Reviewed, UniProtKB/Swiss-Prot Q9YUD3 (REP_BFDV)

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

Beak and feather disease virus (BFDV) [Complete proteome]

Taxonomic identifier

77856 [NCBI]

Taxonomic lineage

Viruses › ssDNA viruses › Circoviridae › Circovirus

Virus host

Psittaciformes [TaxID: 9223]
Gracula [TaxID: 116991]

Protein attributes

Sequence length	289 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.
Catalytic activity	ATP + H2O = ADP + phosphate.
Cofactor	Divalent metal cations, possibly magnesium or manganese 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
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
Gene Ontology (GO)
Biological process	DNA replication Inferred from electronic annotation. Source: UniProtKB-KW protein-DNA covalent cross-linking Inferred from electronic annotation. Source: UniProtKB-KW
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: EC 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...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 289	289	Replication-associated protein		PRO_0000319862
Regions
	Nucleotide binding	165 – 172	8	ATP By similarity
	Motif	4 – 13	10	Nuclear localization signal Potential
	Motif	14 – 17	4	RCR-1 By similarity
	Motif	51 – 56	6	RCR-2 By similarity
	Motif	60 – 80	21	Nuclear localization signal Potential
	Motif	89 – 92	4	RCR-3 By similarity
Sites
	Active site	89	1	For DNA cleavage activity By similarity
	Metal binding	43	1	Divalent metal cation Potential
	Metal binding	51	1	Divalent metal cation Potential
	Metal binding	93	1	Divalent metal cation Potential

Sequences

	Sequence		Length	Mass (Da)
	Q9YUD3-1 [UniParc]. Last modified May 1, 1999. Version 1. Checksum: A52614012B831791	FASTA	289	33,446
	10 20 30 40 50 60 MPSKEGSGCR RWCFTLNNPT DGEIEFVRSL GPDEFYYAIV GREKGEQGTP HLQGYFHFKN 70 80 90 100 110 120 KKRLSALKKL LPRAHFERAK GSDADNEKYC SKEGDVILTL GIVARDGHRA FDGAVAAVMS 130 140 150 160 170 180 GRKMKEVARE FPEVYVRHGR GLHNLSLLVG SSPRDFKTEV DVIYGPPGCG KSRWANEQPG 190 200 210 220 230 240 TKYYKMRGEW WDGYDGEDVV VLDDFYGWLP YCEMLRLCDR YPHKVPVKGA FVEFTSKRII 250 260 270 280 ITSNKPPETW YKEDCDPKPL FRRFTRVWWY NVDKLEQVRP DFLAHPINY

References

[1]

"Psittacine beak and feather disease virus nucleotide sequence analysis and its relationship to porcine circovirus, plant circoviruses, and chicken anaemia virus." Bassami M.R., Berryman D., Wilcox G.E., Raidal S.R. Virology 249:453-459(1998) [PubMed: 9791035] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].

Cross-references

Sequence databases
EMBL GenBank DDBJ	AF080560 Genomic DNA. Translation: AAC69861.1.
3D structure databases
SMR	Q9YUD3. Positions 8-109.
ModBase	Search...
Enzyme and pathway databases
BRENDA	3.6.1.3. 303037.
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_BFDV

Accession

Primary (citable) accession number: Q9YUD3

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 26, 2008
Last sequence update:	May 1, 1999
Last modified:	January 19, 2010
This is version 41 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)