ID   REP_BFDV                Reviewed;         289 AA.
AC   Q9YUD3;
DT   26-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-1999, sequence version 1.
DT   08-NOV-2023, entry version 82.
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   Beak and feather disease virus (BFDV).
OC   Viruses; Monodnaviria; Shotokuvirae; Cressdnaviricota; Arfiviricetes;
OC   Cirlivirales; Circoviridae; Circovirus; Circovirus parrot.
OX   NCBI_TaxID=77856;
OH   NCBI_TaxID=116991; Gracula.
OH   NCBI_TaxID=9223; Psittaciformes.
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=9791035; DOI=10.1006/viro.1998.9324;
RA   Bassami M.R., Berryman D., Wilcox G.E., Raidal S.R.;
RT   "Psittacine beak and feather disease virus nucleotide sequence analysis and
RT   its relationship to porcine circovirus, plant circoviruses, and chicken
RT   anaemia virus.";
RL   Virology 249:453-459(1998).
RN   [2]
RP   INTERACTION WITH CAPSID PROTEIN.
RX   PubMed=16809327; DOI=10.1128/jvi.02559-05;
RA   Heath L., Williamson A.L., Rybicki E.P.;
RT   "The capsid protein of beak and feather disease virus binds to the viral
RT   DNA and is responsible for transporting the replication-associated protein
RT   into the nucleus.";
RL   J. Virol. 80:7219-7225(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, nucleotidyl transferase, ATPase and
CC       helicase activities. ATPase activity is probably carried by the isoform
CC       Rep (By similarity). {ECO:0000250}.
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; Evidence={ECO:0000250};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC       Note=Divalent metal cations, possibly Mg(2+) or Mn(2+). {ECO:0000250};
CC   -!- SUBUNIT: Interacts with the capsid protein; this interaction relocates
CC       Rep into the nucleus. {ECO:0000269|PubMed:16809327}.
CC   -!- SUBCELLULAR LOCATION: Host nucleus {ECO:0000305}.
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; AF080560; AAC69861.1; -; Genomic_DNA.
DR   SMR; Q9YUD3; -.
DR   Proteomes; UP000007454; 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   Gene3D; 3.40.1310.20; -; 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; P-loop containing nucleoside triphosphate hydrolases; 1.
DR   PROSITE; PS52020; CRESS_DNA_REP; 1.
PE   1: Evidence at protein level;
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; Reference proteome; Transferase.
FT   CHAIN           1..289
FT                   /note="Replication-associated protein"
FT                   /id="PRO_0000319862"
FT   DOMAIN          6..103
FT                   /note="CRESS-DNA virus Rep endonuclease"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   MOTIF           4..13
FT                   /note="Nuclear localization signal"
FT                   /evidence="ECO:0000255"
FT   MOTIF           13..16
FT                   /note="RCR-1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   MOTIF           51..53
FT                   /note="RCR-2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   MOTIF           60..80
FT                   /note="Nuclear localization signal"
FT                   /evidence="ECO:0000255"
FT   MOTIF           89..92
FT                   /note="RCR-3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   ACT_SITE        89
FT                   /note="For DNA cleavage activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   BINDING         43
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         51
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         93
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         165..172
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   289 AA;  33446 MW;  A52614012B831791 CRC64;
     MPSKEGSGCR RWCFTLNNPT DGEIEFVRSL GPDEFYYAIV GREKGEQGTP HLQGYFHFKN
     KKRLSALKKL LPRAHFERAK GSDADNEKYC SKEGDVILTL GIVARDGHRA FDGAVAAVMS
     GRKMKEVARE FPEVYVRHGR GLHNLSLLVG SSPRDFKTEV DVIYGPPGCG KSRWANEQPG
     TKYYKMRGEW WDGYDGEDVV VLDDFYGWLP YCEMLRLCDR YPHKVPVKGA FVEFTSKRII
     ITSNKPPETW YKEDCDPKPL FRRFTRVWWY NVDKLEQVRP DFLAHPINY
//