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D3V265

- D3V265_XENBS

UniProt

D3V265 - D3V265_XENBS

Protein

DNA topoisomerase 1

Gene

topA

Organism
Xenorhabdus bovienii (strain SS-2004)
Status
Unreviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 34 (01 Oct 2014)
      Sequence version 1 (20 Apr 2010)
      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 annotationSAAS annotation

    Catalytic activityi

    ATP-independent breakage of single-stranded DNA, followed by passage and rejoining.UniRule annotationSAAS 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 bindingi109 – 1091Magnesium 1; catalyticUniRule annotation
    Metal bindingi109 – 1091Magnesium 2UniRule annotation
    Metal bindingi111 – 1111Magnesium 2UniRule annotation
    Sitei166 – 1661Interaction with DNAUniRule annotation
    Sitei167 – 1671Interaction with DNAUniRule annotation
    Sitei170 – 1701Interaction with DNAUniRule annotation
    Sitei175 – 1751Interaction with DNAUniRule annotation
    Sitei182 – 1821Interaction with DNAUniRule annotation
    Active sitei317 – 3171O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation
    Sitei319 – 3191Interaction with DNAUniRule annotation
    Sitei505 – 5051Interaction with DNAUniRule annotation

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. DNA binding Source: UniProtKB-KW
    3. DNA topoisomerase type I activity Source: UniProtKB-HAMAP
    4. DNA topoisomerase type II (ATP-hydrolyzing) activity Source: InterPro
    5. magnesium ion binding Source: UniProtKB-HAMAP

    GO - Biological processi

    1. DNA topological change Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Isomerase, TopoisomeraseUniRule annotationSAAS annotation

    Keywords - Ligandi

    DNA-bindingUniRule annotationSAAS annotation, MagnesiumUniRule annotationSAAS annotation, Metal-bindingUniRule annotationSAAS annotation

    Enzyme and pathway databases

    BioCyciXBOV406818:GHLH-2275-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA topoisomerase 1UniRule annotation (EC:5.99.1.2UniRule annotation)
    Alternative name(s):
    DNA topoisomerase IUniRule annotation
    Gene namesi
    Name:topAUniRule annotationImported
    Ordered Locus Names:XBJ1_2289Imported
    OrganismiXenorhabdus bovienii (strain SS-2004)Imported
    Taxonomic identifieri406818 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeXenorhabdus
    ProteomesiUP000002045: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    1. chromosome Source: InterPro

    Interactioni

    Subunit structurei

    Monomer.UniRule annotation

    Structurei

    3D structure databases

    ProteinModelPortaliD3V265.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini3 – 140138ToprimUniRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni190 – 1956Interaction with DNAUniRule annotation

    Sequence similaritiesi

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

    Phylogenomic databases

    HOGENOMiHOG000004018.
    KOiK03168.

    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.
    IPR013263. TopoI_Znr_bac.
    IPR028612. Topoisom_1_IA.
    IPR006171. Toprim_domain.
    [Graphical view]
    PANTHERiPTHR11390. PTHR11390. 1 hit.
    PfamiPF08272. Topo_Zn_Ribbon. 2 hits.
    PF01131. 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.

    D3V265-1 [UniParc]FASTAAdd to Basket

    « Hide

    MGKALVIVES PAKAKTINKY LGNDYVVKSS VGHIRDLPTS GAASQKSSNS    50
    STDKNKKKKD EKTALVNRMG VDPYHGWEAD YQILPGKEKV VAELKMLAEK 100
    ADHIYLATDL DREGEAIAWH LREVIGGGEA RFSRVVFNEI TKNAITQAFD 150
    NPGELNIDRV NAQQARRFMD RVVGYMVSPL LWKKVARGLS AGRVQSVAVR 200
    LIVEREREIK AFVPEEYWQL HADLMAKGDI DLHMEVTHEG GKPFKPINAQ 250
    QTQAAVSLLE KARYKVLDRE DRPTSSKPGA PFITSTLQQA ASTRLGFGVK 300
    KTMMMAQRLY EAGHITYMRT DSTNLSQDAL DMVRGYINDQ FGDKYLPKTA 350
    NIYSNKENSQ EAHEAIRPSS VDVMAEELKD MEADAQKLYQ LIWRQFIACQ 400
    MMPAKYDSTT LTIQAGNFEL RAKGRTLRFD GWTKVMPALR KGDEDHTLPV 450
    VEVGTELDLK QLSPSQHFTK PSARFSEASL VRELEKRGIG RPSTYASIIS 500
    TIQDRGYVRG ENRRFYAEKM GEIVNDRLEE NFNELMSYDF TARMEDQLDH 550
    VANNEANWKG VLDEFFTNFS EQLDVASKDP DEGGMRPNPM VSTSIDCPTC 600
    SRPMGIRTAT TGVFLGCSGY TLSPKERCKQ TINLIPENEI LNILEGDEAE 650
    TNALRARHRC KECGTAMDSY LIDNQRKLHV CGNNPACDGY EVEEGEFRIK 700
    GYDGPIVECD KCGSEMHLKM GRFGKYMGCT SEECKNTRKI LRSGEVAPPK 750
    EDPVPLPELP CEKSDAYFVL RDGAAGVFLA ASTFPKSRET RAPLVEELVK 800
    FKDRLPEKLC YLAKAPVADP EGHKTVVRFS RKTKQQYVSS EKNGKATGWA 850
    AFFVDGAWVV KEK 863
    Length:863
    Mass (Da):96,862
    Last modified:April 20, 2010 - v1
    Checksum:iBEBAEDE670B084B5
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    FN667741 Genomic DNA. Translation: CBJ81415.1.
    RefSeqiYP_003468188.1. NC_013892.1.

