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Database: UniProt
Entry: Q59533
LinkDB: Q59533
Original site: Q59533 
ID   GYRB_MYCLE              Reviewed;         678 AA.
AC   Q59533; Q9CDF3;
DT   15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT   27-APR-2001, sequence version 2.
DT   27-MAR-2024, entry version 143.
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, ECO:0000305|PubMed:17325221};
GN   Name=gyrB {ECO:0000255|HAMAP-Rule:MF_01898}; OrderedLocusNames=ML0005;
OS   Mycobacterium leprae (strain TN).
OC   Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Mycobacteriaceae;
OC   Mycobacterium.
OX   NCBI_TaxID=272631;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=8969512; DOI=10.1099/13500872-142-11-3147;
RA   Fsihi H., de Rossi E., Salazar L., Cantoni R., Labo M., Riccardi G.,
RA   Takiff H.E., Eiglmeier K., Bergh S., Cole S.T.;
RT   "Gene arrangement and organization in an approximately 76 kb fragment
RT   encompassing the oriC region of the chromosome of Mycobacterium leprae.";
RL   Microbiology 142:3147-3161(1996).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=TN;
RX   PubMed=11234002; DOI=10.1038/35059006;
RA   Cole S.T., Eiglmeier K., Parkhill J., James K.D., Thomson N.R.,
RA   Wheeler P.R., Honore N., Garnier T., Churcher C.M., Harris D.E.,
RA   Mungall K.L., Basham D., Brown D., Chillingworth T., Connor R.,
RA   Davies R.M., Devlin K., Duthoy S., Feltwell T., Fraser A., Hamlin N.,
RA   Holroyd S., Hornsby T., Jagels K., Lacroix C., Maclean J., Moule S.,
RA   Murphy L.D., Oliver K., Quail M.A., Rajandream M.A., Rutherford K.M.,
RA   Rutter S., Seeger K., Simon S., Simmonds M., Skelton J., Squares R.,
RA   Squares S., Stevens K., Taylor K., Whitehead S., Woodward J.R.,
RA   Barrell B.G.;
RT   "Massive gene decay in the leprosy bacillus.";
RL   Nature 409:1007-1011(2001).
RN   [3]
RP   FUNCTION, ACTIVITY REGULATION, AND SUBUNIT.
RX   PubMed=17325221; DOI=10.1128/aac.01282-06;
RA   Matrat S., Petrella S., Cambau E., Sougakoff W., Jarlier V., Aubry A.;
RT   "Expression and purification of an active form of the Mycobacterium leprae
RT   DNA gyrase and its inhibition by quinolones.";
RL   Antimicrob. Agents Chemother. 51:1643-1648(2007).
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       (PubMed:17325221). Negative supercoiling favors strand separation, and
CC       DNA replication, transcription, recombination and repair, all of which
CC       involve strand separation. Also able to catalyze the interconversion of
CC       other topological isomers of dsDNA rings, including catenanes and
CC       knotted rings. Type II topoisomerases break and join 2 DNA strands
CC       simultaneously in an ATP-dependent manner. {ECO:0000255|HAMAP-
CC       Rule:MF_01898, ECO:0000269|PubMed:17325221}.
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-Rule:MF_01898,
CC         ECO:0000305|PubMed:17325221};
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   -!- ACTIVITY REGULATION: DNA supercoiling is inhibited by fluoroquinolones;
CC       IC(50) 1 ug/ml for sitafloxacin (PubMed:17325221).
CC       {ECO:0000269|PubMed:17325221}.
CC   -!- SUBUNIT: Heterotetramer, composed of two GyrA and two GyrB chains
CC       (PubMed:17325221). In the heterotetramer, GyrA contains the active site
CC       tyrosine that forms a transient covalent intermediate with the DNA,
CC       while GyrB binds cofactors catalyzes ATP hydrolysis.
CC       {ECO:0000255|HAMAP-Rule:MF_01898, ECO:0000269|PubMed:17325221}.
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}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=CAA94712.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR   EMBL; Z70722; CAA94712.1; ALT_INIT; Genomic_DNA.
DR   EMBL; AL583917; CAC29513.1; -; Genomic_DNA.
DR   PIR; E86909; E86909.
DR   RefSeq; NP_301133.1; NC_002677.1.
DR   RefSeq; WP_010907458.1; NC_002677.1.
DR   AlphaFoldDB; Q59533; -.
DR   SMR; Q59533; -.
