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Q9PEV8

- TOP1_XYLFA

UniProt

Q9PEV8 - TOP1_XYLFA

Protein

DNA topoisomerase 1

Gene

topA

Organism
Xylella fastidiosa (strain 9a5c)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 87 (01 Oct 2014)
      Sequence version 1 (01 Oct 2000)
      Previous versions | rss
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    Functioni

    Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone.UniRule annotation

    Catalytic activityi

    ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.UniRule annotation

    Cofactori

    Magnesium. Binds two Mg2+ per subunit.UniRule annotation

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi9 – 91Magnesium 1; catalyticUniRule annotation
    Sitei33 – 331Interaction with DNAUniRule annotation
    Metal bindingi82 – 821Magnesium 1; catalyticUniRule annotation
    Metal bindingi82 – 821Magnesium 2UniRule annotation
    Metal bindingi84 – 841Magnesium 2UniRule annotation
    Sitei143 – 1431Interaction with DNAUniRule annotation
    Sitei144 – 1441Interaction with DNAUniRule annotation
    Sitei147 – 1471Interaction with DNAUniRule annotation
    Sitei159 – 1591Interaction with DNAUniRule annotation
    Active sitei308 – 3081O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation
    Sitei310 – 3101Interaction with DNAUniRule annotation
    Sitei505 – 5051Interaction with DNAUniRule annotation

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-KW
    2. DNA topoisomerase type I activity Source: UniProtKB-HAMAP
    3. magnesium ion binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. DNA topological change Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Isomerase, Topoisomerase

    Keywords - Ligandi

    DNA-binding, Magnesium, Metal-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA topoisomerase 1UniRule annotation (EC:5.99.1.2UniRule annotation)
    Alternative name(s):
    DNA topoisomerase IUniRule annotation
    Omega-protein
    Relaxing enzyme
    Swivelase
    Untwisting enzyme
    Gene namesi
    Name:topAUniRule annotation
    Ordered Locus Names:XF_0920
    OrganismiXylella fastidiosa (strain 9a5c)
    Taxonomic identifieri160492 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXylella
    ProteomesiUP000000812: Chromosome

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 815815DNA topoisomerase 1PRO_0000145172Add
    BLAST

    Interactioni

    Subunit structurei

    Monomer.UniRule annotation

    Protein-protein interaction databases

    STRINGi160492.XF0920.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9PEV8.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini3 – 119117ToprimUniRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni167 – 1726Interaction with DNAUniRule annotation

    Sequence similaritiesi

    Belongs to the type IA topoisomerase family.UniRule annotation
    Contains 1 Toprim domain.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG1754.
    KOiK03168.
    OMAiANEGYER.
    OrthoDBiEOG6S7XQ9.

    Family and domain databases

    Gene3Di1.10.460.10. 2 hits.
    2.70.20.10. 2 hits.
    3.40.50.140. 1 hit.
    HAMAPiMF_00952. Topoisom_1_prok.
    InterProiIPR000380. Topo_IA.
    IPR003601. Topo_IA_2.
    IPR023406. Topo_IA_AS.
    IPR013497. Topo_IA_cen.
    IPR013824. Topo_IA_cen_sub1.
    IPR013825. Topo_IA_cen_sub2.
    IPR023405. Topo_IA_core_domain.
    IPR003602. Topo_IA_DNA-bd.
    IPR005733. TopoI_bac-type.
    IPR028612. Topoisom_1_IA.
    IPR025589. Toprim_C_rpt.
    IPR006171. Toprim_domain.
    [Graphical view]
    PANTHERiPTHR11390. PTHR11390. 1 hit.
    PfamiPF01131. Topoisom_bac. 1 hit.
    PF01751. Toprim. 1 hit.
    PF13368. Toprim_C_rpt. 3 hits.
    [Graphical view]
    PRINTSiPR00417. PRTPISMRASEI.
    SMARTiSM00437. TOP1Ac. 1 hit.
    SM00436. TOP1Bc. 1 hit.
    SM00493. TOPRIM. 1 hit.
    [Graphical view]
    SUPFAMiSSF56712. SSF56712. 1 hit.
    TIGRFAMsiTIGR01051. topA_bact. 1 hit.
    PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q9PEV8-1 [UniParc]FASTAAdd to Basket