    Genome annotation databases

    EnsemblBacteriaiCBJ81415; CBJ81415; XBJ1_2289.
    GeneIDi8831902.
    KEGGixbo:XBJ1_2289.
    PATRICi35299411. VBIXenBov95754_2063.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    FN667741 Genomic DNA. Translation: CBJ81415.1 .
    RefSeqi YP_003468188.1. NC_013892.1.

    3D structure databases

    ProteinModelPortali D3V265.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai CBJ81415 ; CBJ81415 ; XBJ1_2289 .
    GeneIDi 8831902.
    KEGGi xbo:XBJ1_2289.
    PATRICi 35299411. VBIXenBov95754_2063.

    Phylogenomic databases

    HOGENOMi HOG000004018.
    KOi K03168.

    Enzyme and pathway databases

    BioCyci XBOV406818:GHLH-2275-MONOMER.

    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.
    IPR013263. TopoI_Znr_bac.
    IPR028612. Topoisom_1_IA.
    IPR006171. Toprim_domain.
    [Graphical view ]
    PANTHERi PTHR11390. PTHR11390. 1 hit.
    Pfami PF08272. Topo_Zn_Ribbon. 2 hits.
    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. "Complete genome sequence of Xenorhabdus nematophila (strain ATCC 19061 / DSM 3370 / LMG 1036 / NCIB 9965 / AN6)."
      Goodrich-Blair H., Barbazuk B., Bode H.B., Darby C., Du Z., Forst S., Gaudriault S., Goldman B.S., Goodner B., Henkhaus J., Latreille P., Medigue C., Miller N., Norton S., Ogier J.C., Rouy Z., Slater S., Suen G.
      Submitted (FEB-2010) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: SS-2004Imported.
    2. "The entomopathogenic bacterial endosymbionts xenorhabdus and photorhabdus: convergent lifestyles from divergent genomes."
      Chaston J.M., Suen G., Tucker S.L., Andersen A.W., Bhasin A., Bode E., Bode H.B., Brachmann A.O., Cowles C.E., Cowles K.N., Darby C., de Leon L., Drace K., Du Z., Givaudan A., Herbert Tran E.E., Jewell K.A., Knack J.J.
      , Krasomil-Osterfeld K.C., Kukor R., Lanois A., Latreille P., Leimgruber N.K., Lipke C.M., Liu R., Lu X., Martens E.C., Marri P.R., Medigue C., Menard M.L., Miller N.M., Morales-Soto N., Norton S., Ogier J.C., Orchard S.S., Park D., Park Y., Qurollo B.A., Sugar D.R., Richards G.R., Rouy Z., Slominski B., Slominski K., Snyder H., Tjaden B.C., van der Hoeven R., Welch R.D., Wheeler C., Xiang B., Barbazuk B., Gaudriault S., Goodner B., Slater S.C., Forst S., Goldman B.S., Goodrich-Blair H.
      PLoS ONE 6:e27909-e27909(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: SS-2004Imported.

    Entry informationi

    Entry nameiD3V265_XENBS
    AccessioniPrimary (citable) accession number: D3V265
    Entry historyi
    Integrated into UniProtKB/TrEMBL: April 20, 2010
    Last sequence update: April 20, 2010
    Last modified: October 1, 2014
    This is version 34 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiUnreviewed (UniProtKB/TrEMBL)

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteomeImported

    External Data

    Dasty 3