REP_PCV2
ID REP_PCV2 Reviewed; 314 AA.
AC Q8BB16; Q8BB13; Q8BB14; Q8BB15;
DT 25-OCT-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 86.
DE RecName: Full=Replication-associated protein;
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 2 (PCV2).
OC Viruses; Monodnaviria; Shotokuvirae; Cressdnaviricota; Arfiviricetes;
OC Cirlivirales; Circoviridae; Circovirus.
OX NCBI_TaxID=85708;
OH NCBI_TaxID=9823; Sus scrofa (Pig).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORMS REP; REP'; REP3A; REP3B AND
RP REP3C), AND ALTERNATIVE PROMOTER USAGE.
RC STRAIN=Isolate PCV/688;
RX PubMed=12504550; DOI=10.1006/viro.2002.1733;
RA Cheung A.K.;
RT "Transcriptional analysis of porcine circovirus type 2.";
RL Virology 305:168-180(2003).
RN [2]
RP FUNCTION, MUTAGENESIS OF 179-GLY-LYS-180, AND ALTERNATIVE SPLICING.
RC STRAIN=Isolate PCV/688;
RX PubMed=12954212; DOI=10.1016/s0042-6822(03)00373-8;
RA Cheung A.K.;
RT "The essential and nonessential transcription units for viral protein
RT synthesis and DNA replication of porcine circovirus type 2.";
RL Virology 313:452-459(2003).
RN [3]
RP SUBCELLULAR LOCATION, AND NUCLEAR LOCALIZATION SIGNAL.
RX PubMed=19150331; DOI=10.1016/j.bbrc.2009.01.001;
RA Lin W.-L., Chien M.-S., Du Y.-W., Wu P.-C., Huang C.;
RT "The N-terminus of porcine circovirus type 2 replication protein is
RT required for nuclear localization and ori binding activities.";
RL Biochem. Biophys. Res. Commun. 379:1066-1071(2009).
RN [4]
RP REVIEW.
RX PubMed=25011695; DOI=10.1007/s11262-014-1099-z;
RA Lv Q.Z., Guo K.K., Zhang Y.M.;
RT "Current understanding of genomic DNA of porcine circovirus type 2.";
RL Virus Genes 49:1-10(2014).
RN [5]
RP FUNCTION.
RX PubMed=25768890; DOI=10.1016/j.virol.2015.01.004;
RA Cheung A.K.;
RT "Specific functions of the Rep and Rep' proteins of porcine circovirus
RT during copy-release and rolling-circle DNA replication.";
RL Virology 481:43-50(2015).
RN [6]
RP STRUCTURE BY NMR OF 1-116, COFACTOR, AND CHARACTERIZATION.
RX PubMed=17275023; DOI=10.1016/j.jmb.2007.01.002;
RA Vega-Rocha S., Byeon I.-J.L., Gronenborn B., Gronenborn A.M.,
RA Campos-Olivas R.;
RT "Solution structure, divalent metal and DNA binding of the endonuclease
RT domain from the replication initiation protein from porcine circovirus 2.";
RL J. Mol. Biol. 367:473-487(2007).
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:12954212, ECO:0000269|PubMed:25768890}.
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:0000305|PubMed:17275023};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000305|PubMed:17275023};
CC Note=Divalent metal cations, possibly Mg(2+) or Mn(2+).
CC {ECO:0000305|PubMed:17275023};
CC -!- SUBUNIT: Interacts with the capsid protein; this interaction relocates
CC Rep into the nucleus. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Host nucleus {ECO:0000269|PubMed:19150331}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative promoter usage, Alternative splicing; Named isoforms=10;
CC Name=Rep;
CC IsoId=Q8BB16-1; Sequence=Displayed;
CC Name=Rep';
CC IsoId=Q8BB16-2; Sequence=VSP_015884, VSP_015885;
CC Name=NS462;
CC IsoId=Q8BB12-2; Sequence=External;
CC Name=NS642;
CC IsoId=Q8BB12-3; Sequence=External;
CC Name=NS0;
CC IsoId=Q8BB12-1; Sequence=External;
CC Name=NS515;
CC IsoId=Q8BB16-6; Sequence=Not described;
CC Name=NS672;
CC IsoId=Q8BB16-7; Sequence=Not described;
CC Name=Rep3a;
CC IsoId=Q8BB16-3; Sequence=VSP_015883;
CC Name=Rep3b;
CC IsoId=Q8BB16-4; Sequence=VSP_015882;
CC Name=Rep3c;
CC IsoId=Q8BB16-5; Sequence=Not described;
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 -!- MISCELLANEOUS: [Isoform Rep]: Produced by alternative promoter usage.
CC {ECO:0000305|PubMed:12504550}.
CC -!- MISCELLANEOUS: [Isoform Rep']: Produced by alternative splicing of
CC isoform Rep. {ECO:0000305|PubMed:12504550}.
CC -!- MISCELLANEOUS: [Isoform NS515]: Produced by alternative promoter usage.
CC {ECO:0000305|PubMed:12504550}.
CC -!- MISCELLANEOUS: [Isoform NS672]: Produced by alternative promoter usage.
CC {ECO:0000305|PubMed:12504550}.
CC -!- MISCELLANEOUS: [Isoform Rep3a]: Produced by alternative splicing of
CC isoform Rep. {ECO:0000305|PubMed:12504550}.