DR   STRING; 272631.gene:17573814; -.
DR   KEGG; mle:ML0005; -.
DR   PATRIC; fig|272631.5.peg.5; -.
DR   Leproma; ML0005; -.
DR   eggNOG; COG0187; Bacteria.
DR   HOGENOM; CLU_006146_4_1_11; -.
DR   OrthoDB; 9802808at2; -.
DR   Proteomes; UP000000806; 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; IDA:UniProtKB.
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   CDD; cd16928; HATPase_GyrB-like; 1.
DR   CDD; cd00822; TopoII_Trans_DNA_gyrase; 1.
DR   Gene3D; 3.30.230.10; -; 1.
DR   Gene3D; 3.40.50.670; -; 1.
DR   Gene3D; 3.30.565.10; Histidine kinase-like ATPase, C-terminal domain; 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_Su5_D2-typ_SF.
DR   InterPro; IPR014721; Ribsml_uS5_D2-typ_fold_subgr.
DR   InterPro; IPR001241; Topo_IIA.
DR   InterPro; IPR013760; Topo_IIA-like_dom_sf.
DR   InterPro; IPR000565; Topo_IIA_B.
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   NCBIfam; TIGR01059; gyrB; 1.
DR   PANTHER; PTHR45866:SF1; DNA GYRASE SUBUNIT B, MITOCHONDRIAL; 1.
DR   PANTHER; PTHR45866; DNA GYRASE/TOPOISOMERASE SUBUNIT B; 1.
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   PRINTS; PR01159; DNAGYRASEB.
DR   PRINTS; PR00418; TPI2FAMILY.
DR   SMART; SM00387; HATPase_c; 1.
DR   SMART; SM00433; TOP2c; 1.
DR   SUPFAM; SSF55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase; 1.
DR   SUPFAM; SSF54211; Ribosomal protein S5 domain 2-like; 1.
DR   SUPFAM; SSF56719; Type II DNA topoisomerase; 1.
DR   PROSITE; PS00177; TOPOISOMERASE_II; 1.
DR   PROSITE; PS50880; TOPRIM; 1.
PE   1: Evidence at protein level;
KW   ATP-binding; Cytoplasm; DNA-binding; Isomerase; Magnesium; Metal-binding;
KW   Nucleotide-binding; Reference proteome; Topoisomerase.
FT   CHAIN           1..678
FT                   /note="DNA gyrase subunit B"
FT                   /id="PRO_0000145321"
FT   DOMAIN          456..570
FT                   /note="Toprim"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT   BINDING         462
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         535
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         535
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT   BINDING         537
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT   SITE            487
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
FT   SITE            490
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01898"
SQ   SEQUENCE   678 AA;  74674 MW;  F56141BCEF0A9DDA CRC64;
     MAAQRKAQDE YGAASITILE GLEAVRKRPG MYVGSTGERG LHHLIWEVVD NSVDEAMAGY
     ATQVDVRLFD DGSVEVADNG RGIPVAVHAT GVPTVDVVMT QLHAGGKFGG KDSGYNVSGG
     LHGVGVSVVN ALSTRVEVDI KRDGYEWSQF YDKAVPGILK QGEATEATGT TIRFWADPDI
     FETTKYDFGT VARRIQEVAF LNKGLTINLV DERVKQDEVV DDVVSDTAEA PVAMTVEEKS
     TESSAPHKVR HRTFHYPGGL VDFVKHINRT KTPIQQSIID FDGKGAGHEV EVAMQWNGGY
     SESVHTFANT INTHEGGTHE EGFRSALTSV VNKYAKDKKL LKDKDPNLTG DDIREGLAAV
     ISVKVSEPQF EGQTKTKLGN TEVKSFVQRV CNEQLIHWFE ANPVDAKAVV NKAISSAQAR
     IAARKARELV RRKSATDLGG LPGKLADCRS TDPRSSELYV VEGDSAGGSA KSGRDSMFQA
     ILPLRGKIIN VEKARIDRVL KNTEVQAIIT ALGTGIHDEF DISRLRYHKI VLMADADVDG
     QHISTLLLTL LFRFMRPLIE HGYVFLAQPP LYKLKWQRMD PEFAYSDSER DGLLETGLKL
     GKKINKEDGI QRYKGLGEMD AKELWETTMD PSVRVLRQVT LDDAAAADEL FSILMGEDVD
     ARRSFITRNA KDVRFLDV
//
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