REP_PCV1
ID REP_PCV1 Reviewed; 312 AA.
AC Q805H4; O90238; Q6DMP3; Q80QL6; Q80QL7; Q80QL8; Q80QL9;
DT 25-OCT-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 88.
DE RecName: Full=Replication-associated protein;
DE Short=Rep;
DE EC=2.7.7.-;
DE EC=3.1.21.-;
DE EC=3.6.1.-;
DE AltName: Full=ATP-dependent helicase Rep;
DE AltName: Full=RepP;
GN Name=Rep; ORFNames=ORF1;
OS Porcine circovirus 1 (PCV1).
OC Viruses; Monodnaviria; Shotokuvirae; Cressdnaviricota; Arfiviricetes;
OC Cirlivirales; Circoviridae; Circovirus.
OX NCBI_TaxID=133704;
OH NCBI_TaxID=9823; Sus scrofa (Pig).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=Isolate ATCC CCL-33/PK15;
RX PubMed=9787657; DOI=10.1007/s007050050412;
RA Niagro F.D., Forsthoefel A.N., Lawther R.P., Kamalanathan L., Ritchie B.W.,
RA Latimer K.S., Lukert P.D.;
RT "Beak and feather disease virus and porcine circovirus genomes:
RT intermediates between the geminiviruses and plant circoviruses.";
RL Arch. Virol. 143:1723-1744(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORMS REP; REP'; REP3A; REP3B AND
RP REP3C-4A).
RC STRAIN=Isolate ATCC CCL-33/PK15;
RX PubMed=12788629; DOI=10.1016/s0042-6822(03)00096-5;
RA Cheung A.K.;
RT "Comparative analysis of the transcriptional patterns of pathogenic and
RT nonpathogenic porcine circoviruses.";
RL Virology 310:41-49(2003).
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=Isolate IBRS-2;
RA Cao S., Chen H., Ju C.;
RT "Genomic sequence of Porcine circovirus type 1 isolated from IBRS-2 cell
RT line.";
RL Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases.
RN [4]
RP MODEL OF REPLICATION.
RX PubMed=15047840; DOI=10.1128/jvi.78.8.4268-4277.2004;
RA Cheung A.K.;
RT "Detection of template strand switching during initiation and termination
RT of DNA replication of porcine circovirus.";
RL J. Virol. 78:4268-4277(2004).
RN [5]
RP MODEL OF REPLICATION.
RX PubMed=15308698; DOI=10.1128/jvi.78.17.9016-9029.2004;
RA Cheung A.K.;
RT "Palindrome regeneration by template strand-switching mechanism at the
RT origin of DNA replication of porcine circovirus via the rolling-circle
RT melting-pot replication model.";
RL J. Virol. 78:9016-9029(2004).
RN [6]
RP MODEL OF REPLICATION.
RX PubMed=15708589; DOI=10.1016/j.virol.2004.12.016;
RA Cheung A.K.;
RT "Detection of rampant nucleotide reversion at the origin of DNA replication
RT of porcine circovirus type 1.";
RL Virology 333:22-30(2005).
RN [7]
RP FUNCTION.
RX PubMed=16775310; DOI=10.1128/jvi.02506-05;
RA Steinfeldt T., Finsterbusch T., Mankertz A.;
RT "Demonstration of nicking/joining activity at the origin of DNA replication
RT associated with the rep and rep' proteins of porcine circovirus type 1.";
RL J. Virol. 80:6225-6234(2006).
