GYRB_EISEL
ID GYRB_EISEL Reviewed; 478 AA.
AC Q9FAX1;
DT 09-MAY-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2001, sequence version 1.
DT 03-AUG-2022, entry version 78.
DE RecName: Full=DNA gyrase subunit B;
DE EC=5.6.2.2 {ECO:0000255|PROSITE-ProRule:PRU00995};
DE Flags: Fragment;
GN Name=gyrB;
OS Eisenibacter elegans (Flexibacter elegans).
OC Bacteria; Bacteroidetes; Cytophagia; Cytophagales; Microscillaceae;
OC Eisenibacter.
OX NCBI_TaxID=997;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 23112 / DSM 3317 / JCM 21159 / LMG 10750 / NBRC 15055 / NCIMB
RC 1385 / LMG 10750 / NZ-1 / Fx a2;
RA Suzuki M., Yamaguchi K.;
RT "Phylogenetic analysis and taxonomic study of marine Cytophaga like
RT bacteria. Proposal of Haerentibaculum gen. nov. with Haerentibaculum
RT maritimum comb. nov. and Haerentibaculum ovolyticus comb. nov., and two new
RT species.";
RL Submitted (SEP-1999) to the EMBL/GenBank/DDBJ databases.
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.
CC {ECO:0000250|UniProtKB:P0AES6}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP-dependent breakage, passage and rejoining of double-
CC stranded DNA.; EC=5.6.2.2; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU00995};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00995};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00995};
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU00995};
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|PROSITE-
CC ProRule:PRU00995};
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:0000250|UniProtKB:P0AES6}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000250|UniProtKB:P0AES6}.
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.
CC {ECO:0000250|UniProtKB:P0AES6}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase GyrB family.
CC {ECO:0000305}.
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DR EMBL; AB032580; BAB13318.1; -; Genomic_DNA.
DR AlphaFoldDB; Q9FAX1; -.
DR SMR; Q9FAX1; -.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
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-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006265; P:DNA topological change; IEA:InterPro.
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 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; PF01751; Toprim; 1.
DR SMART; SM00433; TOP2c; 1.
DR SUPFAM; SSF54211; SSF54211; 1.
DR SUPFAM; SSF55874; SSF55874; 1.
DR SUPFAM; SSF56719; SSF56719; 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..>478
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000145311"
FT DOMAIN 319..438
FT /note="Toprim"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 325
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 403
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 403
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT BINDING 405
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 350
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT SITE 353
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00995"
FT NON_TER 1
FT NON_TER 478
SQ SEQUENCE 478 AA; 53456 MW; FE90B4C93D9925EE CRC64;
DKDTYKVSGG LHGVGVSCVN ALSSLLVATV HREGKVFQQK YSTGNPQGAV EVVGQSDRTG
TTIYFEPDAT IFATTEYKYE TVSKRLRELS YLNKGIRLTL TDLRETDEQG RHLYEEFFSE
GGLKEFVEHL DSTRQPLLPA PIHVEKTDGD IPVEVALIYN NSYSENVFSY VNNINTHEGG
THVSGFRRAL TRTLKSYADK SGMLEKAKVE ITGDDFREGL TAVISIKVAE PQFEGQTKTK
LGNSDAIGAV DNAVSEILGY YLEENPREAK LIIQKVILAA QARQAARKAR EMVQRKNVMG
GTSLPGKLAD CSDTNPERCE LYLVEGDSAG GSAKQGRDRS FQAILPLRGK ILNVEKAQEY
KIYDNEEIKN MITAMGVTFG TEEDSKALNL TKLRYHKIII MTDADVDGSH IRTLILTFFF
RYMRELIEQG YLYVALPPLY IVKKGKEERY AWSDAERDAI IREIAPEGKE DSVGIQRY
