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Q8BB16

- REP_PCV2

UniProt

Q8BB16 - REP_PCV2

Protein

Replication-associated protein

Gene

Rep

Organism
Porcine circovirus 2 (PCV2)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 59 (01 Oct 2014)
      Sequence version 1 (01 Mar 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.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi48 – 481Divalent metal cationSequence Analysis
    Metal bindingi57 – 571Divalent metal cationSequence Analysis
    Active sitei96 – 961For DNA cleavage activityBy similarity
    Metal bindingi100 – 1001Divalent metal cationSequence Analysis

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi174 – 1818ATPBy 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 2 (PCV2)
    Taxonomic identifieri85708 [NCBI]
    Taxonomic lineageiVirusesssDNA virusesCircoviridaeCircovirus
    Virus hostiSus scrofa (Pig) [TaxID: 9823]
    ProteomesiUP000000470: Genome

    Subcellular locationi

    Host nucleus 1 Publication

    GO - Cellular componenti

    1. host cell nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Host nucleus

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi179 – 1802GK → DI: Complete loss of viral DNA synthesis. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 314314Replication-associated proteinPRO_0000133089Add
    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

    Secondary structure

    1
    314
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi8 – 114
    Beta strandi17 – 237
    Helixi26 – 338
    Helixi37 – 393
    Beta strandi40 – 489
    Beta strandi57 – 6610
    Helixi70 – 778
    Turni78 – 803
    Beta strandi81 – 844
    Helixi90 – 989
    Beta strandi103 – 1086

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2HW0NMR-A2-116[»]
    ProteinModelPortaliQ8BB16.
    SMRiQ8BB16. Positions 2-116.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ8BB16.

    Family & Domainsi

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi4 – 1815Nuclear localization signal1 PublicationAdd
    BLAST
    Motifi19 – 224RCR-1By similarity
    Motifi57 – 626RCR-2By similarity
    Motifi96 – 994RCR-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 (10)i

    Sequence statusi: Complete.

    This entry describes 10 isoformsi produced by alternative promoter usage and alternative splicing. Align

    Isoform Rep (identifier: Q8BB16-1) [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

    MPSKKNGRSG PQPHKRWVFT LNNPSEDERK KIREPPISLF DYFIVGEEGN    50
    EEGRTPHLQG FANFVKKQTF NKVKWYLGAR CHIEKAKGTD QQNKEYCSKE 100
    GNLLIECGAP RSQGQRSDLS TAVSTLLESG SLVTVAEQHP VTFVRNFRGL 150
    AELLKVSGKM QKRDWKTNVH VIVGPPGCGK SKWAANFADP ETTYWKPPRN 200
    KWWDGYHGEE VVVIDDFYGW LPWDDLLRLC DRYPLTVETK GGTVPFLARS 250
    ILITSNQTPL EWYSSTAVPA VEALYRRITS LVFWKNATEQ STEEGGQFVT 300
    LSPPCPEFPY EINY 314

    Note: Produced by alternative promoter usage.

    Length:314
    Mass (Da):35,762
    Last modified:March 1, 2003 - v1
    Checksum:i3FE9D85F2CD656FC
    GO
    Isoform Rep' (identifier: Q8BB16-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         123-178: VSTLLESGSL...VHVIVGPPGC → YSDYQQSDPV...PVRHPFPPMP
         179-314: Missing.

    Note: Produced by alternative splicing of isoform Rep.

    Show »
    Length:178
    Mass (Da):20,240
    Checksum:i0D29BACBE4BECDB0
    GO
    Isoform NS462 (identifier: Q8BB12-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform can be found in the external entry Q8BB12.
    Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
    Length:
    Mass (Da):
    GO
    Isoform NS642 (identifier: Q8BB12-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform can be found in the external entry Q8BB12.
    Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
    Length:
    Mass (Da):
    GO
    Isoform NS0 (identifier: Q8BB12-1) [UniParc]FASTAAdd to Basket

    The sequence of this isoform can be found in the external entry Q8BB12.
    Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.

    Note: Produced by alternative promoter usage.

