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Q8BB16 (REP_PCV2) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 58. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:Rep
ORF Names:ORF1
OrganismPorcine circovirus 2 (PCV2) [Complete proteome]
Taxonomic identifier85708 [NCBI]
Taxonomic lineageVirusesssDNA virusesCircoviridaeCircovirus
Virus hostSus scrofa (Pig) [TaxID: 9823]

Protein attributes

Sequence length314 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.2

Catalytic activity

ATP + H2O = ADP + phosphate.

Cofactor

Divalent metal cations, possibly magnesium or manganese Probable. Ref.4

Subunit structure

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

Subcellular location

Host nucleus Probable Ref.3.

Domain

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 similarities

Belongs to the nanoviruses/circoviruses replication-associated protein family.

Alternative products

This entry describes 10 isoforms produced by alternative promoter usage and alternative splicing. [Align] [Select]
Isoform Rep (identifier: Q8BB16-1)

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.
Note: Produced by alternative promoter usage.
Isoform Rep' (identifier: Q8BB16-2)

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.
Isoform NS462 (identifier: Q8BB12-2)

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.
Isoform NS642 (identifier: Q8BB12-3)

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.
Isoform NS0 (identifier: Q8BB12-1)

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.
Isoform NS515 (identifier: Q8BB16-6)

The sequence of this isoform is not available.
Note: Produced by alternative promoter usage.
Isoform NS672 (identifier: Q8BB16-7)

The sequence of this isoform is not available.
Note: Produced by alternative promoter usage.
Isoform Rep3a (identifier: Q8BB16-3)

The sequence of this isoform differs from the canonical sequence as follows:
     16-249: Missing.
Note: Produced by alternative splicing of isoform Rep.
Isoform Rep3b (identifier: Q8BB16-4)

The sequence of this isoform differs from the canonical sequence as follows:
     16-254: Missing.
Note: Produced by alternative splicing of isoform Rep.
Isoform Rep3c (identifier: Q8BB16-5)

The sequence of this isoform is not available.
Note: Produced by alternative splicing of isoform Rep.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 314314Replication-associated protein
PRO_0000133089

Regions

Nucleotide binding174 – 1818ATP By similarity
Motif4 – 1815Nuclear localization signal Probable
Motif19 – 224RCR-1 By similarity
Motif57 – 626RCR-2 By similarity
Motif96 – 994RCR-3 By similarity

Sites

Active site961For DNA cleavage activity By similarity
Metal binding481Divalent metal cation Potential
Metal binding571Divalent metal cation Potential
Metal binding1001Divalent metal cation Potential

Natural variations

Alternative sequence16 – 254239Missing in isoform Rep3b.
VSP_015882
Alternative sequence16 – 249234Missing in isoform Rep3a.
VSP_015883
Alternative sequence123 – 17856VSTLL…GPPGC → YSDYQQSDPVGMVLLNCCPS CRSSLSEDYFLGILEECYRT IHGGRGPVRHPFPPMP in isoform Rep'.
VSP_015884
Alternative sequence179 – 314136Missing in isoform Rep'.
VSP_015885

Experimental info

Mutagenesis179 – 1802GK → DI: Complete loss of viral DNA synthesis. Ref.2

Secondary structure

.................... 314
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform Rep [UniParc].

Last modified March 1, 2003. Version 1.
Checksum: 3FE9D85F2CD656FC

FASTA31435,762
        10         20         30         40         50         60 
MPSKKNGRSG PQPHKRWVFT LNNPSEDERK KIREPPISLF DYFIVGEEGN EEGRTPHLQG 

        70         80         90        100        110        120 
FANFVKKQTF NKVKWYLGAR CHIEKAKGTD QQNKEYCSKE GNLLIECGAP RSQGQRSDLS 

       130        140        150        160        170        180 
TAVSTLLESG SLVTVAEQHP VTFVRNFRGL AELLKVSGKM QKRDWKTNVH VIVGPPGCGK 

       190        200        210        220        230        240 
SKWAANFADP ETTYWKPPRN KWWDGYHGEE VVVIDDFYGW LPWDDLLRLC DRYPLTVETK 

       250        260        270        280        290        300 
GGTVPFLARS ILITSNQTPL EWYSSTAVPA VEALYRRITS LVFWKNATEQ STEEGGQFVT 

       310 
LSPPCPEFPY EINY 

« Hide

Isoform Rep' [UniParc].

Checksum: 0D29BACBE4BECDB0
Show »

FASTA17820,240
Isoform NS462 [UniParc].

See Q8BB12.

Isoform NS642 [UniParc].

See Q8BB12.

Isoform NS0 [UniParc].

See Q8BB12.

Isoform NS515 (Sequence not available).
Isoform NS672 (Sequence not available).
Isoform Rep3a [UniParc].

Checksum: 0116107E943C6EC8
Show »

FASTA809,003
Isoform Rep3b [UniParc].

Checksum: 4481B5DD3891883E
Show »

FASTA758,475
Isoform Rep3c (Sequence not available).

References

[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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2HW0NMR-A2-116[»]
ProteinModelPortalQ8BB16.
SMRQ8BB16. Positions 2-116.
ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Family and domain databases

Gene3D3.40.50.300. 1 hit.
InterProIPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR027417. P-loop_NTPase.
IPR003365. Viral_rep_N.
[Graphical view]
PfamPF00910. RNA_helicase. 1 hit.
PF02407. Viral_Rep. 1 hit.
[Graphical view]
SUPFAMSSF52540. SSF52540. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceQ8BB16.

Entry information

Entry nameREP_PCV2
AccessionPrimary (citable) accession number: Q8BB16
Secondary accession number(s): Q8BB13, Q8BB14, Q8BB15
Entry history
Integrated into UniProtKB/Swiss-Prot: October 25, 2005
Last sequence update: March 1, 2003
Last modified: April 16, 2014
This is version 58 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references