ID   MREP_SCSVF              Reviewed;         286 AA.
AC   Q9ICP7;
DT   07-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT   01-OCT-2000, sequence version 1.
DT   08-NOV-2023, entry version 65.
DE   RecName: Full=Master replication protein;
DE            Short=M-Rep;
DE            EC=2.7.7.-;
DE            EC=3.1.21.-;
DE            EC=3.6.1.-;
GN   Name=DNA-R; Synonyms=C8;
OS   Subterranean clover stunt virus (strain F) (SCSV).
OC   Viruses; Monodnaviria; Shotokuvirae; Cressdnaviricota; Arfiviricetes;
OC   Mulpavirales; Nanoviridae; Nanovirus; Subterranean clover stunt virus.
OX   NCBI_TaxID=291607;
OH   NCBI_TaxID=3900; Trifolium subterraneum (Subterranean clover).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=10936099; DOI=10.1006/viro.2000.0439;
RA   Timchenko T., Katul L., Sano Y., de Kouchkovsky F., Vetten H.J.,
RA   Gronenborn B.;
RT   "The master rep concept in nanovirus replication: identification of missing
RT   genome components and potential for natural genetic reassortment.";
RL   Virology 274:189-195(2000).
CC   -!- FUNCTION: Essential for the replication of all genomic viral ssDNA
CC       (trans-replication). 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 conserved sequence 5'-A[GT]TATTAC-3' in the intergenic region of
CC       the genome, thereby initiating the rolling circle replication (RCR).
CC       Following cleavage, binds covalently to the 5'-phosphate of DNA as a
CC       tyrosyl ester. The cleavage gives rise to a free 3'-OH that serves as a
CC       primer for the cellular DNA polymerase. The polymerase synthesizes the
CC       (+) strand DNA by rolling circle mechanism. After one round of
CC       replication, a Rep-catalyzed nucleotidyl transfer reaction releases a
CC       circular single-stranded virus genome, thereby terminating the
CC       replication. Displays origin-specific DNA cleavage, nucleotidyl
CC       transferase, ATPase and helicase activities (By similarity).
CC       {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 (By similarity).
CC       {ECO:0000250}.
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}.
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DR   EMBL; AJ290434; CAB96405.1; -; Genomic_DNA.
DR   SMR; Q9ICP7; -.
DR   Proteomes; UP000006543; 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..286
FT                   /note="Master replication protein"
FT                   /id="PRO_0000378521"
FT   DOMAIN          2..96
FT                   /note="CRESS-DNA virus Rep endonuclease"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   MOTIF           9..12
FT                   /note="RCR-1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   MOTIF           41..43
FT                   /note="RCR-2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   MOTIF           50..70
FT                   /note="Nuclear localization signal"
FT                   /evidence="ECO:0000255"
FT   MOTIF           79..82
FT                   /note="RCR-3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   MOTIF           96..102
FT                   /note="Nuclear localization signal"
FT                   /evidence="ECO:0000255"
FT   ACT_SITE        79
FT                   /note="For DNA cleavage activity"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   BINDING         33
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         41
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         84
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         180..188
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   286 AA;  33281 MW;  3E49185793F09C58 CRC64;
     MARQVICWCF TLNNPLAPLS LHESMKYLVY QTEAGDNGTI HYQGYVEMKK RTSLVQMKKL
     LPGAHLEKRR GSQGEARAYA MKEDSRVEGP WEFGEFKEVL EDKLRSVMED MKSTGKRPVE
     YIEDCCNTYD KSSATLREFR GELKKKQAIE EWQLQRQPWM DEVERLMETK DCRRIIWVYG
     PQGGEGKTSY AKHLVKTRDA FYSTGGKTAD IAFAWDHQEL VLFDFPRSFE EYVNYGVIEQ
     LKNGIVQSGK YQSIVKYCNY VEVIVFANFI PRSGMFSEDR IVIVYA
//