GYRB_RICBR
ID GYRB_RICBR Reviewed; 808 AA.
AC Q1RHT8;
DT 23-JAN-2007, integrated into UniProtKB/Swiss-Prot.
DT 16-MAY-2006, sequence version 1.
DT 03-AUG-2022, entry version 100.
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=RBE_0995;
OS Rickettsia bellii (strain RML369-C).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales;
OC Rickettsiaceae; Rickettsieae; Rickettsia; belli group.
OX NCBI_TaxID=336407;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=RML369-C;
RX PubMed=16703114; DOI=10.1371/journal.pgen.0020076;
RA Ogata H., La Scola B., Audic S., Renesto P., Blanc G., Robert C.,
RA Fournier P.-E., Claverie J.-M., Raoult D.;
RT "Genome sequence of Rickettsia bellii illuminates the role of amoebae in
RT gene exchanges between intracellular pathogens.";
RL PLoS Genet. 2:733-744(2006).
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 -!- 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 -!- SIMILARITY: Belongs to the type II topoisomerase GyrB family.
CC {ECO:0000255|HAMAP-Rule:MF_01898}.
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DR EMBL; CP000087; ABE05076.1; -; Genomic_DNA.
DR RefSeq; WP_011477656.1; NC_007940.1.
DR AlphaFoldDB; Q1RHT8; -.
DR SMR; Q1RHT8; -.
DR STRING; 336407.RBE_0995; -.
DR EnsemblBacteria; ABE05076; ABE05076; RBE_0995.
DR KEGG; rbe:RBE_0995; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_4_1_5; -.
DR OMA; LWETTMH; -.
DR OrthoDB; 205481at2; -.
DR Proteomes; UP000001951; 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 3: Inferred from homology;
KW ATP-binding; Cytoplasm; DNA-binding; Isomerase; Magnesium; Metal-binding;
KW Nucleotide-binding; Topoisomerase.
FT CHAIN 1..808
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000273110"
FT DOMAIN 429..544
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 435
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 509
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 509
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 511
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 460
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 463
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
SQ SEQUENCE 808 AA; 90843 MW; 9A6B883F87D5D26F CRC64;
MSEFEEKLNE SSYGADSIKV LKGLEAVRKR PGMYIGDVGD GSGLHHMIYE VVDNAIDEAL
AGYCDLVRVV LNKNGSVTVS DNGRGIPVEI HEEEGISAAE VIMTQLHAGG KFDQNSYKVS
GGLHGVGVSV VNALSDWLEL RIWRNNTEHL IRFNNGITEA PLAVVKENVD KKGTEVTFFP
SVETFTNIEF DFSIIEHRLR ELAFLNSGVK ILLTDNRFEE VKEVEFYYTG GIEAYVKYLD
RAKHAVHSCI VVNADNTESG ISLELAMHWN DSYHENILCF TNNIRQRDGG THLSAFKSGL
TRVITAYLEN TGLNKKAKNA FSGEDTREGI CCVLSVKVPD PKFSSQTKDK LVSSEVRPIV
ENAVYTKVLE WFEEHPADAK LIINKIMEAA NAREAARKAR ELTRRKSVLE VSNLPGKLAD
CHAKDPAVSE LFIVEGDSAG GTAKQGRDSK IQAILPLRGK ILNVERARFD KMLGSDQIGT
LITALGTGVD NREFSLEKLR YHKVIIMTDA DVDGSHIRTL LLTFFYRHMP ELINKGYLYI
AQPPLYKVKK GASELYLKNE QALQDYLVKS AISDATLTLD NKEQLTNENL EELMSKVIKF
NSLLDHASKK FNRSITEILA INDLLNNKIF DNESDSRLKK ALNALNSLEQ SPDKTDWEVL
KHENKIEFFR FSRGLKERKI LLREQLESFE FINISKLALT IFDVFNKQLK LVVKNQEFDI
LTPSILLNTI IECGKKGISV QRFKGLGEMN SDQLWDTTLD PKKRTLMQVR VAEVDEAEGI
FSTLMGDVVE PRRQFIQSNA LNVVNLDV
