ID   REP2_MDV1               Reviewed;         282 AA.
AC   Q9Z0D4;
DT   07-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-1999, sequence version 1.
DT   24-JAN-2024, entry version 83.
DE   RecName: Full=Para-Rep C2;
DE            Short=Rep2;
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 C2;
GN   Name=C2;
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; AB000921; BAA33981.1; -; Genomic_DNA.
DR   SMR; Q9Z0D4; -.
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..282
FT                   /note="Para-Rep C2"
FT                   /id="PRO_0000378522"
FT   DOMAIN          1..99
FT                   /note="CRESS-DNA virus Rep endonuclease"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   MOTIF           7..10
FT                   /note="RCR-1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   MOTIF           47..49
FT                   /note="RCR-2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   MOTIF           56..77
FT                   /note="Nuclear localization signal"
FT                   /evidence="ECO:0000255"
FT   MOTIF           86..89
FT                   /note="RCR-3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   MOTIF           99..105
FT                   /note="Nuclear localization signal"
FT                   /evidence="ECO:0000255"
FT   ACT_SITE        86
FT                   /note="For DNA cleavage activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   BINDING         38
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         47
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   282 AA;  32682 MW;  6E8CE00C0BB7462E CRC64;
     MASKRWCFTL NYKTALERET FISLFSRDEL NYFVCGDEIA PTTGQKHLQG YVSMKKLIRL
     GGLKKKFGSI AHWEIAKGDD FQNRDYCTKE TLIAEIGAPV KKGSNRRKIM EIYEEDPEEM
     KLRDPDTALR CKAKKLREEY CSEVSVFSLR PWQIELHRAL MEVPDDRTII WAYGPDGGEG
     KSTFAKELIK YGWFYTAGGK TQDILYMYAQ DPERNIAFDV PRCSSEMMNY QAMEMMKNRV
     FASTKYRPVD LCIRKKVHLI VFANVAPDPT KLSEDRIVII NC
//