    Length:23
    Mass (Da):2,725
    GO
    Isoform NS515 (identifier: Q8BB16-6)

    Sequence is not available

    Note: Produced by alternative promoter usage.

    Length:
    Mass (Da):
    Isoform NS672 (identifier: Q8BB16-7)

    Sequence is not available

    Note: Produced by alternative promoter usage.

    Length:
    Mass (Da):
    Isoform Rep3a (identifier: Q8BB16-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         16-249: Missing.

    Note: Produced by alternative splicing of isoform Rep.

    Show »
    Length:80
    Mass (Da):9,003
    Checksum:i0116107E943C6EC8
    GO
    Isoform Rep3b (identifier: Q8BB16-4) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         16-254: Missing.

    Note: Produced by alternative splicing of isoform Rep.

    Show »
    Length:75
    Mass (Da):8,475
    Checksum:i4481B5DD3891883E
    GO
    Isoform Rep3c (identifier: Q8BB16-5)

    Sequence is not available

    Note: Produced by alternative splicing of isoform Rep.

    Length:
    Mass (Da):

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei16 – 254239Missing in isoform Rep3b. CuratedVSP_015882Add
    BLAST
    Alternative sequencei16 – 249234Missing in isoform Rep3a. CuratedVSP_015883Add
    BLAST
    Alternative sequencei123 – 17856VSTLL…GPPGC → YSDYQQSDPVGMVLLNCCPS CRSSLSEDYFLGILEECYRT IHGGRGPVRHPFPPMP in isoform Rep'. CuratedVSP_015884Add
    BLAST
    Alternative sequencei179 – 314136Missing in isoform Rep'. CuratedVSP_015885Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY094619 Genomic DNA. Translation: AAM21844.1.
    AY094619 Genomic DNA. Translation: AAM21845.1.
    AY094619 Genomic DNA. Translation: AAM21846.1.
    AY094619 Genomic DNA. Translation: AAM21847.1.

    Keywords - Coding sequence diversityi

    Alternative promoter usage, Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AY094619 Genomic DNA. Translation: AAM21844.1 .
    AY094619 Genomic DNA. Translation: AAM21845.1 .
    AY094619 Genomic DNA. Translation: AAM21846.1 .
    AY094619 Genomic DNA. Translation: AAM21847.1 .

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2HW0 NMR - A 2-116 [» ]
    ProteinModelPortali Q8BB16.
    SMRi Q8BB16. Positions 2-116.
    ModBasei Search...
    MobiDBi Search...

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Miscellaneous databases

    EvolutionaryTracei Q8BB16.

    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. "Transcriptional analysis of porcine circovirus type 2."
      Cheung A.K.
      Virology 305:168-180(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORMS REP; REP'; REP3A; REP3B AND REP3C), ALTERNATIVE PROMOTER USAGE.
      Strain: Isolate PCV/688.
    2. "The essential and nonessential transcription units for viral protein synthesis and DNA replication of porcine circovirus type 2."
      Cheung A.K.
      Virology 313:452-459(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, MUTAGENESIS OF 179-GLY-LYS-180.
      Strain: Isolate PCV/688.
    3. "The N-terminus of porcine circovirus type 2 replication protein is required for nuclear localization and ori binding activities."
      Lin W.-L., Chien M.-S., Du Y.-W., Wu P.-C., Huang C.
      Biochem. Biophys. Res. Commun. 379:1066-1071(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, NUCLEAR LOCALIZATION SIGNAL.
    4. "Solution structure, divalent metal and DNA binding of the endonuclease domain from the replication initiation protein from porcine circovirus 2."
      Vega-Rocha S., Byeon I.-J.L., Gronenborn B., Gronenborn A.M., Campos-Olivas R.
      J. Mol. Biol. 367:473-487(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR OF 1-116, COFACTOR, CHARACTERIZATION.

    Entry informationi

    Entry nameiREP_PCV2
    AccessioniPrimary (citable) accession number: Q8BB16
    Secondary accession number(s): Q8BB13, Q8BB14, Q8BB15
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 25, 2005
    Last sequence update: March 1, 2003
    Last modified: October 1, 2014
    This is version 59 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

    3D-structure, Complete proteome, Multifunctional enzyme

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3