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Protein

Replication-associated protein

Gene

Rep

Organism
Porcine circovirus 1 (isolate China) (PCV1)
Status
Reviewed-Annotation score: 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 similarity1 Publication

Catalytic activityi

ATP + H2O = ADP + phosphate.

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Divalent metal cations, possibly Mg2+ or Mn2+.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi45Divalent metal cationSequence analysis1
Metal bindingi54Divalent metal cationSequence analysis1
Active sitei93For DNA cleavage activityBy similarity1
Metal bindingi97Divalent metal cationSequence analysis1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi171 – 178ATPBy similarity8

GO - Molecular functioni

GO - Biological processi

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]
Proteomesi
  • UP000007023 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Host nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001330881 – 312Replication-associated proteinAdd BLAST312

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.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi4 – 15Nuclear localization signalSequence analysisAdd BLAST12
Motifi16 – 19RCR-1By similarity4
Motifi54 – 59RCR-2By similarity6
Motifi63 – 84Nuclear localization signalSequence analysisAdd BLAST22
Motifi93 – 96RCR-3By similarity4

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. AlignAdd to basket

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)DescriptionActionsGraphical viewLength
Sequence conflicti185A → T in AAC34819 (PubMed:9787657).Curated1

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti179Q → R in strain: Isolate IBRS-2. 1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_01587813 – 251Missing in isoform Rep3b. CuratedAdd BLAST239
Alternative sequenceiVSP_01587913 – 247RWVFT…FLARS → SGILVPAATSRKRKEPTSRI KNTAVKKATYLSSVELRGTR GSAATCLLL in isoform Rep3c-4a. CuratedAdd BLAST235
Alternative sequenceiVSP_01587713 – 246Missing in isoform Rep3a. CuratedAdd BLAST234
Alternative sequenceiVSP_015880120 – 168VSTLL…TAVHV → YFDYQQSGPPGMVLLNCCPS CRSSLSEDYYFAILEDCWRT IHGGTRRPI in isoform Rep'. CuratedAdd BLAST49
Alternative sequenceiVSP_015881169 – 312Missing in isoform Rep'. CuratedAdd BLAST144

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.
KEGGivg:7693233.

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.
RefSeqiNP_065678.1. NC_001792.2.

3D structure databases

ProteinModelPortaliQ805H4.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi7693233.
KEGGivg:7693233.

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.
ProtoNetiSearch...

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 5, 2016
This is version 71 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.