GYRB_STRCO
ID GYRB_STRCO Reviewed; 686 AA.
AC P35886;
DT 01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-1994, sequence version 1.
DT 03-AUG-2022, entry version 140.
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=SCO3874;
GN ORFNames=SCH18.11c;
OS Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145).
OC Bacteria; Actinobacteria; Streptomycetales; Streptomycetaceae;
OC Streptomyces; Streptomyces albidoflavus group.
OX NCBI_TaxID=100226;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=A3(2) / NRRL B-16638;
RX PubMed=7828880; DOI=10.1016/0378-1119(94)90628-9;
RA Calcutt M.J.;
RT "Gene organization in the dnaA-gyrA region of the Streptomyces coelicolor
RT chromosome.";
RL Gene 151:23-28(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-471 / A3(2) / M145;
RX PubMed=12000953; DOI=10.1038/417141a;
RA Bentley S.D., Chater K.F., Cerdeno-Tarraga A.-M., Challis G.L.,
RA Thomson N.R., James K.D., Harris D.E., Quail M.A., Kieser H., Harper D.,
RA Bateman A., Brown S., Chandra G., Chen C.W., Collins M., Cronin A.,
RA Fraser A., Goble A., Hidalgo J., Hornsby T., Howarth S., Huang C.-H.,
RA Kieser T., Larke L., Murphy L.D., Oliver K., O'Neil S., Rabbinowitsch E.,
RA Rajandream M.A., Rutherford K.M., Rutter S., Seeger K., Saunders D.,
RA Sharp S., Squares R., Squares S., Taylor K., Warren T., Wietzorrek A.,
RA Woodward J.R., Barrell B.G., Parkhill J., Hopwood D.A.;
RT "Complete genome sequence of the model actinomycete Streptomyces coelicolor
RT A3(2).";
RL Nature 417:141-147(2002).
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; L27063; AAA65215.1; -; Genomic_DNA.
DR EMBL; AL939118; CAB92994.1; -; Genomic_DNA.
DR RefSeq; NP_628061.1; NC_003888.3.
DR RefSeq; WP_011029285.1; NC_003888.3.
DR AlphaFoldDB; P35886; -.
DR SMR; P35886; -.
DR STRING; 100226.SCO3874; -.
DR GeneID; 1099310; -.
DR KEGG; sco:SCO3874; -.
DR PATRIC; fig|100226.15.peg.3947; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_4_1_11; -.
DR InParanoid; P35886; -.
DR OMA; LWETTMH; -.
DR PhylomeDB; P35886; -.
DR Proteomes; UP000001973; 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:0034335; F:DNA negative supercoiling activity; IEA:UniProt.
DR GO; GO:0003918; F:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006265; P:DNA topological change; IBA:GO_Central.
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..686
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000145346"
FT DOMAIN 465..579
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT REGION 1..29
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 471
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 544
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 544
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 546
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 496
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 499
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
SQ SEQUENCE 686 AA; 75464 MW; 50333794CBC83866 CRC64;
MADSGNPNEN NPSTDTGVND AVSTSHGDAS ASYDASAITV LEGLDAVRKR PGMYIGSTGE
RGLHHLVQEV VDNSVDEALA GHADTIDVTI LPDGGVRVVD NGRGIPVGIV PSEGKPAVEV
VLTVLHAGGK FGGGGYAVSG GLHGVGVSVV NALSTRVAVE VKTDGYRWTQ EYKLGVPTAS
LARHEATEET GTTVTFWADG DIFETTDYSF ETLSRRFQEM AFLNKGLKIN LTDERESAKA
TAGADEAGED EKHEVKSVSY HYEGGIVDFV TYLNSRKGEL VHPTVIDLEA EDKDKSLSLE
VAMQWNGGYT EGVYSFANII HTHEGGTHEE GFRAALTSLI NKYARDKKLL REKDDNLTGD
DIREGLTAII SVKLAEPQFE GQTKTKLGNT EVKTFVQKVV YEHLTDWLDR NPNEAADIIR
KGIQAAHARV AARKARDLTR RKGLLESASL PGKLSDCQSN DPTKCEIFIV EGDSAGGSAK
SGRNPQYQAI LPIRGKILNV EKARIDRILQ NQEIQAMISA FGTGVHEDFD IEKLRYHKII
LMADADVDGQ HINTLLLTFL FRFMRPLVES GHVYLSRPPL YKIKWGRDDF EYAYSDRERD
ALIEMGRQAG KRIREDSVQR FKGLGEMNAE ELRITTMDQE HRVLGQVTLD DAAQADDLFS
VLMGEDVEAR RAFIQRNAKD VRFLDI
