GYRB_CLOAB
ID GYRB_CLOAB Reviewed; 637 AA.
AC P94604;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 29-AUG-2001, sequence version 2.
DT 03-AUG-2022, entry version 135.
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=CA_C0006;
OS Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / LMG 5710
OS / VKM B-1787).
OC Bacteria; Firmicutes; Clostridia; Eubacteriales; Clostridiaceae;
OC Clostridium.
OX NCBI_TaxID=272562;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787;
RA Ullmann S., Duerre P.;
RT "Nucleotide sequence and molecular characterization of the DNA gyrase genes
RT from Clostridium acetobutylicum.";
RL Anaerobe 2:239-248(1996).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 824 / DSM 792 / JCM 1419 / LMG 5710 / VKM B-1787;
RX PubMed=11466286; DOI=10.1128/jb.183.16.4823-4838.2001;
RA Noelling J., Breton G., Omelchenko M.V., Makarova K.S., Zeng Q., Gibson R.,
RA Lee H.M., Dubois J., Qiu D., Hitti J., Wolf Y.I., Tatusov R.L., Sabathe F.,
RA Doucette-Stamm L.A., Soucaille P., Daly M.J., Bennett G.N., Koonin E.V.,
RA Smith D.R.;
RT "Genome sequence and comparative analysis of the solvent-producing
RT bacterium Clostridium acetobutylicum.";
RL J. Bacteriol. 183:4823-4838(2001).
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; U35453; AAB41130.1; -; Genomic_DNA.
DR EMBL; AE001437; AAK77993.1; -; Genomic_DNA.
DR PIR; F96900; F96900.
DR PIR; T46555; T46555.
DR RefSeq; NP_346653.1; NC_003030.1.
DR RefSeq; WP_010963335.1; NC_003030.1.
DR AlphaFoldDB; P94604; -.
DR SMR; P94604; -.
DR STRING; 272562.CA_C0006; -.
DR EnsemblBacteria; AAK77993; AAK77993; CA_C0006.
DR GeneID; 44996479; -.
DR KEGG; cac:CA_C0006; -.
DR PATRIC; fig|272562.8.peg.185; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_4_1_9; -.
DR OMA; LWETTMH; -.
DR OrthoDB; 205481at2; -.
DR Proteomes; UP000000814; 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; -; 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_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; Reference proteome; Topoisomerase.
FT CHAIN 1..637
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000145306"
FT DOMAIN 420..534
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 426
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 499
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 499
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 501
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 451
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 454
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT CONFLICT 32
FT /note="S -> T (in Ref. 1; AAB41130)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 637 AA; 71614 MW; BF10BDEA0A86DDEA CRC64;
MSEKNEIYDE SQIQVLEGLE AVRKRPGMYI GSTGTRGLHH LVYEIVDNSI DEALAGYCSH
IKVFIHKDNS VTVSDDGRGM PIGIHHKMKK PTVEVIMTIL HAGGKFGGGA YRVSGGLHGV
GASVVNALSE TCEVEVKTEG HIWKQTYHRG KVASPFEKIG DSDEHGTKIY FKPDPEIFED
TEYDYDTLSQ RLRELAFLNK GIKIELTDER HDKNEIFHYE GGLKSFVSYL NRNKEVVFKE
PIYVEGSIDS NYSVEIALQY NDGYNENIFS FANNIHTIEG GTHLAGFKTA LTRVINDYAK
KFGYLKENDK NLSGEDIREG LTAVVSVKLT EPQFEGQTKT KLGNTEVRGI VDSIISERVS
TYLEENPQIG KLVIDKALVA SRAREAAKKA REITRRKSVL ESTSLPGKLA DCSSKDAEEC
EIYIVEGDSA GGSAKQGRNR RFQAILPLRG KIMNVEKQRI DKILNSEEIK AMATAFGGGI
GKDFDVSKLR YHKIIIMTDA DVDGAHIRTL ILTFFYRYMT ELISEGHVFI AQPPLYKVTK
TRKEYYAYSD KELEDVLQDV GGKDKNTDIQ RYKGLGEMNP EQLWETTMNP EQRTLIKVNI
EDAMAADEIF TILMGDKVDP RRKFIEENAT KVVNLDV
