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Q805H4

- REP_PCV1C

UniProt

Q805H4 - REP_PCV1C

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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

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

Mg2+By similarity, Mn2+By similarityNote: Divalent metal cations, possibly Mg(2+) or Mn(2+).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
Complete GO annotation...

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-KW
Complete GO annotation...

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

        10         20         30         40         50
MPSKKSGPQP HKRWVFTLNN PSEEEKNKIR ELPISLFDYF VCGEEGLEEG
60 70 80 90 100
RTPHLQGFAN FAKKQTFNKV KWYFGARCHI EKAKGTDQQN KEYCSKEGHI
110 120 130 140 150
LIECGAPRNQ GKRSDLSTAV STLLETGSLV TVAEQFPVTY VRNFRGLAEL
160 170 180 190 200
LKVSGKMQQR DWKTAVHVIV GPPGCGKSQW ARNFAEPSDT YWKPSRNKWW
210 220 230 240 250
DGYHGEEVVV LDDFYGWLPW DDLLRLCDRY PLTVETKGGT VPFLARSILI
260 270 280 290 300
TSNQAPQEWY SSTAVPAVEA LYRRITTLQF WKTAGEQSTE VPEGRFEAVD
310
PPCALFPYKI NY
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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: November 26, 2014
This is version 65 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