ID A9ILB0_BART1 Unreviewed; 816 AA.
AC A9ILB0;
DT 05-FEB-2008, integrated into UniProtKB/TrEMBL.
DT 05-FEB-2008, sequence version 1.
DT 24-JAN-2024, entry version 117.
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 ECO:0000313|EMBL:CAK00544.1};
GN OrderedLocusNames=BT_0041 {ECO:0000313|EMBL:CAK00544.1};
OS Bartonella tribocorum (strain CIP 105476 / IBS 506).
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC Bartonellaceae; Bartonella.
OX NCBI_TaxID=382640 {ECO:0000313|EMBL:CAK00544.1, ECO:0000313|Proteomes:UP000001592};
RN [1] {ECO:0000313|EMBL:CAK00544.1, ECO:0000313|Proteomes:UP000001592}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CIP 105476 / IBS 506 {ECO:0000313|Proteomes:UP000001592};
RX PubMed=18037886; DOI=10.1038/ng.2007.38;
RA Saenz H.L., Engel P., Stoeckli M.C., Lanz C., Raddatz G.,
RA Vayssier-Taussat M., Birtles R., Schuster S.C., Dehio C.;
RT "Genomic analysis of Bartonella identifies type IV secretion systems as
RT host adaptability factors.";
RL Nat. Genet. 39:1469-1476(2007).
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; AM260525; CAK00544.1; -; Genomic_DNA.
DR RefSeq; WP_012230336.1; NC_010161.1.
DR AlphaFoldDB; A9ILB0; -.
DR KEGG; btr:BT_0041; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_4_1_5; -.
DR OMA; LWETTMH; -.
DR Proteomes; UP000001592; 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; 3.30.230.10; -; 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};
KW Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW Rule:MF_01898}.
FT DOMAIN 435..550
FT /note="Toprim"
FT /evidence="ECO:0000259|PROSITE:PS50880"
FT BINDING 441
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 466
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 469
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
SQ SEQUENCE 816 AA; 90289 MW; EB5A68DB0019B2CF CRC64;
MSDEITSPTQ STSPTKGDDY GAASIKVLKG LDAVRKRPGM YIGDTDDGSG LHHMVYEVVD
NAIDEALAGH ATLVNVTLHA DGSCSVRDNG RGIPTDIHPT EGISAAEVIM TQLHAGGKFD
QNSYKVSGGL HGVGVSVVNA LSVWLKLQIR RNGKIHEISF THGVADAPLK VVGDCDQESG
TEIRFLPSSE TFTMVEFDFE TLERRLRELA FLNSGVHILL VDERHADIKA VELHYEGGLI
EFVKYIDQSK KALLDTPIYI ASEKDGMSVD VALWWNDSYH EKVLCFTNNI PQRDGGTHLI
GFRSALTRQI NGYAESSGIA KKEKVNLTGD DCREGLTAIL SVKVPDPKFS SQTKDKLVSS
EVRPIVENLV NEGLSTWLEE HPNEAKLLIS KVVEAATARE AARKARELTR RKGALDITSL
PGKLADCQER DPAKSEIFIV EGDSAGGSAK SGRSRQNQAI LPLRGKILNV ERARFDRMLS
SDMIGTLITA LGTSIGKDEF SPDKLRYHKI IIMTDADVDG AHIRTLLLTF FFRQMPELIE
RGHLYIAQPP LYKVSRGKSS QYIKNEAAFE EFLIDTGLEE TTLELSTGEV RAGADLYQLA
KDARVFRQLL NGLHTRYDRN VVEQAAIVGA FNPEAFATQE KAQKIAEAVE HRLNLIADDM
EQGWSGQYIE DGSLCFERIL RGVKDVITLD AGLINSADAR QIDRISQNFS DLYHPPLLLR
RKDKTERIFG PMSLLESIFT NGKKGITLQR YKGLGEMNAE QLWETTLDPN ARSLLQVKIN
DATDADSLFS RLMGDEVEPR RIFIQDNALS VANLDI
//