ID   REP3_MDV1               Reviewed;         284 AA.
AC   Q9Z0D3;
DT   07-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-1999, sequence version 1.
DT   24-JAN-2024, entry version 79.
DE   RecName: Full=Para-Rep C3;
DE            Short=Rep3;
DE            EC=2.7.7.-;
DE            EC=3.1.21.-;
DE            EC=3.6.1.-;
DE   AltName: Full=Replication-associated protein of non-essential DNA C3;
GN   Name=C3;
OS   Milk vetch dwarf virus (isolate N) (MDV).
OC   Viruses; Monodnaviria; Shotokuvirae; Cressdnaviricota; Arfiviricetes;
OC   Mulpavirales; Nanoviridae; Nanovirus; Milk vetch dwarf virus.
OX   NCBI_TaxID=291605;
OH   NCBI_TaxID=47065; Astragalus sinicus (Chinese milk vetch).
OH   NCBI_TaxID=3847; Glycine max (Soybean) (Glycine hispida).
OH   NCBI_TaxID=3885; Phaseolus vulgaris (Kidney bean) (French bean).
OH   NCBI_TaxID=3888; Pisum sativum (Garden pea) (Lathyrus oleraceus).
OH   NCBI_TaxID=3906; Vicia faba (Broad bean) (Faba vulgaris).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=9880029; DOI=10.1099/0022-1317-79-12-3111;
RA   Sano Y., Wada M., Hashimoto Y., Matsumoto T., Kojima M.;
RT   "Sequences of ten circular ssDNA components associated with the milk vetch
RT   dwarf virus genome.";
RL   J. Gen. Virol. 79:3111-3118(1998).
CC   -!- FUNCTION: Initiates and terminates the replication only of its own
CC       subviral DNA molecule. The closed circular ssDNA genome is first
CC       converted to a superhelical dsDNA. Rep binds a specific hairpin at the
CC       genome origin of replication. Introduces an endonucleolytic nick within
CC       the intergenic region of the genome, thereby initiating the rolling
CC       circle replication (RCR). Following cleavage, binds covalently to the
CC       5'-phosphate of DNA as a tyrosyl ester. The cleavage gives rise to a
CC       free 3'-OH that serves as a primer for the cellular DNA polymerase. The
CC       polymerase synthesizes the (+) strand DNA by rolling circle mechanism.
CC       After one round of replication, a Rep-catalyzed nucleotidyl transfer
CC       reaction releases a circular single-stranded virus genome, thereby
CC       terminating the replication. Displays origin-specific DNA cleavage,
CC       nucleotidyl transferase, ATPase and helicase activities (By
CC       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: Homooligomer (Potential). Rep binds to repeated DNA motifs
CC       (iterons) (By similarity). {ECO:0000250, ECO:0000305}.
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   -!- MISCELLANEOUS: The genome of nanoviruses is composed of six to eight
CC       segments. In addition, some isolates contain subviral DNAs.
CC   -!- SIMILARITY: Belongs to the nanoviridea/circoviridae replication-
CC       associated protein family. {ECO:0000305}.
CC   -!- CAUTION: This protein is encoded by a subviral DNA that is not present
CC       in all isolates of the virus. {ECO:0000305}.
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DR   EMBL; AB000922; BAA33982.1; -; Genomic_DNA.
DR   SMR; Q9Z0D3; -.
DR   Proteomes; UP000008236; 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; IPR003365; Viral_rep_N.
DR   Pfam; PF00910; RNA_helicase; 1.
DR   Pfam; PF02407; Viral_Rep; 1.
DR   PROSITE; PS52020; CRESS_DNA_REP; 1.
PE   3: Inferred from homology;
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..284
FT                   /note="Para-Rep C3"
FT                   /id="PRO_0000378524"
FT   DOMAIN          3..98
FT                   /note="CRESS-DNA virus Rep endonuclease"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   MOTIF           10..13
FT                   /note="RCR-1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   MOTIF           42..44
FT                   /note="RCR-2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   MOTIF           51..71
FT                   /note="Nuclear localization signal"
FT                   /evidence="ECO:0000255"
FT   MOTIF           81..84
FT                   /note="RCR-3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   MOTIF           98..104
FT                   /note="Nuclear localization signal"
FT                   /evidence="ECO:0000255"
FT   ACT_SITE        81
FT                   /note="For DNA cleavage activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   BINDING         36
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         42
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         86
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         174..182
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   284 AA;  33349 MW;  C9C880B8459B3355 CRC64;
     MPTVQSTCWV FTLNFKGEIP ILPFNERVQY ACWQHERVGH DHLQGFIQMK AQQSLGQMKA
     IIPGAHFEKM RALNSDQAKA YAMKEDTRIE GPWEYGKYIK KGSHKRKIME RFEDDPEEMK
     IEDPSLYRRC LSRKMTEEQR STAEWNYDMK PWQDQVIQEI EETPDYRKII WVYGPKGGEG
     KSTFARYLSL KQGWGYLPGG PTHDMLHIIS GEPKNNWVFD IPRVASEYVN YGVLEQVKNR
     VMVNTKYEPI VIRDDNHPVH VIVFANCMPD FTKISEDRMK IVHC
//