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Q9PHK2

- TOP1P_XYLFA

UniProt

Q9PHK2 - TOP1P_XYLFA

Protein

DNA topoisomerase I, plasmid

Gene

XF_a0003

Organism
Xylella fastidiosa (strain 9a5c)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 104 (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 bindingi7 – 71Magnesium 1; catalyticUniRule annotation
    Sitei31 – 311Interaction with DNAUniRule annotation
    Metal bindingi79 – 791Magnesium 1; catalyticUniRule annotation
    Metal bindingi79 – 791Magnesium 2UniRule annotation
    Metal bindingi81 – 811Magnesium 2UniRule annotation
    Sitei134 – 1341Interaction with DNAUniRule annotation
    Sitei135 – 1351Interaction with DNAUniRule annotation
    Sitei138 – 1381Interaction with DNAUniRule annotation
    Sitei143 – 1431Interaction with DNAUniRule annotation
    Active sitei287 – 2871O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation
    Sitei289 – 2891Interaction with DNAUniRule annotation
    Sitei483 – 4831Interaction with DNAUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri563 – 58927C4-type 1Add
    BLAST
    Zinc fingeri613 – 64331C4-type 2Add
    BLAST

    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, Zinc

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA topoisomerase I, plasmidUniRule annotation (EC:5.99.1.2UniRule annotation)
    Alternative name(s):
    Omega-protein
    Relaxing enzyme
    Swivelase
    Untwisting enzyme
    Gene namesi
    Ordered Locus Names:XF_a0003
    Encoded oniPlasmid pXF510 Publication
    OrganismiXylella fastidiosa (strain 9a5c)
    Taxonomic identifieri160492 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaXanthomonadalesXanthomonadaceaeXylella
    ProteomesiUP000000812: Plasmid pXF51

    Subcellular locationi

    GO - Cellular componenti

    1. chromosome Source: InterPro

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 660660DNA topoisomerase I, plasmidPRO_0000145174Add
    BLAST

    Interactioni

    Subunit structurei

    Monomer.UniRule annotation

    Protein-protein interaction databases

    STRINGi160492.XFa0003.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9PHK2.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 110110ToprimUniRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni158 – 1636Interaction with DNAUniRule annotation

    Sequence similaritiesi

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

    Zinc finger

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri563 – 58927C4-type 1Add
    BLAST
    Zinc fingeri613 – 64331C4-type 2Add
    BLAST

    Keywords - Domaini

    Repeat, Zinc-finger

    Phylogenomic databases

    eggNOGiCOG0551.
    KOiK03168.
    OMAiHRTDNPN.
    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.
    IPR013498. Topo_IA_Znf.
    IPR005733. TopoI_bac-type.
    IPR028612. Topoisom_1_IA.
    IPR006171. Toprim_domain.
    [Graphical view]
    PANTHERiPTHR11390. PTHR11390. 1 hit.
    PfamiPF01131. Topoisom_bac. 1 hit.
    PF01751. Toprim. 1 hit.
    PF01396. zf-C4_Topoisom. 1 hit.
    [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.

    Q9PHK2-1 [UniParc]FASTAAdd to Basket

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    MKLMIIESPG KIEKLSTILG DGWKIAASVG HVRDLPQKEM GVAAPDFKPS    50
    YELTERGEGV VAKLKNLLKQ ADSVYLATDP DREGEAISWH LQQCLKLSNP 100
    LRVTFNEITA NAVKASLVAP RTIDVKRVAA QEARRVLDRL VGYMVSPELS 150
    RLTGKRLSAG RVQSPAVRLV VEREREIKAF KVTNHFGAML FFADAKTSGE 200
    WSAEWLTKPK FVAEDNPYFM DRDFAAAVAQ VKAVVVKSFD ESEAKRSPPP 250
    PFTTSTMQQA ASVTLGVDPK AAMDAAQKLY EQGHITYHRT DNPNVSDESL 300
    GDIYAVSVKL GLDIAEKPRK FKAPAGAQVG HPAVTPTHWE VEEAGETSDQ 350
    KALYKLIRLR AIACQLADAR YAVRTVRLEA AQPVGGKNVE FEARGRTLIY 400
    QGWLKLIAGD QTEEEDGNEK ESSNPIPVCA PGECLDVARG KLLEKKTKPP 450
    SHYTQATLVK KLESEGIGRP ATYAAIMDNI VSRGYVKTEK KYLFPTETGE 500
    LIVDSLVGKF EFLDLGFTRE IEESLDRIAQ GESGYKAVIA KVHDQLNMEL 550
    STLQVSATPK HPCQECGKPL RRIPGKNGHF WGCSGYPDCS VTFPDEGGKP 600
    GQKKPVEVSN FACVKCGNPL KHLVKKGKGG YDFWGCSGFK EGCKATYEDK 650
    KGKPNFEKAK 660
    Length:660
    Mass (Da):72,556
    Last modified:October 1, 2000 - v1
    Checksum:iAC4A5F000A503A1F
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE003851 Genomic DNA. Translation: AAF85572.1.
    PIRiC82861.
    RefSeqiNP_061659.1. NC_002490.1.

    Genome annotation databases

    EnsemblBacteriaiAAF85572; AAF85572; XF_a0003.
    GeneIDi1125448.
    KEGGixfa:XFa0003.
    PATRICi24135901. VBIXylFas578_2957.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE003851 Genomic DNA. Translation: AAF85572.1 .
    PIRi C82861.
    RefSeqi NP_061659.1. NC_002490.1.

    3D structure databases

    ProteinModelPortali Q9PHK2.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 160492.XFa0003.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAF85572 ; AAF85572 ; XF_a0003 .
    GeneIDi 1125448.
    KEGGi xfa:XFa0003.
    PATRICi 24135901. VBIXylFas578_2957.

    Phylogenomic databases

    eggNOGi COG0551.
    KOi K03168.
    OMAi HRTDNPN.
    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.
    IPR013498. Topo_IA_Znf.
    IPR005733. TopoI_bac-type.
    IPR028612. Topoisom_1_IA.
    IPR006171. Toprim_domain.
    [Graphical view ]
    PANTHERi PTHR11390. PTHR11390. 1 hit.
    Pfami PF01131. Topoisom_bac. 1 hit.
    PF01751. Toprim. 1 hit.
    PF01396. zf-C4_Topoisom. 1 hit.
    [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.
    2. "Genetic organization of Plasmid pXF51 from the plant pathogen Xylella fastidiosa."
      Marques M.V., da Silva A.M., Gomes S.L.
      Plasmid 45:184-199(2001) [PubMed] [Europe PMC] [Abstract]
      Cited for: DISCUSSION OF SEQUENCE.

    Entry informationi

    Entry nameiTOP1P_XYLFA
    AccessioniPrimary (citable) accession number: Q9PHK2
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 20, 2001
    Last sequence update: October 1, 2000
    Last modified: October 1, 2014
    This is version 104 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, Plasmid, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3