GYRB_CAUVN
ID GYRB_CAUVN Reviewed; 805 AA.
AC B8GXQ0; P48197;
DT 16-JUN-2009, integrated into UniProtKB/Swiss-Prot.
DT 03-MAR-2009, sequence version 1.
DT 03-AUG-2022, entry version 98.
DE RecName: Full=DNA gyrase subunit B {ECO:0000255|HAMAP-Rule:MF_01898};
DE EC=5.6.2.2 {ECO:0000255|HAMAP-Rule:MF_01898};
GN Name=gyrB {ECO:0000255|HAMAP-Rule:MF_01898}; OrderedLocusNames=CCNA_00159;
OS Caulobacter vibrioides (strain NA1000 / CB15N) (Caulobacter crescentus).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Caulobacterales;
OC Caulobacteraceae; Caulobacter.
OX NCBI_TaxID=565050;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NA1000 / CB15N;
RX PubMed=20472802; DOI=10.1128/jb.00255-10;
RA Marks M.E., Castro-Rojas C.M., Teiling C., Du L., Kapatral V.,
RA Walunas T.L., Crosson S.;
RT "The genetic basis of laboratory adaptation in Caulobacter crescentus.";
RL J. Bacteriol. 192:3678-3688(2010).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-196, AND INDUCTION.
RC STRAIN=NA1000 / CB15N;
RX PubMed=9079919; DOI=10.1128/jb.179.7.2319-2330.1997;
RA Roberts R.C., Shapiro L.;
RT "Transcription of genes encoding DNA replication proteins is coincident
RT with cell cycle control of DNA replication in Caulobacter crescentus.";
RL J. Bacteriol. 179:2319-2330(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-187.
RX PubMed=8226640; DOI=10.1128/jb.175.21.6970-6981.1993;
RA Rizzo M.F., Shapiro L., Gober J.;
RT "Asymmetric expression of the gyrase B gene from the replication-competent
RT chromosome in the Caulobacter crescentus predivisional cell.";
RL J. Bacteriol. 175:6970-6981(1993).
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:0000255|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:0000255|HAMAP-
CC Rule:MF_01898};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01898};
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000255|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:0000255|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:0000255|HAMAP-Rule:MF_01898}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_01898}.
CC -!- INDUCTION: Transcription is induced just prior to the onset of DNA
CC replication, at the swarmer-to-stalked-cell transition, lasts through
CC the stalked-cell phase and then decreases in the predivisional cell.
CC {ECO:0000269|PubMed:9079919}.
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:0000255|HAMAP-
CC Rule:MF_01898}.
CC -!- MISCELLANEOUS: This protein may be 16 amino acids longer at the N-
CC terminus, in which case it would overlap with the stop codon for recF,
CC the upstream gene, with which is might be translationally coupled
CC (PubMed:9079919). {ECO:0000305|PubMed:9079919}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase GyrB family.
CC {ECO:0000255|HAMAP-Rule:MF_01898}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAB51450.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=AAC43046.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
CC Sequence=ACL93626.2; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR EMBL; CP001340; ACL93626.2; ALT_INIT; Genomic_DNA.
DR EMBL; U37793; AAB51450.1; ALT_INIT; Genomic_DNA.
DR EMBL; U00592; AAC43046.2; ALT_INIT; Genomic_DNA.
DR RefSeq; YP_002515534.4; NC_011916.1.
DR AlphaFoldDB; B8GXQ0; -.
DR SMR; B8GXQ0; -.
DR PRIDE; B8GXQ0; -.
DR EnsemblBacteria; ACL93626; ACL93626; CCNA_00159.
DR GeneID; 7332413; -.
DR KEGG; ccs:CCNA_00159; -.
DR PATRIC; fig|565050.3.peg.157; -.
DR HOGENOM; CLU_006146_0_1_5; -.
DR OMA; LWETTMH; -.
DR OrthoDB; 205481at2; -.
DR PhylomeDB; B8GXQ0; -.
DR Proteomes; UP000001364; 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; cd03366; TOPRIM_TopoIIA_GyrB; 1.
DR Gene3D; 3.30.230.10; -; 1.
DR Gene3D; 3.30.565.10; -; 1.
DR Gene3D; 3.40.50.670; -; 2.
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_S5_D2-typ_fold.
DR InterPro; IPR014721; Ribosomal_S5_D2-typ_fold_subgr.
DR InterPro; IPR001241; Topo_IIA.
DR InterPro; IPR013760; Topo_IIA-like_dom_sf.
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 Pfam; PF00204; DNA_gyraseB; 1.
DR Pfam; PF00986; DNA_gyraseB_C; 1.
DR Pfam; PF02518; HATPase_c; 1.
DR Pfam; PF01751; Toprim; 1.
DR SMART; SM00387; HATPase_c; 1.
DR SMART; SM00433; TOP2c; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR SUPFAM; SSF55874; SSF55874; 1.
DR SUPFAM; SSF56719; SSF56719; 1.
DR TIGRFAMs; TIGR01059; gyrB; 1.
DR PROSITE; PS00177; TOPOISOMERASE_II; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 2: Evidence at transcript level;
KW ATP-binding; Cytoplasm; DNA-binding; Isomerase; Magnesium; Metal-binding;
KW Nucleotide-binding; Reference proteome; Topoisomerase.
FT CHAIN 1..805
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000378314"
FT DOMAIN 435..550
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 441
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|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:0000255|HAMAP-Rule:MF_01898"
FT BINDING 515
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 517
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 466
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 469
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT CONFLICT 127
FT /note="V -> D (in Ref. 3; AAC43046)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 805 AA; 88212 MW; FD39481D9A64ADE0 CRC64;
MTTEEAAAQY GADSIKVLKG LDAVRKRPGM YIGDTDDGSG LHHMVYEVVD NAIDEALAGH
ATKVQVILNA DGSVTVTDDG RGIPVDMHEG EGVSAAEVIM TQLHAGGKFD QNSYKVSGGL
HGVGVSVVNA LSDWLELLIH RNGKVHQMRF ERGDAVTSLK VTGDSPVRTE GPKAGETLTG
TEVTFFPSKD TFAFIEFDRK TLEHRLRELA FLNSGVTIWF KDHRDVEPWE EKLFYEGGIE
AFVRHLDKAK TPLLKAPIAV KGVKDKVEID LALWWNDSYH EQMLCFTNNI PQRDGGTHLS
AFRAALTRII TSYAESSGIL KKEKVSLGGE DSREGLTCVL SVKVPDPKFS SQTKDKLVSS
EVRPAVEGLV SEGLSTWFEE HPNEAKAIVT KIAEAAAARE AARKARELTR RKSALDITSL
PGKLADCSER DPAKSEIFIV EGDSAGGSAK QARNRDNQAV LPLRGKILNV ERARFDKMLS
SDQIGTLITA LGAGIGRDDF NPDKVRYHKI VLMTDADVDG AHIRTLLLTF FYRQMPELIE
RGYIYIAQPP LYKASKGKSS RYLKDDAEMD AFLVDEGVDG AELDLASGER MTGQDLLALV
QTCRSAKANI DRLAARAPAT AIEQAALSGL LGESPNAAAA ATRLDLYAEE GDGPWSGERG
DTGFVFSRVR RGVSERVVLD DVLLHAADAR RLAERAVKLT EIFSGRAIFR RKDKSTTVRG
PLDLVNAVLD AGRKGLTIQR YKGLGEMNPD QLWETTLDAE ARTLLQVRVN HADDADDMFS
RLMGDLVEPR REFIQENALD AEVDV