CC -!- MISCELLANEOUS: [Isoform Rep3b]: Produced by alternative splicing of
CC isoform Rep. {ECO:0000305|PubMed:12504550}.
CC -!- MISCELLANEOUS: [Isoform Rep3c]: Produced by alternative splicing of
CC isoform Rep. {ECO:0000305|PubMed:12504550}.
CC -!- SIMILARITY: Belongs to the nanoviruses/circoviruses replication-
CC associated protein family. {ECO:0000305}.
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DR EMBL; AY094619; AAM21844.1; -; Genomic_DNA.
DR EMBL; AY094619; AAM21845.1; -; Genomic_DNA.
DR EMBL; AY094619; AAM21846.1; -; Genomic_DNA.
DR EMBL; AY094619; AAM21847.1; -; Genomic_DNA.
DR PDB; 2HW0; NMR; -; A=2-116.
DR PDB; 6WDZ; X-ray; 2.03 A; A/D/G=2-116.
DR PDBsum; 2HW0; -.
DR PDBsum; 6WDZ; -.
DR BMRB; Q8BB16; -.
DR SMR; Q8BB16; -.
DR EvolutionaryTrace; Q8BB16; -.
DR Proteomes; UP000000470; 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 1: Evidence at protein level;
KW 3D-structure; Alternative promoter usage; Alternative splicing;
KW ATP-binding; Covalent protein-DNA linkage; DNA replication; DNA-binding;
KW Endonuclease; Helicase; Host nucleus; Hydrolase; Metal-binding;
KW Multifunctional enzyme; Nuclease; Nucleotide-binding;
KW Nucleotidyltransferase; Transferase.
FT CHAIN 1..314
FT /note="Replication-associated protein"
FT /id="PRO_0000133089"
FT REGION 1..29
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 4..18
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000269|PubMed:19150331"
FT MOTIF 19..23
FT /note="RCR-1"
FT /evidence="ECO:0000250|UniProtKB:P27260"
FT MOTIF 55..61
FT /note="RCR-2"
FT /evidence="ECO:0000250|UniProtKB:P27260"
FT MOTIF 96..99
FT /note="RCR-3"
FT /evidence="ECO:0000250|UniProtKB:P27260"
FT ACT_SITE 96
FT /note="For DNA cleavage activity"
FT /evidence="ECO:0000250|UniProtKB:P27260"
FT BINDING 48
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255"
FT BINDING 57
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255"
FT BINDING 100
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255"
FT BINDING 174..181
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P27260"
FT VAR_SEQ 16..254
FT /note="Missing (in isoform Rep3b)"
FT /evidence="ECO:0000305"
FT /id="VSP_015882"
FT VAR_SEQ 16..249
FT /note="Missing (in isoform Rep3a)"
FT /evidence="ECO:0000305"
FT /id="VSP_015883"
FT VAR_SEQ 123..178
FT /note="VSTLLESGSLVTVAEQHPVTFVRNFRGLAELLKVSGKMQKRDWKTNVHVIVG
FT PPGC -> YSDYQQSDPVGMVLLNCCPSCRSSLSEDYFLGILEECYRTIHGGRGPVRHP
FT FPPMP (in isoform Rep')"
FT /evidence="ECO:0000305"
FT /id="VSP_015884"
FT VAR_SEQ 179..314
FT /note="Missing (in isoform Rep')"
FT /evidence="ECO:0000305"
FT /id="VSP_015885"
FT MUTAGEN 179..180
FT /note="GK->DI: Complete loss of viral DNA synthesis."
FT /evidence="ECO:0000269|PubMed:12954212"
FT STRAND 8..11
FT /evidence="ECO:0007829|PDB:2HW0"
FT STRAND 14..23
FT /evidence="ECO:0007829|PDB:6WDZ"
FT HELIX 26..33
FT /evidence="ECO:0007829|PDB:6WDZ"
FT HELIX 37..39
FT /evidence="ECO:0007829|PDB:6WDZ"
FT STRAND 40..48
FT /evidence="ECO:0007829|PDB:6WDZ"
FT STRAND 57..68
FT /evidence="ECO:0007829|PDB:6WDZ"
FT HELIX 70..77
FT /evidence="ECO:0007829|PDB:6WDZ"
FT TURN 78..80
FT /evidence="ECO:0007829|PDB:2HW0"
FT STRAND 82..85
FT /evidence="ECO:0007829|PDB:6WDZ"
FT HELIX 90..98
FT /evidence="ECO:0007829|PDB:6WDZ"
FT STRAND 103..108
FT /evidence="ECO:0007829|PDB:6WDZ"
SQ SEQUENCE 314 AA; 35762 MW; 3FE9D85F2CD656FC CRC64;
MPSKKNGRSG PQPHKRWVFT LNNPSEDERK KIREPPISLF DYFIVGEEGN EEGRTPHLQG
FANFVKKQTF NKVKWYLGAR CHIEKAKGTD QQNKEYCSKE GNLLIECGAP RSQGQRSDLS
TAVSTLLESG SLVTVAEQHP VTFVRNFRGL AELLKVSGKM QKRDWKTNVH VIVGPPGCGK
SKWAANFADP ETTYWKPPRN KWWDGYHGEE VVVIDDFYGW LPWDDLLRLC DRYPLTVETK
GGTVPFLARS ILITSNQTPL EWYSSTAVPA VEALYRRITS LVFWKNATEQ STEEGGQFVT
LSPPCPEFPY EINY
