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Q1RIM1

- TOP1_RICBR

UniProt

Q1RIM1 - TOP1_RICBR

Protein

DNA topoisomerase 1

Gene

topA

Organism
Rickettsia bellii (strain RML369-C)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi
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    • History
      Entry version 67 (01 Oct 2014)
      Sequence version 1 (16 May 2006)
      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 bindingi80 – 801Magnesium 1; catalyticUniRule annotation
    Metal bindingi80 – 801Magnesium 2UniRule annotation
    Metal bindingi82 – 821Magnesium 2UniRule annotation
    Sitei142 – 1421Interaction with DNAUniRule annotation
    Sitei143 – 1431Interaction with DNAUniRule annotation
    Sitei146 – 1461Interaction with DNAUniRule annotation
    Sitei158 – 1581Interaction with DNAUniRule annotation
    Active sitei304 – 3041O-(5'-phospho-DNA)-tyrosine intermediateUniRule annotation
    Sitei306 – 3061Interaction with DNAUniRule annotation
    Sitei499 – 4991Interaction with DNAUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Zinc fingeri600 – 62728C4-typeAdd
    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

    Enzyme and pathway databases

    BioCyciRBEL336407:GJCY-733-MONOMER.
    RETL1328306-WGS:GSTH-1662-MONOMER.

    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:RBE_0712
    OrganismiRickettsia bellii (strain RML369-C)
    Taxonomic identifieri336407 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRickettsialesRickettsiaceaeRickettsieaeRickettsiabelli group
    ProteomesiUP000001951: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    1. chromosome Source: InterPro

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 800800DNA topoisomerase 1PRO_0000273104Add
    BLAST

    Interactioni

    Subunit structurei

    Monomer.UniRule annotation

    Protein-protein interaction databases

    STRINGi336407.RBE_0712.

    Structurei

    3D structure databases

    ProteinModelPortaliQ1RIM1.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 111111ToprimUniRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni166 – 1716Interaction 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 fingeri600 – 62728C4-typeAdd
    BLAST

    Keywords - Domaini

    Zinc-finger

    Phylogenomic databases

    eggNOGiCOG1754.
    HOGENOMiHOG000004020.
    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.
    IPR013498. Topo_IA_Znf.
    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. 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. 2 hits.
    TIGRFAMsiTIGR01051. topA_bact. 1 hit.
    PROSITEiPS00396. TOPOISOMERASE_I_PROK. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q1RIM1-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKLVIVESPA KAKTINKYLG DEFKVIASFG HIRDLPSKKG SVIPDENFSM    50
    KYDISEKAGK YVDAIIKDAK KAESVYLATD PDREGESISW HIAEVIKEKN 100
    KVKSDDFFKR VAFNEITKKA ITHAIENPRK LDNNLVNAQQ ARRALDYLVG 150
    FTLSPLLWRK LPGCKSAGRV QSVALRLICE REDEIERFKS EEYWDISLKM 200
    LNSNNELFTA KLTHINDQKL EKFSITNDKE AKDLTEKLKS QNFHVDKIEK 250
    KQQKRQPQPP FITSSLQQEA ARKLGFSAKK TMQIAQKLYE GVDIGKETIG 300
    LITYMRTDGV TLSNDAVDEI RKLINKDYGD KYLPSSPRIY KSKVKNAQEA 350
    HEAIRPTNIN YIPNDLKEKL EKDYYKLYEL IWKRTIACQM ENVIMDLVNA 400
    TLASENKEYL ARANGSTIAF DGFYKVYRES IDDEAEEENK MLPPLKEQEH 450
    LKTKEIIPNQ HFTEPPPRYS EASLVKKLEE LGIGRPSTYA TILSVLQDRK 500
    YVTLEKKRFI PEELGRLVTV FLVGFFKKYV EYDFTAGLEN ELDEIAAGKL 550
    EWKSALGNFW NGFNHNIESV NKQNITEIIS YVQQALDYHI FGENKDSKVC 600
    PSCKTGELSL KLGKFGAFLA CSNYPECNFR KSIVSGNDNN EADGEAKDIV 650
    NENKVLGKDK EGIEIYLKKG PYGPYIQYGE QVDSKIKPKR SPLPAGLNQN 700
    DITLDMALKL LSLPLKIGNH KESGEEVLVG YGKFGPYIKY MGKFISIPKK 750
    YDFLNLSLDD AMKLIEEKLN AIAAKQPNPL NMDEVTNLVD KKIKVKKTKK 800
    Length:800
    Mass (Da):91,229
    Last modified:May 16, 2006 - v1
    Checksum:i686E7F5561AF337D
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000087 Genomic DNA. Translation: ABE04793.1.
    RefSeqiYP_537882.1. NC_007940.1.

    Genome annotation databases

    EnsemblBacteriaiABE04793; ABE04793; RBE_0712.
    GeneIDi3995312.
    KEGGirbe:RBE_0712.
    PATRICi17882904. VBIRicBel102610_0817.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CP000087 Genomic DNA. Translation: ABE04793.1 .
    RefSeqi YP_537882.1. NC_007940.1.

    3D structure databases

    ProteinModelPortali Q1RIM1.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 336407.RBE_0712.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai ABE04793 ; ABE04793 ; RBE_0712 .
    GeneIDi 3995312.
    KEGGi rbe:RBE_0712.
    PATRICi 17882904. VBIRicBel102610_0817.

    Phylogenomic databases

    eggNOGi COG1754.
    HOGENOMi HOG000004020.
    KOi K03168.
    OMAi ANEGYER.
    OrthoDBi EOG6S7XQ9.

    Enzyme and pathway databases

    BioCyci RBEL336407:GJCY-733-MONOMER.
    RETL1328306-WGS:GSTH-1662-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.
    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. 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. 2 hits.
    TIGRFAMsi TIGR01051. topA_bact. 1 hit.
    PROSITEi PS00396. TOPOISOMERASE_I_PROK. 1 hit.
    PS50880. TOPRIM. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Genome sequence of Rickettsia bellii illuminates the role of amoebae in gene exchanges between intracellular pathogens."
      Ogata H., La Scola B., Audic S., Renesto P., Blanc G., Robert C., Fournier P.-E., Claverie J.-M., Raoult D.
      PLoS Genet. 2:733-744(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: RML369-C.

    Entry informationi

    Entry nameiTOP1_RICBR
    AccessioniPrimary (citable) accession number: Q1RIM1
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: January 23, 2007
    Last sequence update: May 16, 2006
    Last modified: October 1, 2014
    This is version 67 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

    Documents

    1. Rickettsia bellii strain RML369-C
      Rickettsia bellii (strain RML369-C): entries and gene names
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3