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TOP1_XYLFA
ID   TOP1_XYLFA              Reviewed;         815 AA.
AC   Q9PEV8;
DT   16-JUN-2003, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2000, sequence version 1.
DT   03-AUG-2022, entry version 120.
DE   RecName: Full=DNA topoisomerase 1 {ECO:0000255|HAMAP-Rule:MF_00952};
DE            EC=5.6.2.1 {ECO:0000255|HAMAP-Rule:MF_00952};
DE   AltName: Full=DNA topoisomerase I {ECO:0000255|HAMAP-Rule:MF_00952};
DE   AltName: Full=Omega-protein;
DE   AltName: Full=Relaxing enzyme;
DE   AltName: Full=Swivelase;
DE   AltName: Full=Untwisting enzyme;
GN   Name=topA {ECO:0000255|HAMAP-Rule:MF_00952}; OrderedLocusNames=XF_0920;
OS   Xylella fastidiosa (strain 9a5c).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Xanthomonadales;
OC   Xanthomonadaceae; Xylella.
OX   NCBI_TaxID=160492;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=9a5c;
RX   PubMed=10910347; DOI=10.1038/35018003;
RA   Simpson A.J.G., Reinach F.C., Arruda P., Abreu F.A., Acencio M.,
RA   Alvarenga R., Alves L.M.C., Araya J.E., Baia G.S., Baptista C.S.,
RA   Barros M.H., Bonaccorsi E.D., Bordin S., Bove J.M., Briones M.R.S.,
RA   Bueno M.R.P., Camargo A.A., Camargo L.E.A., Carraro D.M., Carrer H.,
RA   Colauto N.B., Colombo C., Costa F.F., Costa M.C.R., Costa-Neto C.M.,
RA   Coutinho L.L., Cristofani M., Dias-Neto E., Docena C., El-Dorry H.,
RA   Facincani A.P., Ferreira A.J.S., Ferreira V.C.A., Ferro J.A., Fraga J.S.,
RA   Franca S.C., Franco M.C., Frohme M., Furlan L.R., Garnier M., Goldman G.H.,
RA   Goldman M.H.S., Gomes S.L., Gruber A., Ho P.L., Hoheisel J.D.,
RA   Junqueira M.L., Kemper E.L., Kitajima J.P., Krieger J.E., Kuramae E.E.,
RA   Laigret F., Lambais M.R., Leite L.C.C., Lemos E.G.M., Lemos M.V.F.,
RA   Lopes S.A., Lopes C.R., Machado J.A., Machado M.A., Madeira A.M.B.N.,
RA   Madeira H.M.F., Marino C.L., Marques M.V., Martins E.A.L., Martins E.M.F.,
RA   Matsukuma A.Y., Menck C.F.M., Miracca E.C., Miyaki C.Y.,
RA   Monteiro-Vitorello C.B., Moon D.H., Nagai M.A., Nascimento A.L.T.O.,
RA   Netto L.E.S., Nhani A. Jr., Nobrega F.G., Nunes L.R., Oliveira M.A.,
RA   de Oliveira M.C., de Oliveira R.C., Palmieri D.A., Paris A., Peixoto B.R.,
RA   Pereira G.A.G., Pereira H.A. Jr., Pesquero J.B., Quaggio R.B.,
RA   Roberto P.G., Rodrigues V., de Rosa A.J.M., de Rosa V.E. Jr., de Sa R.G.,
RA   Santelli R.V., Sawasaki H.E., da Silva A.C.R., da Silva A.M.,
RA   da Silva F.R., Silva W.A. Jr., da Silveira J.F., Silvestri M.L.Z.,
RA   Siqueira W.J., de Souza A.A., de Souza A.P., Terenzi M.F., Truffi D.,
RA   Tsai S.M., Tsuhako M.H., Vallada H., Van Sluys M.A., Verjovski-Almeida S.,
RA   Vettore A.L., Zago M.A., Zatz M., Meidanis J., Setubal J.C.;
RT   "The genome sequence of the plant pathogen Xylella fastidiosa.";
RL   Nature 406:151-159(2000).
CC   -!- FUNCTION: Releases the supercoiling and torsional tension of DNA, which
CC       is introduced during the DNA replication and transcription, by
CC       transiently cleaving and rejoining one strand of the DNA duplex.
CC       Introduces a single-strand break via transesterification at a target
CC       site in duplex DNA. The scissile phosphodiester is attacked by the
CC       catalytic tyrosine of the enzyme, resulting in the formation of a DNA-
CC       (5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH
CC       DNA strand. The free DNA strand then undergoes passage around the
CC       unbroken strand, thus removing DNA supercoils. Finally, in the
CC       religation step, the DNA 3'-OH attacks the covalent intermediate to
CC       expel the active-site tyrosine and restore the DNA phosphodiester
CC       backbone. {ECO:0000255|HAMAP-Rule:MF_00952}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP-independent breakage of single-stranded DNA, followed by
CC         passage and rejoining.; EC=5.6.2.1; Evidence={ECO:0000255|HAMAP-
CC         Rule:MF_00952};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00952};
CC       Note=Binds two Mg(2+) per subunit. {ECO:0000255|HAMAP-Rule:MF_00952};
CC   -!- SUBUNIT: Monomer. {ECO:0000255|HAMAP-Rule:MF_00952}.
CC   -!- SIMILARITY: Belongs to the type IA topoisomerase family.
CC       {ECO:0000255|HAMAP-Rule:MF_00952}.
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DR   EMBL; AE003849; AAF83730.1; -; Genomic_DNA.
DR   PIR; B82746; B82746.
DR   RefSeq; WP_010893440.1; NC_002488.3.
DR   AlphaFoldDB; Q9PEV8; -.
