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Q805H4

- REP_PCV1C

UniProt

Q805H4 - REP_PCV1C

Protein

Replication-associated protein

Gene

Rep

Organism
Porcine circovirus 1 (isolate China) (PCV1)
Status
Reviewed - Annotation score: 5 out of 5- Protein inferred from homologyi
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    • History
      Entry version 63 (01 Oct 2014)
      Sequence version 1 (01 Jun 2003)
      Previous versions | rss
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    Functioni

    Essential for the replication of viral ssDNA. The closed circular ssDNA genome is first converted to a superhelical dsDNA. Rep and/or Rep' binds a specific hairpin at the genome origin of replication. Introduces an endonucleolytic nick within the conserved sequence 5'-AGTATTAC-3' in 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. ATPase activity is probably carried by the isoform Rep 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 bindingi45 – 451Divalent metal cationSequence Analysis
    Metal bindingi54 – 541Divalent metal cationSequence Analysis
    Active sitei93 – 931For DNA cleavage activityBy similarity
    Metal bindingi97 – 971Divalent metal cationSequence Analysis

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi171 – 1788ATPBy 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:
    Replication-associated protein (EC:2.7.7.-, EC:3.1.21.-, EC:3.6.1.3)
    Alternative name(s):
    ATP-dependent helicase Rep
    RepP
    Gene namesi
    Name:Rep
    ORF Names:ORF1
    OrganismiPorcine circovirus 1 (isolate China) (PCV1)
    Taxonomic identifieri654929 [NCBI]
    Taxonomic lineageiVirusesssDNA virusesCircoviridaeCircovirus
    Virus hostiSus scrofa (Pig) [TaxID: 9823]
    ProteomesiUP000007023: 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 – 312312Replication-associated proteinPRO_0000133088Add
    BLAST

    Keywords - PTMi

    Covalent protein-DNA linkage

    Interactioni

    Subunit structurei

    Interacts with the capsid protein; this interaction relocates Rep into the nucleus.By similarity

    Structurei

    3D structure databases

    ProteinModelPortaliQ805H4.
    SMRiQ805H4. Positions 2-113.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi4 – 1512Nuclear localization signalSequence AnalysisAdd
    BLAST
    Motifi16 – 194RCR-1By similarity
    Motifi54 – 596RCR-2By similarity
    Motifi63 – 8422Nuclear localization signalSequence AnalysisAdd
    BLAST
    Motifi93 – 964RCR-3By similarity

    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

    Gene3Di3.40.50.300. 1 hit.
    InterProiIPR000605. Helicase_SF3_ssDNA/RNA_vir.
    IPR027417. P-loop_NTPase.
    IPR003365. Viral_rep_N.
    [Graphical view]
    PfamiPF00910. RNA_helicase. 1 hit.
    PF02407. Viral_Rep. 1 hit.
    [Graphical view]
    SUPFAMiSSF52540. SSF52540. 1 hit.

    Sequences (5)i

    Sequence statusi: Complete.

    This entry describes 5 isoformsi produced by alternative splicing. Align

    Isoform Rep (identifier: Q805H4-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MPSKKSGPQP HKRWVFTLNN PSEEEKNKIR ELPISLFDYF VCGEEGLEEG    50
    RTPHLQGFAN FAKKQTFNKV KWYFGARCHI EKAKGTDQQN KEYCSKEGHI 100
    LIECGAPRNQ GKRSDLSTAV STLLETGSLV TVAEQFPVTY VRNFRGLAEL 150
    LKVSGKMQQR DWKTAVHVIV GPPGCGKSQW ARNFAEPSDT YWKPSRNKWW 200
    DGYHGEEVVV LDDFYGWLPW DDLLRLCDRY PLTVETKGGT VPFLARSILI 250
    TSNQAPQEWY SSTAVPAVEA LYRRITTLQF WKTAGEQSTE VPEGRFEAVD 300
    PPCALFPYKI NY 312
    Length:312
    Mass (Da):35,635
    Last modified:June 1, 2003 - v1
    Checksum:iE3A5AFDD8BE0C3CF
    GO
    Isoform Rep' (identifier: Q805H4-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         120-168: VSTLLETGSL...QRDWKTAVHV → YFDYQQSGPP...TIHGGTRRPI
         169-312: Missing.

    Show »
    Length:168
    Mass (Da):19,273
    Checksum:i7B6F8BD1A844A86E
    GO
    Isoform Rep3a (identifier: Q805H4-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         13-246: Missing.

    Show »
    Length:78
    Mass (Da):8,785
    Checksum:iEFDD5391CD903AC2
    GO
    Isoform Rep3b (identifier: Q805H4-4) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         13-251: Missing.

    Show »
    Length:73
    Mass (Da):8,257
    Checksum:iEDC8D7895E4364A0
    GO
    Isoform Rep3c-4a (identifier: Q805H4-5) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         13-247: RWVFTLNNPS...GGTVPFLARS → SGILVPAATS...RGSAATCLLL

    Show »
    Length:126
    Mass (Da):13,882
    Checksum:iB9F35549EFBD9C26
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti185 – 1851A → T in AAC34819. (PubMed:9787657)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti179 – 1791Q → R in strain: Isolate IBRS-2.

