Replication-associated protein - Porcine circovirus 2 (PCV2)

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Q8BB16 (REP_PCV2) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 55. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

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 names

Name:	Rep
ORF Names:	ORF1

Organism

Porcine circovirus 2 (PCV2) [Complete proteome]

Taxonomic identifier

85708 [NCBI]

Taxonomic lineage

Viruses › ssDNA viruses › Circoviridae › Circovirus

Virus host

Sus scrofa (Pig) [TaxID: 9823]

Protein attributes

Sequence length	314 AA.
Sequence status	Complete.
Protein existence	Evidence 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.

Ontologies

Keywords
Biological process	DNA replication
Cellular component	Host nucleus
Coding sequence diversity	Alternative promoter usage Alternative splicing
Ligand	ATP-binding DNA-binding Metal-binding Nucleotide-binding
Molecular function	Endonuclease Helicase Hydrolase Nuclease Nucleotidyltransferase Transferase
PTM	Covalent protein-DNA linkage
Technical term	3D-structure Complete proteome Multifunctional enzyme
Gene Ontology (GO)
Biological_process	ATP catabolic process Inferred from electronic annotation. Source: GOC DNA replication Inferred from electronic annotation. Source: UniProtKB-KW nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC protein-DNA covalent cross-linking Inferred from electronic annotation. Source: InterPro
Cellular_component	host cell nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATPase activity, uncoupled Inferred from electronic annotation. Source: InterPro DNA binding Inferred from electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: InterPro RNA helicase activity Inferred from electronic annotation. Source: InterPro endodeoxyribonuclease activity, producing 5'-phosphomonoesters Inferred from electronic annotation. Source: InterPro metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW nucleotidyltransferase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

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 key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 314

314

Replication-associated protein

PRO_0000133089

Regions

Nucleotide binding

174 – 181

ATP By similarity

Motif

4 – 18

Nuclear localization signal Probable

Motif

19 – 22

RCR-1 By similarity

Motif

57 – 62

RCR-2 By similarity

Motif

96 – 99

RCR-3 By similarity

Sites

Active site

For DNA cleavage activity By similarity

Metal binding

Divalent metal cation Potential

Metal binding

Divalent metal cation Potential

Metal binding

100

Divalent metal cation Potential

Natural variations

Alternative sequence

16 – 254

239

Missing in isoform Rep3b.

VSP_015882

Alternative sequence

16 – 249

234

Missing in isoform Rep3a.

VSP_015883

Alternative sequence

123 – 178

VSTLL…GPPGC → YSDYQQSDPVGMVLLNCCPS CRSSLSEDYFLGILEECYRT IHGGRGPVRHPFPPMP in isoform Rep'.

VSP_015884

Alternative sequence

179 – 314

136

Missing in isoform Rep'.

VSP_015885

Experimental info

Mutagenesis

179 – 180

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

Secondary structure

314

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

Isoform Rep [UniParc].

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

FASTA

314

35,762

        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 »

FASTA

178

20,240

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 »

FASTA

9,003

Isoform Rep3b [UniParc].

Checksum: 4481B5DD3891883E
Show »

FASTA

8,475

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

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2HW0	NMR	-	A	2-116	[»]

ProteinModelPortal

Q8BB16.

SMR

Q8BB16. Positions 2-116.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

InterPro

IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR003365. Viral_rep_N.
[Graphical view]

Pfam

PF00910. RNA_helicase. 1 hit.
PF02407. Viral_Rep. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q8BB16.

Entry information

Entry name

REP_PCV2

Accession

Primary (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 3, 2013
This is version 55 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program

Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Alternative products

Sequence annotation (Features)

Molecule processing

Regions

Sites

Natural variations

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protocols and materials databases

Family and domain databases

Other

Entry information

Relevant documents