DR   SMR; Q9PEV8; -.
DR   STRING; 160492.XF_0920; -.
DR   EnsemblBacteria; AAF83730; AAF83730; XF_0920.
DR   KEGG; xfa:XF_0920; -.
DR   eggNOG; COG0550; Bacteria.
DR   eggNOG; COG1754; Bacteria.
DR   HOGENOM; CLU_002929_0_1_6; -.
DR   OMA; PECKYTR; -.
DR   Proteomes; UP000000812; Chromosome.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0003917; F:DNA topoisomerase type I (single strand cut, ATP-independent) 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   CDD; cd00186; TOP1Ac; 1.
DR   CDD; cd03363; TOPRIM_TopoIA_TopoI; 1.
DR   Gene3D; 1.10.290.10; -; 1.
DR   Gene3D; 1.10.460.10; -; 1.
DR   Gene3D; 2.70.20.10; -; 1.
DR   HAMAP; MF_00952; Topoisom_1_prok; 1.
DR   InterPro; IPR000380; Topo_IA.
DR   InterPro; IPR003601; Topo_IA_2.
DR   InterPro; IPR023406; Topo_IA_AS.
DR   InterPro; IPR013497; Topo_IA_cen.
DR   InterPro; IPR013824; Topo_IA_cen_sub1.
DR   InterPro; IPR013825; Topo_IA_cen_sub2.
DR   InterPro; IPR013826; Topo_IA_cen_sub3.
DR   InterPro; IPR023405; Topo_IA_core_domain.
DR   InterPro; IPR003602; Topo_IA_DNA-bd_dom.
DR   InterPro; IPR005733; TopoI_bac-type.
DR   InterPro; IPR028612; Topoisom_1_IA.
DR   InterPro; IPR025589; Toprim_C_rpt.
DR   InterPro; IPR006171; TOPRIM_domain.
DR   InterPro; IPR034149; TOPRIM_TopoI.
DR   PANTHER; PTHR42785; PTHR42785; 2.
DR   Pfam; PF01131; Topoisom_bac; 1.
DR   Pfam; PF01751; Toprim; 1.
DR   Pfam; PF13368; Toprim_C_rpt; 3.
DR   PRINTS; PR00417; PRTPISMRASEI.
DR   SMART; SM00437; TOP1Ac; 1.
DR   SMART; SM00436; TOP1Bc; 1.
DR   SMART; SM00493; TOPRIM; 1.
DR   SUPFAM; SSF56712; SSF56712; 1.
DR   TIGRFAMs; TIGR01051; topA_bact; 1.
DR   PROSITE; PS00396; TOPOISOMERASE_I_PROK; 1.
DR   PROSITE; PS50880; TOPRIM; 1.
PE   3: Inferred from homology;
KW   DNA-binding; Isomerase; Magnesium; Metal-binding; Reference proteome;
KW   Topoisomerase.
FT   CHAIN           1..815
FT                   /note="DNA topoisomerase 1"
FT                   /id="PRO_0000145172"
FT   DOMAIN          3..119
FT                   /note="Toprim"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT   REGION          167..172
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT   REGION          760..815
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        770..809
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        308
FT                   /note="O-(5'-phospho-DNA)-tyrosine intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT   BINDING         9
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_00952"
FT   BINDING         82
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_00952"
FT   BINDING         82
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT   BINDING         84
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT   SITE            33
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT   SITE            143
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT   SITE            144
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT   SITE            147
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT   SITE            159
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT   SITE            310
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
FT   SITE            505
FT                   /note="Interaction with DNA"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00952"
SQ   SEQUENCE   815 AA;  91803 MW;  65BC01306E1EB1C5 CRC64;
     MPKHLLIVES PAKAKTINKY LGKDFTVLAS YGHVRDLVPK EGAVDPENGF AMRYDLIDKN
     EKHVEAITKA AKTADSIYLA TDPDREGEAI SWHISEILKE RGLLKDKPMQ RIVFTEITPR
     AIKEAIQKPR MIASDLVDAQ QARRALDYLV GFNLSPVLWR KVQRGLSAGR VQSPALRMIV
     EREEEIEAFI TREYWSIHAE CAHPAQHFSA KLIKLDGQKF EQFTITDSDT AAAAQRRIQQ
     VAQGRLHITD VTNKERKRRP APPFITSTLQ QEASRKLGFT TRKTMQIAQK LYEGIALGEE
     GSVGLITYMR TDSVNLSLDA LSEIRDIIAR DYGTNALPDK PNVYTTKSKN AQEAHEAVRP
     TSALRTPTQV APYLSNEEHR LYELVWKRAV ASQMIPAILN TTSVDLAAGN EHVFRATGTT
     VVVQGFLAVY EEGKDNKNAE DDDEGRKLPV MKTGENVPLE RILTEQHFTQ PPPRYTEAAL
     VKALEEYGIG RPSTYASIIQ TLLFRKYVDM EGRSFRPTDI GRAVSKFLAS HFTRYVDYDF
     TAHLEDELDA ISRGEEEWIP LMKKFWVPFK ELVEDKKDSL DKTDAGSVRL LGIDPTSGKE
     VSGRIGRFGP MVQIGTVDDE EKPRFASLRP NQSIYSISLE EAIELFKMPR VLGEDQSQQV
     SVGIGRFGPF AKRGSTYVSL KSEDDPYTID LARATFLINE KEEIARNRII KNFENSQIQV
     LNGRFGPYIS DGKLNGKIPK DREPASLTLE EAQQLLIDTG KPARKNFSTK KTATKNETRK
     QTTKKRTTDA KATKKVSDKP VKKQIKKRIA PNITE
 
 
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