GYRB_MYCLE
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 03-AUG-2022, entry version 135.
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; Actinobacteria; Corynebacteriales; 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.ML0005; -.
DR EnsemblBacteria; CAC29513; CAC29513; CAC29513.
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 OMA; LWETTMH; -.
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 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 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 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
