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Protein

Replication-associated protein

Gene

Rep

Organism
Porcine circovirus 2 (PCV2)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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+1 Publication, Mn2+1 PublicationNote: Divalent metal cations, possibly Mg2+ or Mn2+.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi48Divalent metal cationSequence analysis1
Metal bindingi57Divalent metal cationSequence analysis1
Active sitei96For DNA cleavage activityBy similarity1
Metal bindingi100Divalent metal cationSequence analysis1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi174 – 181ATPBy 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 2 (PCV2)
Taxonomic identifieri85708 [NCBI]
Taxonomic lineageiVirusesssDNA virusesCircoviridaeCircovirus
Virus hostiSus scrofa (Pig) [TaxID: 9823]
Proteomesi
  • UP000000470 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Host nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi179 – 180GK → DI: Complete loss of viral DNA synthesis. 1 Publication2

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001330891 – 314Replication-associated proteinAdd BLAST314

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

1314
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi8 – 11Combined sources4
Beta strandi17 – 23Combined sources7
Helixi26 – 33Combined sources8
Helixi37 – 39Combined sources3
Beta strandi40 – 48Combined sources9
Beta strandi57 – 66Combined sources10
Helixi70 – 77Combined sources8
Turni78 – 80Combined sources3
Beta strandi81 – 84Combined sources4
Helixi90 – 98Combined sources9
Beta strandi103 – 108Combined sources6

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2HW0NMR-A2-116[»]
ProteinModelPortaliQ8BB16.
SMRiQ8BB16.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ8BB16.

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi4 – 18Nuclear localization signal1 PublicationAdd BLAST15
Motifi19 – 22RCR-1By similarity4
Motifi57 – 62RCR-2By similarity6
Motifi96 – 99RCR-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 (10)i

Sequence statusi: Complete.

This entry describes 10 isoformsi produced by alternative promoter usage and alternative splicing. AlignAdd to basket

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

        10         20         30         40         50
MPSKKNGRSG PQPHKRWVFT LNNPSEDERK KIREPPISLF DYFIVGEEGN
60 70 80 90 100
EEGRTPHLQG FANFVKKQTF NKVKWYLGAR CHIEKAKGTD QQNKEYCSKE
110 120 130 140 150
GNLLIECGAP RSQGQRSDLS TAVSTLLESG SLVTVAEQHP VTFVRNFRGL
160 170 180 190 200
AELLKVSGKM QKRDWKTNVH VIVGPPGCGK SKWAANFADP ETTYWKPPRN
210 220 230 240 250
KWWDGYHGEE VVVIDDFYGW LPWDDLLRLC DRYPLTVETK GGTVPFLARS
260 270 280 290 300
ILITSNQTPL EWYSSTAVPA VEALYRRITS LVFWKNATEQ STEEGGQFVT
310
LSPPCPEFPY EINY
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)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_01588216 – 254Missing in isoform Rep3b. CuratedAdd BLAST239
Alternative sequenceiVSP_01588316 – 249Missing in isoform Rep3a. CuratedAdd BLAST234
Alternative sequenceiVSP_015884123 – 178VSTLL…GPPGC → YSDYQQSDPVGMVLLNCCPS CRSSLSEDYFLGILEECYRT IHGGRGPVRHPFPPMP in isoform Rep'. CuratedAdd BLAST56
Alternative sequenceiVSP_015885179 – 314Missing in isoform Rep'. CuratedAdd BLAST136

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2HW0NMR-A2-116[»]
ProteinModelPortaliQ8BB16.
SMRiQ8BB16.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiQ8BB16.

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_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: November 2, 2016
This is version 67 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

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.