ID   REP1_FBNY2              Reviewed;         278 AA.
AC   Q66862;
DT   25-OCT-2005, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   27-MAR-2024, entry version 104.
DE   RecName: Full=Para-Rep C1;
DE            Short=Rep1;
DE            EC=2.7.7.-;
DE            EC=3.1.21.-;
DE            EC=3.6.1.-;
DE   AltName: Full=ATP-dependent helicase C1;
DE   AltName: Full=Replication-associated protein of non-essential DNA C1;
GN   Name=C1; ORFNames=ORF1;
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=7844570; DOI=10.1099/0022-1317-76-2-475;
RA   Katul L., Maiss E., Vetten V.J.;
RT   "Sequence analysis of a faba bean necrotic yellows virus DNA component
RT   containing a putative replicase gene.";
RL   J. Gen. Virol. 76:475-479(1995).
RN   [2]
RP   FUNCTION, AND MUTAGENESIS OF TYR-78 AND LYS-177.
RX   PubMed=10559333; DOI=10.1128/jvi.73.12.10173-10182.1999;
RA   Timchenko T., de Kouchkovsky F., Katul L., David C., Vetten H.J.,
RA   Gronenborn B.;
RT   "A single Rep protein initiates replication of multiple genome components
RT   of faba bean necrotic yellows virus, a single-stranded DNA virus of
RT   plants.";
RL   J. Virol. 73:10173-10182(1999).
RN   [3]
RP   REVIEW.
RX   PubMed=14741122; DOI=10.1016/j.vetmic.2003.10.015;
RA   Gronenborn B.;
RT   "Nanoviruses: genome organisation and protein function.";
RL   Vet. Microbiol. 98:103-109(2004).
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.
CC       {ECO:0000269|PubMed:10559333}.
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}.
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; X80879; CAA56847.1; -; Genomic_DNA.
DR   SMR; Q66862; -.
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; IDA:CACAO.
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   GO; GO:0019071; P:viral DNA cleavage involved in viral genome maturation; IDA:CACAO.
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   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; Transferase.
FT   CHAIN           1..278
FT                   /note="Para-Rep C1"
FT                   /id="PRO_0000222439"
FT   DOMAIN          1..95
FT                   /note="CRESS-DNA virus Rep endonuclease"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   MOTIF           8..11
FT                   /note="RCR-1"
FT                   /evidence="ECO:0000250"
FT   MOTIF           39..41
FT                   /note="RCR-2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   MOTIF           48..69
FT                   /note="Nuclear localization signal"
FT                   /evidence="ECO:0000255"
FT   MOTIF           78..81
FT                   /note="RCR-3"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU01364"
FT   MOTIF           95..101
FT                   /note="Nuclear localization signal"
FT                   /evidence="ECO:0000255"
FT   ACT_SITE        78
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         39
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         83
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         176..178
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000305"
FT   MUTAGEN         78
FT                   /note="Y->F: Complete loss of DNA cleavage and nucleotidyl
FT                   transfer activity."
FT                   /evidence="ECO:0000269|PubMed:10559333"
FT   MUTAGEN         177
FT                   /note="K->A: Complete loss of ATPase activity."
FT                   /evidence="ECO:0000269|PubMed:10559333"
SQ   SEQUENCE   278 AA;  32382 MW;  4D9F4451F4EA2DED CRC64;
     MACSNWVFTR NFQGALPLLS FDERVQYAVW QHERGTHDHI QGVIQLKKKA RFSTVKEIIG
     GNPHVEKMKG TIEEASAYVQ KEETRVAGPW SYGDLLKRGS HRRKTMERYL EDPEEMQLKD
     PDTALRCNAK RLKEDFMKEK TKLQLRPWQK ELHDLILTEP DDRTIIWVYG PDGGEGKSMF
     AKELIKYGWF YTAGGKTQDI LYMYAQDPER NIAFDVPRCS SEMMNYQAME MMKNRCFAST
     KYRSVDLCCN KNVHLVVFAN VAYDPTKISE DRIVIINC
//