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Q87009

- REP2_SCSVF

UniProt

Q87009 - REP2_SCSVF

Protein

Para-Rep C2

Gene

C2

Organism
Subterranean clover stunt virus (strain F) (SCSV)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi
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    • History
      Entry version 51 (01 Oct 2014)
      Sequence version 1 (01 Nov 1996)
      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 bindingi37 – 371Divalent metal cationSequence Analysis
    Metal bindingi45 – 451Divalent metal cationSequence Analysis
    Active sitei84 – 841For DNA cleavage activityBy similarity

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi172 – 1809ATPBy 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 C2 (EC:2.7.7.-, EC:3.1.21.-, EC:3.6.1.3)
    Short name:
    Rep2
    Alternative name(s):
    Replication-associated protein of non-essential DNA C2
    Gene namesi
    Name:C2
    OrganismiSubterranean clover stunt virus (strain F) (SCSV)
    Taxonomic identifieri291607 [NCBI]
    Taxonomic lineageiVirusesssDNA virusesNanoviridaeNanovirus
    Virus hostiMedicago arabica [TaxID: 70936]
    Medicago lupulina [TaxID: 47085]
    Medicago minima [TaxID: 70957]
    Phaseolus vulgaris (Kidney bean) (French bean) [TaxID: 3885]
    Pisum sativum (Garden pea) [TaxID: 3888]
    Trifolium cernuum [TaxID: 74509]
    Trifolium dubium (Suckling clover) (Lesser trefoil) [TaxID: 97021]
    Trifolium glomeratum [TaxID: 74514]
    Trifolium pratense (Red clover) [TaxID: 57577]
    Trifolium repens (Creeping white clover) [TaxID: 3899]
    Trifolium subterraneum (Subterranean clover) [TaxID: 3900]
    Vicia faba (Broad bean) (Faba vulgaris) [TaxID: 3906]
    Wisteria sinensis [TaxID: 20997]
    ProteomesiUP000006543: 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 – 280280Para-Rep C2PRO_0000378523Add
    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

    ProteinModelPortaliQ87009.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi7 – 104RCR-1By similarity
    Motifi45 – 506RCR-2By similarity
    Motifi54 – 7522Nuclear localization signalSequence AnalysisAdd
    BLAST
    Motifi84 – 874RCR-3By similarity
    Motifi97 – 1037Nuclear 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.

    Q87009-1 [UniParc]FASTAAdd to Basket

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    MARRYCFTLN YATEIERETF LSLFSQDELN YFVVGDETAT TGQKHLQGFV    50
    SFKNKIRLGG LKKKFGNRAH WEIARGSDSQ NRDYCCKETL ISEIGIPVMK 100
    GSNKRKTMEI YEEDPEEMQL KDPDTALRCK AKKLKEEYCS CYDFQKLRPW 150
    QIELHAALMA EPDDRSIIWV YGSDGGEGKT SFAKELIRYG WFYTAGGKTQ 200
    DVLYMYAQDP ERNIAFDVPR CSSEMMNYQA MEMLKNRVFA STKYRPVDLC 250
    IRKLVHLIVF ANVAPDPTRI SEDRLVIINC 280
    Length:280
    Mass (Da):32,473
    Last modified:November 1, 1996 - v1
    Checksum:iBAE273C64B04D6E3
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U16731 Genomic DNA. Translation: AAA68018.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U16731 Genomic DNA. Translation: AAA68018.1 .

    3D structure databases

    ProteinModelPortali Q87009.
    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. "Sequence of subterranean clover stunt virus DNA: affinities with the geminiviruses."
      Boevink P.C., Chu P.W.G., Keese P.K.
      Virology 207:354-361(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].

    Entry informationi

    Entry nameiREP2_SCSVF
    AccessioniPrimary (citable) accession number: Q87009
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 7, 2009
    Last sequence update: November 1, 1996
    Last modified: October 1, 2014
    This is version 51 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, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3