CC -!- FUNCTION: Essential for the replication of viral ssDNA. The closed
CC circular ssDNA genome is first converted to a superhelical dsDNA. Rep
CC and/or Rep' binds a specific hairpin at the genome origin of
CC replication. Introduces an endonucleolytic nick within the conserved
CC sequence 5'-AGTATTAC-3' in the intergenic region of the genome, thereby
CC initiating the rolling circle replication (RCR). Following cleavage,
CC binds covalently to the 5'-phosphate of DNA as a tyrosyl ester. The
CC cleavage gives rise to a free 3'-OH that serves as a primer for the
CC cellular DNA polymerase. The polymerase synthesizes the (+) strand DNA
CC by rolling circle mechanism. After one round of replication, a Rep-
CC catalyzed nucleotidyl transfer reaction releases a circular single-
CC stranded virus genome, thereby terminating the replication. Displays
CC origin-specific DNA cleavage, and nucleotidyl transferase.
CC {ECO:0000269|PubMed:16775310}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:456216;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000269|PubMed:16775310};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000303|PubMed:16775310};
CC Note=Divalent metal cations, possibly Mg(2+) or Mn(2+).
CC {ECO:0000303|PubMed:16775310};
CC -!- SUBUNIT: Interacts with the capsid protein; this interaction relocates
CC Rep into the nucleus. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Host nucleus {ECO:0000305}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=5;
CC Name=Rep;
CC IsoId=Q805H4-1; Sequence=Displayed;
CC Name=Rep';
CC IsoId=Q805H4-2; Sequence=VSP_015880, VSP_015881;
CC Name=Rep3a;
CC IsoId=Q805H4-3; Sequence=VSP_015877;
CC Name=Rep3b;
CC IsoId=Q805H4-4; Sequence=VSP_015878;
CC Name=Rep3c-4a;
CC IsoId=Q805H4-5; Sequence=VSP_015879;
CC -!- DOMAIN: There are 3 rolling circle replication (RCR) motifs. RCR-2 is
CC probably involved in metal coordination. RCR-3 is required for
CC phosphodiester bond cleavage for initiation of RCR.
CC -!- SIMILARITY: Belongs to the nanoviruses/circoviruses replication-
CC associated protein family. {ECO:0000305}.
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DR EMBL; AF071879; AAC34819.1; -; Genomic_DNA.
DR EMBL; AY193712; AAO39666.1; -; Genomic_DNA.
DR EMBL; AY184287; AAN77859.1; -; Genomic_DNA.
DR EMBL; AY184287; AAN77860.1; -; Genomic_DNA.
DR EMBL; AY184287; AAN77861.1; -; Genomic_DNA.
DR EMBL; AY184287; AAN77862.1; -; Genomic_DNA.
DR EMBL; AY184287; AAN77863.1; -; Genomic_DNA.
DR EMBL; AY660574; AAT72755.1; -; Genomic_DNA.
DR RefSeq; NP_065678.1; NC_001792.2.
DR SMR; Q805H4; -.
DR GeneID; 7693233; -.
DR KEGG; vg:7693233; -.
DR Proteomes; UP000007023; Genome.
DR Proteomes; UP000115772; Genome.
DR Proteomes; UP000136520; Genome.
DR Proteomes; UP000180335; Genome.
DR GO; GO:0042025; C:host cell nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016887; F:ATP hydrolysis activity; IEA:RHEA.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0016888; F:endodeoxyribonuclease activity, producing 5'-phosphomonoesters; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016779; F:nucleotidyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR GO; GO:0003724; F:RNA helicase activity; IEA:InterPro.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR GO; GO:0018142; P:protein-DNA covalent cross-linking; IEA:InterPro.
DR GO; GO:0039684; P:rolling circle single-stranded viral DNA replication; IDA:UniProtKB.
DR Gene3D; 3.40.50.300; -; 1.
DR InterPro; IPR000605; Helicase_SF3_ssDNA/RNA_vir.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR003365; Viral_rep_N.
DR Pfam; PF00910; RNA_helicase; 1.
DR Pfam; PF02407; Viral_Rep; 1.
DR SUPFAM; SSF52540; SSF52540; 1.
