNSEVMGA
VDQAVGEALN YYLEEHPKEA KMVVDKVILA AQARVAARKA RESVQRKSPM SGGGMPGKLA
DCSSKDPEEC ELFLVEGDSA GGSAKQGRDR RFQAILPLRG KILNVEKAMW HKAFESDEVN
NIIQALGIRF GVDGEDSKEA NIDKLRYKKV IIMTDADVDG SHIDTLIMTL FFRYFPQVIR
NGYLYIATPP LYLCKKGKVE EYCWTDQQRQ KFIDTYGGGS ENAVHTQRYK GLGEMNPEQL
WSTTMNPENR MLKQISIENA AEVDYIFSML MGEDVGPRRD FIEKNATYAN IDA
//
