GYRB_MYCGE
ID GYRB_MYCGE Reviewed; 650 AA.
AC P47249; Q49307;
DT 01-FEB-1996, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-1996, sequence version 1.
DT 03-AUG-2022, entry version 131.
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=MG003;
OS Mycoplasma genitalium (strain ATCC 33530 / DSM 19775 / NCTC 10195 / G37)
OS (Mycoplasmoides genitalium).
OC Bacteria; Tenericutes; Mollicutes; Mycoplasmataceae; Mycoplasma.
OX NCBI_TaxID=243273;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 33530 / DSM 19775 / NCTC 10195 / G37;
RX PubMed=8083173; DOI=10.1128/jb.176.18.5814-5819.1994;
RA Bailey C.C., Bott K.F.;
RT "An unusual gene containing a dnaJ N-terminal box flanks the putative
RT origin of replication of Mycoplasma genitalium.";
RL J. Bacteriol. 176:5814-5819(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33530 / DSM 19775 / NCTC 10195 / G37;
RX PubMed=7569993; DOI=10.1126/science.270.5235.397;
RA Fraser C.M., Gocayne J.D., White O., Adams M.D., Clayton R.A.,
RA Fleischmann R.D., Bult C.J., Kerlavage A.R., Sutton G.G., Kelley J.M.,
RA Fritchman J.L., Weidman J.F., Small K.V., Sandusky M., Fuhrmann J.L.,
RA Nguyen D.T., Utterback T.R., Saudek D.M., Phillips C.A., Merrick J.M.,
RA Tomb J.-F., Dougherty B.A., Bott K.F., Hu P.-C., Lucier T.S.,
RA Peterson S.N., Smith H.O., Hutchison C.A. III, Venter J.C.;
RT "The minimal gene complement of Mycoplasma genitalium.";
RL Science 270:397-403(1995).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 199-304; 404-507 AND 605-650.
RC STRAIN=ATCC 33530 / DSM 19775 / NCTC 10195 / G37;
RX PubMed=8253680; DOI=10.1128/jb.175.24.7918-7930.1993;
RA Peterson S.N., Hu P.-C., Bott K.F., Hutchison C.A. III;
RT "A survey of the Mycoplasma genitalium genome by using random sequencing.";
RL J. Bacteriol. 175:7918-7930(1993).
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; U09251; AAA57071.1; -; Genomic_DNA.
DR EMBL; L43967; AAC71219.1; -; Genomic_DNA.
DR EMBL; U02187; AAD12471.1; -; Genomic_DNA.
DR EMBL; U02199; AAD12487.1; -; Genomic_DNA.
DR EMBL; U02211; AAD12503.1; -; Genomic_DNA.
DR PIR; C64200; C64200.
DR RefSeq; WP_009885560.1; NZ_AAGX01000001.1.
DR AlphaFoldDB; P47249; -.
DR SMR; P47249; -.
DR STRING; 243273.MG_003; -.
DR EnsemblBacteria; AAC71219; AAC71219; MG_003.
DR KEGG; mge:MG_003; -.
DR eggNOG; COG0187; Bacteria.
DR HOGENOM; CLU_006146_4_1_14; -.
DR OMA; LWETTMH; -.
DR OrthoDB; 205481at2; -.
DR BioCyc; MGEN243273:G1GJ2-3-MON; -.
DR Proteomes; UP000000807; 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; 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..650
FT /note="DNA gyrase subunit B"
FT /id="PRO_0000145319"
FT DOMAIN 435..549
FT /note="Toprim"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT REGION 400..422
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 441
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 514
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 514
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT BINDING 516
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 466
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT SITE 469
FT /note="Interaction with DNA"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
SQ SEQUENCE 650 AA; 73605 MW; 750BA6035A5CB55E CRC64;
MEENNKANIY DSSSIKVLEG LEAVRKRPGM YIGSTGEEGL HHMIWEIVDN SIDEAMGGFA
SFVKLTLEDN FVTRVEDDGR GIPVDIHPKT NRSTVETVFT VLHAGGKFDN DSYKVSGGLH
GVGASVVNAL SSSFKVWVFR QNKKYFLSFS DGGKVIGDLV QEGNSEKEHG TIVEFVPDFS
VMEKSDYKQT VIVSRLQQLA FLNKGIRIDF VDNRKQNPQS FSWKYDGGLV EYIHHLNNEK
EPLFNEVIAD EKTETVKAVN RDENYTVKVE VAFQYNKTYN QSIFSFCNNI NTTEGGTHVE
GFRNALVKII NRFAVENKFL KDSDEKINRD DVCEGLTAII SIKHPNPQYE GQTKKKLGNT
EVRPLVNSVV SEIFERFMLE NPQEANAIIR KTLLAQEARR RSQEARELTR RKSPFDSGSL
PGKLADCTTR DPSISELYIV EGDSAGGTAK TGRDRYFQAI LPLRGKILNV EKSNFEQIFN
NAEISALVMA IGCGIKPDFE LEKLRYSKIV IMTDADVDGA HIRTLLLTFF FRFMYPLVEQ
GNIFIAQPPL YKVSYSHKDL YMHTDVQLEQ WKSQNPNVKF GLQRYKGLGE MDALQLWETT
MDPKVRTLLK VTVEDASIAD KAFSLLMGDE VPPRREFIEK NARSVKNIDI
