ID   MREP_FBNY2              Reviewed;         286 AA.
AC   O39828;
DT   26-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT   01-JAN-1998, sequence version 1.
DT   27-MAR-2024, entry version 103.
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.-;
DE   AltName: Full=ATP-dependent helicase C2;
DE   AltName: Full=Replication-associated protein 2;
DE            Short=Rep2;
GN   Name=DNA-R; Synonyms=C2;
OS   Faba bean necrotic yellows virus (isolate SV292-88) (FBNYV).
OC   Viruses; Monodnaviria; Shotokuvirae; Cressdnaviricota; Arfiviricetes;
OC   Mulpavirales; Nanoviridae; Nanovirus; Faba bean necrotic yellows virus.
OX   NCBI_TaxID=291604;
OH   NCBI_TaxID=3827; Cicer arietinum (Chickpea) (Garbanzo).
OH   NCBI_TaxID=3864; Lens culinaris (Lentil) (Cicer lens).
OH   NCBI_TaxID=3885; Phaseolus vulgaris (Kidney bean) (French bean).
OH   NCBI_TaxID=3906; Vicia faba (Broad bean) (Faba vulgaris).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=9217049; DOI=10.1006/viro.1997.8611;
RA   Katul L., Maiss E., Morozov S.Y., Vetten H.J.;
RT   "Analysis of six DNA components of the faba bean necrotic yellows virus
RT   genome and their structural affinity to related plant virus genomes.";
RL   Virology 233:247-259(1997).
RN   [2]
RP   STRUCTURE BY NMR OF 2-95, COFACTOR, AND CHARACTERIZATION.
RX   PubMed=17472345; DOI=10.1021/bi700159q;
RA   Vega-Rocha S., Gronenborn B., Gronenborn A.M., Campos-Olivas R.;
RT   "Solution structure of the endonuclease domain from the master replication
RT   initiator protein of the nanovirus faba bean necrotic yellows virus and
RT   comparison with the corresponding geminivirus and circovirus structures.";
RL   Biochemistry 46:6201-6212(2007).
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.
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:17472345};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000305|PubMed:17472345};
CC       Note=Divalent metal cations, possibly Mg(2+) or Mn(2+).
CC       {ECO:0000305|PubMed:17472345};
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}.
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DR   EMBL; Y11405; CAA72209.1; -; Genomic_DNA.
DR   PDB; 2HWT; NMR; -; A=2-95.
DR   PDB; 6H8O; X-ray; 1.15 A; A/B=2-96.
DR   PDBsum; 2HWT; -.
DR   PDBsum; 6H8O; -.
DR   BMRB; O39828; -.
DR   SMR; O39828; -.
DR   EvolutionaryTrace; O39828; -.
DR   Proteomes; UP000008666; 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; IDA:CACAO.
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   1: Evidence at protein level;
KW   3D-structure; ATP-binding; Covalent protein-DNA linkage; DNA replication;
KW   DNA-binding; Endonuclease; Helicase; Host nucleus; Hydrolase;
KW   Metal-binding; Multifunctional enzyme; Nuclease; Nucleotide-binding;
KW   Nucleotidyltransferase; Transferase.
FT   CHAIN           1..286
FT                   /note="Master replication protein"
FT                   /id="PRO_0000318772"
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         186..188
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   STRAND          4..14
FT                   /evidence="ECO:0007829|PDB:6H8O"
FT   STRAND          25..34
FT                   /evidence="ECO:0007829|PDB:6H8O"
FT   STRAND          40..52
FT                   /evidence="ECO:0007829|PDB:6H8O"
FT   HELIX           54..60
FT                   /evidence="ECO:0007829|PDB:6H8O"
FT   STRAND          64..68
FT                   /evidence="ECO:0007829|PDB:6H8O"
FT   HELIX           73..79
FT                   /evidence="ECO:0007829|PDB:6H8O"
FT   HELIX           83..85
FT                   /evidence="ECO:0007829|PDB:2HWT"
FT   STRAND          86..94
FT                   /evidence="ECO:0007829|PDB:6H8O"
SQ   SEQUENCE   286 AA;  33141 MW;  FE878BF9336D23CD CRC64;
     MARQVICWCF TLNNPLSPLS LHDSMKYLVY QTEQGEAGNI HFQGYIEMKK RTSLAGMKKL
     IPGAHFEKRR GTQGEARAYS MKEDTRLEGP WEYGEFVPTI EDKLREVMND MKITGKRPIE
     YIEECCNTYD KSASTLREFR GELKKKKAIS SWELQRKPWM GEVDALLQER DGRRIIWVYG
     PQGGEGKTSY AKHLVKTRDA FYSTGGKTAD IAFAWDHQEL VLFDFPRSFE EYVNYGVIEQ
     LKNGIIQSGK YQSVIKYSDY VEVIVFANFT PRSGMFSEDR IVYVYA
//