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Q9Z0D3

- REP3_MDV1

UniProt

Q9Z0D3 - REP3_MDV1

Protein

Para-Rep C3

Gene

C3

Organism
Milk vetch dwarf virus (isolate N) (MDV)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi
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    • History
      Entry version 48 (01 Oct 2014)
      Sequence version 1 (01 May 1999)
      Previous versions | rss
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    Functioni

    Initiates and terminates the replication only of its own subviral DNA molecule. The closed circular ssDNA genome is first converted to a superhelical dsDNA. Rep binds a specific hairpin at the genome origin of replication. Introduces an endonucleolytic nick within the intergenic region of the genome, thereby initiating the rolling circle replication (RCR). Following cleavage, binds covalently to the 5'-phosphate of DNA as a tyrosyl ester. The cleavage gives rise to a free 3'-OH that serves as a primer for the cellular DNA polymerase. The polymerase synthesizes the (+) strand DNA by rolling circle mechanism. After one round of replication, a Rep-catalyzed nucleotidyl transfer reaction releases a circular single-stranded virus genome, thereby terminating the replication. Displays origin-specific DNA cleavage, nucleotidyl transferase, ATPase and helicase activities By similarity.By similarity

    Catalytic activityi

    ATP + H2O = ADP + phosphate.

    Cofactori

    Divalent metal cations, possibly magnesium or manganese.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi36 – 361Divalent metal cationSequence Analysis
    Metal bindingi42 – 421Divalent metal cationSequence Analysis
    Active sitei81 – 811For DNA cleavage activityBy similarity
    Metal bindingi86 – 861Divalent metal cationSequence Analysis

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi174 – 1829ATPBy similarity

    GO - Molecular functioni

    1. ATPase activity, uncoupled Source: InterPro
    2. ATP binding Source: UniProtKB-KW
    3. DNA binding Source: UniProtKB-KW
    4. endodeoxyribonuclease activity, producing 5'-phosphomonoesters Source: InterPro
    5. metal ion binding Source: UniProtKB-KW
    6. nucleotidyltransferase activity Source: UniProtKB-KW
    7. RNA binding Source: InterPro
    8. RNA helicase activity Source: InterPro

    GO - Biological processi

    1. DNA replication Source: UniProtKB-KW
    2. protein-DNA covalent cross-linking Source: InterPro

    Keywords - Molecular functioni

    Endonuclease, Helicase, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase

    Keywords - Biological processi

    DNA replication

    Keywords - Ligandi

    ATP-binding, DNA-binding, Metal-binding, Nucleotide-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Para-Rep C3 (EC:2.7.7.-, EC:3.1.21.-, EC:3.6.1.3)
    Short name:
    Rep3
    Alternative name(s):
    Replication-associated protein of non-essential DNA C3
    Gene namesi
    Name:C3
    OrganismiMilk vetch dwarf virus (isolate N) (MDV)
    Taxonomic identifieri291605 [NCBI]
    Taxonomic lineageiVirusesssDNA virusesNanoviridaeNanovirus
    Virus hostiAstragalus sinicus (Chinese milk vetch) [TaxID: 47065]
    Glycine max (Soybean) (Glycine hispida) [TaxID: 3847]
    Phaseolus vulgaris (Kidney bean) (French bean) [TaxID: 3885]
    Pisum sativum (Garden pea) [TaxID: 3888]
    Vicia faba (Broad bean) (Faba vulgaris) [TaxID: 3906]
    ProteomesiUP000008236: Genome

    Subcellular locationi

    Host nucleus Curated

    GO - Cellular componenti

    1. host cell nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Host nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 284284Para-Rep C3PRO_0000378524Add
    BLAST

    Keywords - PTMi

    Covalent protein-DNA linkage

    Interactioni

    Subunit structurei

    Homooligomer Potential. Rep binds to repeated DNA motifs (iterons) By similarity.By similarityCurated

    Structurei

    3D structure databases

    ProteinModelPortaliQ9Z0D3.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi11 – 144RCR-1By similarity
    Motifi42 – 476RCR-2By similarity
    Motifi51 – 7121Nuclear localization signalSequence AnalysisAdd
    BLAST
    Motifi81 – 844RCR-3By similarity
    Motifi98 – 1047Nuclear localization signalSequence Analysis

    Domaini

    There are 3 rolling circle replication (RCR) motifs. RCR-2 is probably involved in metal coordination. RCR-3 is required for phosphodiester bond cleavage for initiation of RCR.

    Sequence similaritiesi

    Family and domain databases

    InterProiIPR000605. Helicase_SF3_ssDNA/RNA_vir.
    IPR003365. Viral_rep_N.
    [Graphical view]
    PfamiPF00910. RNA_helicase. 1 hit.
    PF02407. Viral_Rep. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q9Z0D3-1 [UniParc]FASTAAdd to Basket

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    MPTVQSTCWV FTLNFKGEIP ILPFNERVQY ACWQHERVGH DHLQGFIQMK    50
    AQQSLGQMKA IIPGAHFEKM RALNSDQAKA YAMKEDTRIE GPWEYGKYIK 100
    KGSHKRKIME RFEDDPEEMK IEDPSLYRRC LSRKMTEEQR STAEWNYDMK 150
    PWQDQVIQEI EETPDYRKII WVYGPKGGEG KSTFARYLSL KQGWGYLPGG 200
    PTHDMLHIIS GEPKNNWVFD IPRVASEYVN YGVLEQVKNR VMVNTKYEPI 250
    VIRDDNHPVH VIVFANCMPD FTKISEDRMK IVHC 284
    Length:284
    Mass (Da):33,349
    Last modified:May 1, 1999 - v1
    Checksum:iC9C880B8459B3355
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB000922 Genomic DNA. Translation: BAA33982.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AB000922 Genomic DNA. Translation: BAA33982.1 .

    3D structure databases

    ProteinModelPortali Q9Z0D3.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Family and domain databases

    InterProi IPR000605. Helicase_SF3_ssDNA/RNA_vir.
    IPR003365. Viral_rep_N.
    [Graphical view ]
    Pfami PF00910. RNA_helicase. 1 hit.
    PF02407. Viral_Rep. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Sequences of ten circular ssDNA components associated with the milk vetch dwarf virus genome."
      Sano Y., Wada M., Hashimoto Y., Matsumoto T., Kojima M.
      J. Gen. Virol. 79:3111-3118(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].

    Entry informationi

    Entry nameiREP3_MDV1
    AccessioniPrimary (citable) accession number: Q9Z0D3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 7, 2009
    Last sequence update: May 1, 1999
    Last modified: October 1, 2014
    This is version 48 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programViral Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    The genome of nanoviruses is composed of six to eight segments. In addition, some isolates contain subviral DNAs.

    Caution

    This protein is encoded by a subviral DNA that is not present in all isolates of the virus.Curated

    Keywords - Technical termi

    Complete proteome, Multifunctional enzyme

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3