    « Hide

    MPKHLLIVES PAKAKTINKY LGKDFTVLAS YGHVRDLVPK EGAVDPENGF    50
    AMRYDLIDKN EKHVEAITKA AKTADSIYLA TDPDREGEAI SWHISEILKE 100
    RGLLKDKPMQ RIVFTEITPR AIKEAIQKPR MIASDLVDAQ QARRALDYLV 150
    GFNLSPVLWR KVQRGLSAGR VQSPALRMIV EREEEIEAFI TREYWSIHAE 200
    CAHPAQHFSA KLIKLDGQKF EQFTITDSDT AAAAQRRIQQ VAQGRLHITD 250
    VTNKERKRRP APPFITSTLQ QEASRKLGFT TRKTMQIAQK LYEGIALGEE 300
    GSVGLITYMR TDSVNLSLDA LSEIRDIIAR DYGTNALPDK PNVYTTKSKN 350
    AQEAHEAVRP TSALRTPTQV APYLSNEEHR LYELVWKRAV ASQMIPAILN 400
    TTSVDLAAGN EHVFRATGTT VVVQGFLAVY EEGKDNKNAE DDDEGRKLPV 450
    MKTGENVPLE RILTEQHFTQ PPPRYTEAAL VKALEEYGIG RPSTYASIIQ 500
    TLLFRKYVDM EGRSFRPTDI GRAVSKFLAS HFTRYVDYDF TAHLEDELDA 550
    ISRGEEEWIP LMKKFWVPFK ELVEDKKDSL DKTDAGSVRL LGIDPTSGKE 600
    VSGRIGRFGP MVQIGTVDDE EKPRFASLRP NQSIYSISLE EAIELFKMPR 650
    VLGEDQSQQV SVGIGRFGPF AKRGSTYVSL KSEDDPYTID LARATFLINE 700
    KEEIARNRII KNFENSQIQV LNGRFGPYIS DGKLNGKIPK DREPASLTLE 750
    EAQQLLIDTG KPARKNFSTK KTATKNETRK QTTKKRTTDA KATKKVSDKP 800
    VKKQIKKRIA PNITE 815
    Length:815
    Mass (Da):91,803
    Last modified:October 1, 2000 - v1
    Checksum:i65BC01306E1EB1C5
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE003849 Genomic DNA. Translation: AAF83730.1.
    PIRiB82746.
    RefSeqiNP_298210.1. NC_002488.3.

    Genome annotation databases

    EnsemblBacteriaiAAF83730; AAF83730; XF_0920.
    GeneIDi1126456.
    KEGGixfa:XF0920.
    PATRICi24131894. VBIXylFas578_0986.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE003849 Genomic DNA. Translation: AAF83730.1 .
    PIRi B82746.
    RefSeqi NP_298210.1. NC_002488.3.

    3D structure databases

    ProteinModelPortali Q9PEV8.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 160492.XF0920.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAF83730 ; AAF83730 ; XF_0920 .
    GeneIDi 1126456.
    KEGGi xfa:XF0920.
    PATRICi 24131894. VBIXylFas578_0986.

    Phylogenomic databases

    eggNOGi COG1754.
    KOi K03168.
    OMAi ANEGYER.
    OrthoDBi EOG6S7XQ9.

