GYRB_STRPN
ID GYRB_STRPN Reviewed; 648 AA.
AC P0A4L9; P48373;
DT 15-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 15-MAR-2005, sequence version 1.
DT 03-AUG-2022, entry version 111.
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=SP_0806;
OS Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC Streptococcus.
OX NCBI_TaxID=170187;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=533;
RX PubMed=7608096; DOI=10.1128/jb.177.14.4166-4170.1995;
RA Munoz R., Bustamante M., de la Campa A.G.;
RT "Ser-127-to-Leu substitution in the DNA gyrase B subunit of Streptococcus
RT pneumoniae is implicated in novobiocin resistance.";
RL J. Bacteriol. 177:4166-4170(1995).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-334 / TIGR4;
RX PubMed=11463916; DOI=10.1126/science.1061217;
RA Tettelin H., Nelson K.E., Paulsen I.T., Eisen J.A., Read T.D.,
RA Peterson S.N., Heidelberg J.F., DeBoy R.T., Haft D.H., Dodson R.J.,
RA Durkin A.S., Gwinn M.L., Kolonay J.F., Nelson W.C., Peterson J.D.,
RA Umayam L.A., White O., Salzberg S.L., Lewis M.R., Radune D.,
RA Holtzapple E.K., Khouri H.M., Wolf A.M., Utterback T.R., Hansen C.L.,
RA McDonald L.A., Feldblyum T.V., Angiuoli S.V., Dickinson T., Hickey E.K.,
RA Holt I.E., Loftus B.J., Yang F., Smith H.O., Venter J.C., Dougherty B.A.,
RA Morrison D.A., Hollingshead S.K., Fraser C.M.;
RT "Complete genome sequence of a virulent isolate of Streptococcus
RT pneumoniae.";
RL Science 293:498-506(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; X83917; CAA58771.1; -; Genomic_DNA.
DR EMBL; AE005672; AAK74943.1; -; Genomic_DNA.
DR PIR; F95093; F95093.
DR RefSeq; WP_000134039.1; NZ_AKVY01000001.1.
DR AlphaFoldDB; P0A4L9; -.
DR SMR; P0A4L9; -.
DR STRING; 170187.SP_0806; -.
DR BindingDB; P0A4L9; -.
DR ChEMBL; CHEMBL1075021; -.
DR DrugBank; DB01044; Gatifloxacin.
DR DrugCentral; P0A4L9; -.
DR EnsemblBacteria; AAK74943; AAK74943; SP_0806.
DR GeneID; 60234325; -.
DR KEGG; spn:SP_0806; -.
DR eggNOG; COG0187; Bacteria.
DR OMA; LWETTMH; -.
DR PhylomeDB; P0A4L9; -.
DR BioCyc; SPNE170187:G1FZB-825-MON; -.
DR PRO; PR:P0A4L9; -.
DR Proteomes; UP000000585; 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 GO; GO:0046677; P:response to antibiotic; IEA:UniProtKB-KW.
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 Antibiotic resistance; ATP-binding; Cytoplasm; DNA-binding; Isomerase;
KW Magnesium; Metal-binding; Nucleotide-binding; Topoisomerase.
FT CHAIN 1..648
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000145347"
FT DOMAIN 427..541
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 433
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 506
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 506
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 508
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 458
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 461
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT VARIANT 127
FT /note="S -> L (confers novobiocin resistance)"
FT CONFLICT 88
FT /note="D -> G (in Ref. 1; CAA58771)"
FT /evidence="ECO:0000305"
FT CONFLICT 107
FT /note="A -> S (in Ref. 1; CAA58771)"
FT /evidence="ECO:0000305"
FT CONFLICT 304
FT /note="D -> S (in Ref. 1; CAA58771)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 648 AA; 72238 MW; 976A0B030BC892C4 CRC64;
MTEEIKNLQA QDYDASQIQV LEGLEAVRMR PGMYIGSTSK EGLHHLVWEI VDNSIDEALA
GFASHIQVFI EPDDSITVVD DGRGIPVDIQ EKTGRPAVET VFTVLHAGGK FGGGGYKVSG
GLHGVGSSVV NALSTQLDVH VHKNGKIHYQ EYRRGHVVAD LEIVGDTDKT GTTVHFTPDP
KIFTETTIFD FDKLNKRIQE LAFLNRGLQI SITDKRQGLE QTKHYHYEGG IASYVEYINE
NKDVIFDTPI YTDGEMDDIT VEVAMQYTTG YHENVMSFAN NIHTHEGGTH EQGFRTALTR
VINDYARKNK LLKDNEDNLT GEDVREGLTA VISVKHPNPQ FEGQTKTKLG NSEVVKITNR
LFSEAFSDFL MENPQIAKRI VEKGILAAKA RVAAKRAREV TRKKSGLEIS NLPGKLADCS
SNNPAETELF IVEGDSAGGS AKSGRNREFQ AILPIRGKIL NVEKASMDKI LANEEIRSLF
TAMGTGFGAE FDVSKARYQK LVLMTDADVD GAHIRTLLLT LIYRYMKPIL EAGYVYIAQP
PIYGVKVGSE IKEYIQPGAD QEIKLQEALA RYSEGRTKPT IQRYKGLGEM DDHQLWETTM
DPEHRLMARV SVDDAAEADK IFDMLMGDRV EPRREFIEEN AVYSTLDV