PE 3: Inferred from homology;
KW Alternative splicing; ATP-binding; Covalent protein-DNA linkage;
KW DNA replication; DNA-binding; Endonuclease; Helicase; Host nucleus;
KW Hydrolase; Metal-binding; Multifunctional enzyme; Nuclease;
KW Nucleotide-binding; Nucleotidyltransferase; Reference proteome;
KW Transferase.
FT CHAIN 1..312
FT /note="Replication-associated protein"
FT /id="PRO_0000133088"
FT MOTIF 4..15
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000250|UniProtKB:Q8BB16"
FT MOTIF 16..20
FT /note="RCR-1"
FT /evidence="ECO:0000250|UniProtKB:P27260"
FT MOTIF 52..58
FT /note="RCR-2"
FT /evidence="ECO:0000250|UniProtKB:P27260"
FT MOTIF 93..96
FT /note="RCR-3"
FT /evidence="ECO:0000250|UniProtKB:P27260"
FT ACT_SITE 93
FT /note="For DNA cleavage activity"
FT /evidence="ECO:0000250|UniProtKB:P27260"
FT BINDING 45
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255"
FT BINDING 54
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255"
FT BINDING 97
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255"
FT BINDING 171..178
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P27260"
FT VAR_SEQ 13..251
FT /note="Missing (in isoform Rep3b)"
FT /evidence="ECO:0000305"
FT /id="VSP_015878"
FT VAR_SEQ 13..247
FT /note="RWVFTLNNPSEEEKNKIRELPISLFDYFVCGEEGLEEGRTPHLQGFANFAKK
FT QTFNKVKWYFGARCHIEKAKGTDQQNKEYCSKEGHILIECGAPRNQGKRSDLSTAVSTL
FT LETGSLVTVAEQFPVTYVRNFRGLAELLKVSGKMQQRDWKTAVHVIVGPPGCGKSQWAR
FT NFAEPSDTYWKPSRNKWWDGYHGEEVVVLDDFYGWLPWDDLLRLCDRYPLTVETKGGTV
FT PFLARS -> SGILVPAATSRKRKEPTSRIKNTAVKKATYLSSVELRGTRGSAATCLLL
FT (in isoform Rep3c-4a)"
FT /evidence="ECO:0000305"
FT /id="VSP_015879"
FT VAR_SEQ 13..246
FT /note="Missing (in isoform Rep3a)"
FT /evidence="ECO:0000305"
FT /id="VSP_015877"
FT VAR_SEQ 120..168
FT /note="VSTLLETGSLVTVAEQFPVTYVRNFRGLAELLKVSGKMQQRDWKTAVHV ->
FT YFDYQQSGPPGMVLLNCCPSCRSSLSEDYYFAILEDCWRTIHGGTRRPI (in
FT isoform Rep')"
FT /evidence="ECO:0000305"
FT /id="VSP_015880"
FT VAR_SEQ 169..312
FT /note="Missing (in isoform Rep')"
FT /evidence="ECO:0000305"
FT /id="VSP_015881"
FT VARIANT 179
FT /note="Q -> R (in strain: Isolate IBRS-2)"
FT CONFLICT 185
FT /note="A -> T (in Ref. 1; AAC34819)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 312 AA; 35635 MW; E3A5AFDD8BE0C3CF CRC64;
MPSKKSGPQP HKRWVFTLNN PSEEEKNKIR ELPISLFDYF VCGEEGLEEG RTPHLQGFAN
FAKKQTFNKV KWYFGARCHI EKAKGTDQQN KEYCSKEGHI LIECGAPRNQ GKRSDLSTAV
STLLETGSLV TVAEQFPVTY VRNFRGLAEL LKVSGKMQQR DWKTAVHVIV GPPGCGKSQW
ARNFAEPSDT YWKPSRNKWW DGYHGEEVVV LDDFYGWLPW DDLLRLCDRY PLTVETKGGT
VPFLARSILI TSNQAPQEWY SSTAVPAVEA LYRRITTLQF WKTAGEQSTE VPEGRFEAVD
PPCALFPYKI NY
