Q805H4 (REP_PCV1C) Reviewed, UniProtKB/Swiss-Prot

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 1 (isolate China) (PCV1) [Reference proteome]

Taxonomic identifier

654929 [NCBI]

Taxonomic lineage

Viruses › ssDNA viruses › Circoviridae › Circovirus › Porcine circovirus 1

Virus host

Sus scrofa (Pig) [TaxID: 9823]

Protein attributes

Sequence length	312 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

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.7
Catalytic activity	ATP + H2O = ADP + phosphate.
Cofactor	Divalent metal cations, possibly magnesium or manganese By similarity.
Subunit structure	Interacts with the capsid protein; this interaction relocates Rep into the nucleus By similarity.
Subcellular location	Host nucleus Potential.
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	Complete proteome Multifunctional enzyme Reference proteome
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 5 isoforms produced by alternative splicing. [Align] [Select]

Isoform Rep (identifier: Q805H4-1)

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.

Isoform Rep' (identifier: Q805H4-2)

The sequence of this isoform differs from the canonical sequence as follows:
     120-168: VSTLLETGSL...QRDWKTAVHV → YFDYQQSGPP...TIHGGTRRPI
     169-312: Missing.

Isoform Rep3a (identifier: Q805H4-3)

The sequence of this isoform differs from the canonical sequence as follows:
     13-246: Missing.

Isoform Rep3b (identifier: Q805H4-4)

The sequence of this isoform differs from the canonical sequence as follows:
     13-251: Missing.

Isoform Rep3c-4a (identifier: Q805H4-5)

The sequence of this isoform differs from the canonical sequence as follows:
     13-247: RWVFTLNNPS...GGTVPFLARS → SGILVPAATS...RGSAATCLLL

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 312	312	Replication-associated protein		PRO_0000133088
Regions
	Nucleotide binding	171 – 178	8	ATP By similarity
	Motif	4 – 15	12	Nuclear localization signal Potential
	Motif	16 – 19	4	RCR-1 By similarity
	Motif	54 – 59	6	RCR-2 By similarity
	Motif	63 – 84	22	Nuclear localization signal Potential
	Motif	93 – 96	4	RCR-3 By similarity
Sites
	Active site	93	1	For DNA cleavage activity By similarity
	Metal binding	45	1	Divalent metal cation Potential
	Metal binding	54	1	Divalent metal cation Potential
	Metal binding	97	1	Divalent metal cation Potential
Natural variations
	Alternative sequence	13 – 251	239	Missing in isoform Rep3b.		VSP_015878
	Alternative sequence	13 – 247	235	RWVFT…FLARS → SGILVPAATSRKRKEPTSRI KNTAVKKATYLSSVELRGTR GSAATCLLL in isoform Rep3c-4a.		VSP_015879
	Alternative sequence	13 – 246	234	Missing in isoform Rep3a.		VSP_015877
	Alternative sequence	120 – 168	49	VSTLL…TAVHV → YFDYQQSGPPGMVLLNCCPS CRSSLSEDYYFAILEDCWRT IHGGTRRPI in isoform Rep'.		VSP_015880
	Alternative sequence	169 – 312	144	Missing in isoform Rep'.		VSP_015881
	Natural variant	179	1	Q → R in strain: Isolate IBRS-2.
Experimental info
	Sequence conflict	185	1	A → T in AAC34819. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform Rep [UniParc]. Last modified June 1, 2003. Version 1. Checksum: E3A5AFDD8BE0C3CF	FASTA	312	35,635
	10 20 30 40 50 60 MPSKKSGPQP HKRWVFTLNN PSEEEKNKIR ELPISLFDYF VCGEEGLEEG RTPHLQGFAN 70 80 90 100 110 120 FAKKQTFNKV KWYFGARCHI EKAKGTDQQN KEYCSKEGHI LIECGAPRNQ GKRSDLSTAV 130 140 150 160 170 180 STLLETGSLV TVAEQFPVTY VRNFRGLAEL LKVSGKMQQR DWKTAVHVIV GPPGCGKSQW 190 200 210 220 230 240 ARNFAEPSDT YWKPSRNKWW DGYHGEEVVV LDDFYGWLPW DDLLRLCDRY PLTVETKGGT 250 260 270 280 290 300 VPFLARSILI TSNQAPQEWY SSTAVPAVEA LYRRITTLQF WKTAGEQSTE VPEGRFEAVD 310 PPCALFPYKI NY
	Isoform Rep' [UniParc]. Checksum: 7B6F8BD1A844A86E	FASTA	168	19,273
	10 20 30 40 50 60 MPSKKSGPQP HKRWVFTLNN PSEEEKNKIR ELPISLFDYF VCGEEGLEEG RTPHLQGFAN 70 80 90 100 110 120 FAKKQTFNKV KWYFGARCHI EKAKGTDQQN KEYCSKEGHI LIECGAPRNQ GKRSDLSTAY 130 140 150 160 FDYQQSGPPG MVLLNCCPSC RSSLSEDYYF AILEDCWRTI HGGTRRPI
	Isoform Rep3a [UniParc]. Checksum: EFDD5391CD903AC2	FASTA	78	8,785
	10 20 30 40 50 60 MPSKKSGPQP HKSILITSNQ APQEWYSSTA VPAVEALYRR ITTLQFWKTA GEQSTEVPEG 70 RFEAVDPPCA LFPYKINY
	Isoform Rep3b [UniParc]. Checksum: EDC8D7895E4364A0	FASTA	73	8,257
	10 20 30 40 50 60 MPSKKSGPQP HKSNQAPQEW YSSTAVPAVE ALYRRITTLQ FWKTAGEQST EVPEGRFEAV 70 DPPCALFPYK INY
	Isoform Rep3c-4a [UniParc]. Checksum: B9F35549EFBD9C26	FASTA	126	13,882
	10 20 30 40 50 60 MPSKKSGPQP HKSGILVPAA TSRKRKEPTS RIKNTAVKKA TYLSSVELRG TRGSAATCLL 70 80 90 100 110 120 LILITSNQAP QEWYSSTAVP AVEALYRRIT TLQFWKTAGE QSTEVPEGRF EAVDPPCALF PYKINY

References

[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.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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.
RefSeq	NP_065678.1. NC_001792.2.
3D structure databases
ProteinModelPortal	Q805H4.
SMR	Q805H4. Positions 2-113.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	7693233.
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...

Entry information

Entry name

REP_PCV1C

Accession

Primary (citable) accession number: Q805H4
Secondary accession number(s): O90238 , Q6DMP3, Q80QL6, Q80QL7, Q80QL8, Q80QL9

Entry history

Integrated into UniProtKB/Swiss-Prot:	October 25, 2005
Last sequence update:	June 1, 2003
Last modified:	April 3, 2013
This is version 59 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program