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei13 – 251239Missing in isoform Rep3b. CuratedVSP_015878Add
    BLAST
    Alternative sequencei13 – 247235RWVFT…FLARS → SGILVPAATSRKRKEPTSRI KNTAVKKATYLSSVELRGTR GSAATCLLL in isoform Rep3c-4a. CuratedVSP_015879Add
    BLAST
    Alternative sequencei13 – 246234Missing in isoform Rep3a. CuratedVSP_015877Add
    BLAST
    Alternative sequencei120 – 16849VSTLL…TAVHV → YFDYQQSGPPGMVLLNCCPS CRSSLSEDYYFAILEDCWRT IHGGTRRPI in isoform Rep'. CuratedVSP_015880Add
    BLAST
    Alternative sequencei169 – 312144Missing in isoform Rep'. CuratedVSP_015881Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF071879 Genomic DNA. Translation: AAC34819.1.
    AY193712 Genomic DNA. Translation: AAO39666.1.
    AY184287 Genomic DNA. Translation: AAN77859.1.
    AY184287 Genomic DNA. Translation: AAN77860.1.
    AY184287 Genomic DNA. Translation: AAN77861.1.
    AY184287 Genomic DNA. Translation: AAN77862.1.
    AY184287 Genomic DNA. Translation: AAN77863.1.
    AY660574 Genomic DNA. Translation: AAT72755.1.
    RefSeqiNP_065678.1. NC_001792.2.

    Genome annotation databases

    GeneIDi7693233.

    Keywords - Coding sequence diversityi

    Alternative promoter usage, Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF071879 Genomic DNA. Translation: AAC34819.1 .
    AY193712 Genomic DNA. Translation: AAO39666.1 .
    AY184287 Genomic DNA. Translation: AAN77859.1 .
    AY184287 Genomic DNA. Translation: AAN77860.1 .
    AY184287 Genomic DNA. Translation: AAN77861.1 .
    AY184287 Genomic DNA. Translation: AAN77862.1 .
    AY184287 Genomic DNA. Translation: AAN77863.1 .
    AY660574 Genomic DNA. Translation: AAT72755.1 .
    RefSeqi NP_065678.1. NC_001792.2.

    3D structure databases

    ProteinModelPortali Q805H4.
    SMRi Q805H4. Positions 2-113.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 7693233.

    Family and domain databases

    Gene3Di 3.40.50.300. 1 hit.
    InterProi IPR000605. Helicase_SF3_ssDNA/RNA_vir.
    IPR027417. P-loop_NTPase.
    IPR003365. Viral_rep_N.
    [Graphical view ]
    Pfami PF00910. RNA_helicase. 1 hit.
    PF02407. Viral_Rep. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52540. SSF52540. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Beak and feather disease virus and porcine circovirus genomes: intermediates between the geminiviruses and plant circoviruses."
      Niagro F.D., Forsthoefel A.N., Lawther R.P., Kamalanathan L., Ritchie B.W., Latimer K.S., Lukert P.D.
      Arch. Virol. 143:1723-1744(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "Comparative analysis of the transcriptional patterns of pathogenic and nonpathogenic porcine circoviruses."
      Cheung A.K.
      Virology 310:41-49(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORMS REP; REP'; REP3A; REP3B AND REP3C-4A).
    3. "Genomic sequence of Porcine circovirus type 1 isolated from IBRS-2 cell line."
      Cao S., Chen H., Ju C.
      Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: Isolate IBRS-2.
    4. "Detection of template strand switching during initiation and termination of DNA replication of porcine circovirus."
      Cheung A.K.
      J. Virol. 78:4268-4277(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: MODEL OF REPLICATION.
    5. "Palindrome regeneration by template strand-switching mechanism at the origin of DNA replication of porcine circovirus via the rolling-circle melting-pot replication model."
      Cheung A.K.
      J. Virol. 78:9016-9029(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: MODEL OF REPLICATION.
    6. "Detection of rampant nucleotide reversion at the origin of DNA replication of porcine circovirus type 1."
      Cheung A.K.
      Virology 333:22-30(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: MODEL OF REPLICATION.
    7. "Demonstration of nicking/joining activity at the origin of DNA replication associated with the rep and rep' proteins of porcine circovirus type 1."
      Steinfeldt T., Finsterbusch T., Mankertz A.
      J. Virol. 80:6225-6234(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.

    Entry informationi

    Entry nameiREP_PCV1C
    AccessioniPrimary (citable) accession number: Q805H4
    Secondary accession number(s): O90238
    , Q6DMP3, Q80QL6, Q80QL7, Q80QL8, Q80QL9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 25, 2005
    Last sequence update: June 1, 2003
    Last modified: October 1, 2014
    This is version 63 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programViral Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Multifunctional enzyme, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3