    Family and domain databases

    Gene3Di 1.10.460.10. 2 hits.
    2.70.20.10. 2 hits.
    3.40.50.140. 1 hit.
    HAMAPi MF_00952. Topoisom_1_prok.
    InterProi IPR000380. Topo_IA.
    IPR003601. Topo_IA_2.
    IPR023406. Topo_IA_AS.
    IPR013497. Topo_IA_cen.
    IPR013824. Topo_IA_cen_sub1.
    IPR013825. Topo_IA_cen_sub2.
    IPR023405. Topo_IA_core_domain.
    IPR003602. Topo_IA_DNA-bd.
    IPR005733. TopoI_bac-type.
    IPR028612. Topoisom_1_IA.
    IPR025589. Toprim_C_rpt.
    IPR006171. Toprim_domain.
    [Graphical view ]
    PANTHERi PTHR11390. PTHR11390. 1 hit.
    Pfami PF01131. Topoisom_bac. 1 hit.
    PF01751. Toprim. 1 hit.
    PF13368. Toprim_C_rpt. 3 hits.
    [Graphical view ]
    PRINTSi PR00417. PRTPISMRASEI.
    SMARTi SM00437. TOP1Ac. 1 hit.
    SM00436. TOP1Bc. 1 hit.
    SM00493. TOPRIM. 1 hit.
    [Graphical view ]
    SUPFAMi SSF56712. SSF56712. 1 hit.
    TIGRFAMsi TIGR01051. topA_bact. 1 hit.
    PROSITEi PS00396. TOPOISOMERASE_I_PROK. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "The genome sequence of the plant pathogen Xylella fastidiosa."
      Simpson A.J.G., Reinach F.C., Arruda P., Abreu F.A., Acencio M., Alvarenga R., Alves L.M.C., Araya J.E., Baia G.S., Baptista C.S., Barros M.H., Bonaccorsi E.D., Bordin S., Bove J.M., Briones M.R.S., Bueno M.R.P., Camargo A.A., Camargo L.E.A.
      , Carraro D.M., Carrer H., Colauto N.B., Colombo C., Costa F.F., Costa M.C.R., Costa-Neto C.M., Coutinho L.L., Cristofani M., Dias-Neto E., Docena C., El-Dorry H., Facincani A.P., Ferreira A.J.S., Ferreira V.C.A., Ferro J.A., Fraga J.S., Franca S.C., Franco M.C., Frohme M., Furlan L.R., Garnier M., Goldman G.H., Goldman M.H.S., Gomes S.L., Gruber A., Ho P.L., Hoheisel J.D., Junqueira M.L., Kemper E.L., Kitajima J.P., Krieger J.E., Kuramae E.E., Laigret F., Lambais M.R., Leite L.C.C., Lemos E.G.M., Lemos M.V.F., Lopes S.A., Lopes C.R., Machado J.A., Machado M.A., Madeira A.M.B.N., Madeira H.M.F., Marino C.L., Marques M.V., Martins E.A.L., Martins E.M.F., Matsukuma A.Y., Menck C.F.M., Miracca E.C., Miyaki C.Y., Monteiro-Vitorello C.B., Moon D.H., Nagai M.A., Nascimento A.L.T.O., Netto L.E.S., Nhani A. Jr., Nobrega F.G., Nunes L.R., Oliveira M.A., de Oliveira M.C., de Oliveira R.C., Palmieri D.A., Paris A., Peixoto B.R., Pereira G.A.G., Pereira H.A. Jr., Pesquero J.B., Quaggio R.B., Roberto P.G., Rodrigues V., de Rosa A.J.M., de Rosa V.E. Jr., de Sa R.G., Santelli R.V., Sawasaki H.E., da Silva A.C.R., da Silva A.M., da Silva F.R., Silva W.A. Jr., da Silveira J.F., Silvestri M.L.Z., Siqueira W.J., de Souza A.A., de Souza A.P., Terenzi M.F., Truffi D., Tsai S.M., Tsuhako M.H., Vallada H., Van Sluys M.A., Verjovski-Almeida S., Vettore A.L., Zago M.A., Zatz M., Meidanis J., Setubal J.C.
      Nature 406:151-159(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 9a5c.

    Entry informationi

    Entry nameiTOP1_XYLFA
    AccessioniPrimary (citable) accession number: Q9PEV8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 16, 2003
    Last sequence update: October 1, 2000
    Last modified: October 1, 2014
    This is version 87 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3