GYRB_CYTHU
ID GYRB_CYTHU Reviewed; 478 AA.
AC Q9LCK1;
DT 01-DEC-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 89.
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 Cytophaga hutchinsonii.
OC Bacteria; Bacteroidetes; Cytophagia; Cytophagales; Cytophagaceae;
OC Cytophaga.
OX NCBI_TaxID=985;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=IAM 12607;
RX PubMed=10555336; DOI=10.1099/00207713-49-4-1551;
RA Suzuki M., Nakagawa Y., Harayama S., Yamamoto S.;
RT "Phylogenetic analysis of genus Marinilabilia and related bacteria based on
RT the amino acid sequences of GyrB and amended description of Marinilabilia
RT salmonicolor with Marinilabilia agarovorans as its subjective synonym.";
RL Int. J. Syst. Bacteriol. 49:1551-1557(1999).
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; AB015037; BAA90686.1; -; Genomic_DNA.
DR AlphaFoldDB; Q9LCK1; -.
DR SMR; Q9LCK1; -.
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_0000145308"
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; 53701 MW; 42DCCEF290C05144 CRC64;
DKDSYKVSGG LHGVGVSCVN ALSTDMKVTV YSHGKVHQQE YKKGIPQYDV KEIGESDLHG
TKVQFLPDDT IFTSSEYKYE TIANRLRELS FLNKGIRITL QDHRQVDAEG KSEIEMFHSE
GGLREFVDYL DSTREKLIPT PLYMESDKGP IPVEVAMLYN TSYSENVFSY VNNINTIEGG
THVAGFRRAL TRTLKSYADK SGMLEKLKME VTGDDFREGL TAVISVKVQE PQFEGQTKTK
LGNSDVMGAV DQVVGEMLNT YLEENPKEAK IIVQKVILAA QARNAARKAR EMVQRKNVLS
GSGLPGKLAD CSESDPEKCE LYLVEGDSAG GSAKQGRDRK YHAILPLRGK ILNVEKAQEH
RIYENDEIKN MITALGVSFG TEEGEKVLNL TKLRYHKVII MTDADIDGSH IRTLILTFFF
RYMRALIDGG HVYIAQPPLY LVKRGKEEKY CWTEEQREAA VKELAKDGKE DSVGIQRY
