ID   REP_ICMV                Reviewed;         351 AA.
AC   Q82676;
DT   26-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   03-AUG-2022, entry version 83.
DE   RecName: Full=Replication-associated protein;
DE            Short=Rep;
DE            EC=2.7.7.-;
DE            EC=3.1.21.-;
DE   AltName: Full=Protein AC1;
DE   AltName: Full=Protein AL1;
GN   ORFNames=AC1, AL1;
OS   Indian cassava mosaic virus (ICMV).
OC   Viruses; Monodnaviria; Shotokuvirae; Cressdnaviricota; Repensiviricetes;
OC   Geplafuvirales; Geminiviridae; Begomovirus.
OX   NCBI_TaxID=31600;
OH   NCBI_TaxID=3983; Manihot esculenta (Cassava) (Jatropha manihot).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=8245859; DOI=10.1099/0022-1317-74-11-2437;
RA   Hong Y.G., Robinson D.J., Harrison B.D.;
RT   "Nucleotide sequence evidence for the occurrence of three distinct
RT   whitefly-transmitted geminiviruses in cassava.";
RL   J. Gen. Virol. 74:2437-2443(1993).
RN   [2]
RP   CHARACTERIZATION OF THE HELICASE ACTIVITY.
RX   PubMed=17142233; DOI=10.1093/nar/gkl903;
RA   Choudhury N.R., Malik P.S., Singh D.K., Islam M.N., Kaliappan K.,
RA   Mukherjee S.K.;
RT   "The oligomeric Rep protein of Mungbean yellow mosaic India virus (MYMIV)
RT   is a likely replicative helicase.";
RL   Nucleic Acids Res. 34:6362-6377(2006).
CC   -!- FUNCTION: Essential for the replication of viral ssDNA. The closed
CC       circular ssDNA genome is first converted to a superhelical dsDNA. Rep
CC       binds a specific region at the genome origin of replication. It
CC       introduces an endonucleolytic nick within the conserved sequence 5'-
CC       TAATATTAC-3' in the intergenic region of the genome present in all
CC       geminiviruses, 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   -!- 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. Interacts with the replication enhancer protein
CC       (REn). Interacts with host retinoblastoma-related protein 1 (RBR1), and
CC       may thereby induce the transcription of host replicative enzymes even
CC       if the cell is not dividing anymore. Interacts with host PCNA.
CC       Interacts with host SCE1 protein (By similarity). {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Host nucleus {ECO:0000250}.
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   -!- SIMILARITY: Belongs to the geminiviridae Rep protein family.
CC       {ECO:0000305}.
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DR   EMBL; Z24758; CAA80891.1; -; Genomic_DNA.
DR   PIR; JQ2327; JQ2327.
DR   RefSeq; NP_047233.1; NC_001932.1.
DR   SMR; Q82676; -.
DR   GeneID; 991061; -.
DR   KEGG; vg:991061; -.
DR   Proteomes; UP000007210; 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:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0016888; F:endodeoxyribonuclease activity, producing 5'-phosphomonoesters; IEA:InterPro.
DR   GO; GO:0004386; F:helicase activity; IEA:UniProtKB-KW.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0016779; F:nucleotidyltransferase activity; IEA:UniProtKB-KW.
DR   GO; GO:0005198; F:structural molecule activity; IEA:InterPro.
DR   GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR   InterPro; IPR001301; Gemini_AL1_CLV.
DR   InterPro; IPR001191; Gemini_AL1_REP.
DR   InterPro; IPR022690; Gemini_AL1_REP_cat-dom.
DR   InterPro; IPR022692; Gemini_AL1_REP_central.
DR   Pfam; PF00799; Gemini_AL1; 1.
DR   Pfam; PF08283; Gemini_AL1_M; 1.
DR   PRINTS; PR00227; GEMCOATAL1.
DR   PRINTS; PR00228; GEMCOATCLVL1.
PE   1: Evidence at protein level;
KW   ATP-binding; Covalent protein-DNA linkage; DNA replication; DNA-binding;
KW   Endonuclease; Helicase; Host nucleus; Host-virus interaction; Hydrolase;
KW   Metal-binding; Multifunctional enzyme; Nuclease; Nucleotide-binding;
KW   Nucleotidyltransferase; Reference proteome; Transferase.
FT   CHAIN           1..351
FT                   /note="Replication-associated protein"
FT                   /id="PRO_0000320111"
FT   REGION          143..153
FT                   /note="Binding to RBR1"
FT                   /evidence="ECO:0000250"
FT   REGION          156..176
FT                   /note="Oligomerization"
FT                   /evidence="ECO:0000250"
FT   MOTIF           15..19
FT                   /note="RCR-1"
FT   MOTIF           57..62
FT                   /note="RCR-2"
FT   MOTIF           103..106
FT                   /note="RCR-3"
FT   ACT_SITE        103
FT                   /note="For DNA cleavage activity"
FT                   /evidence="ECO:0000250"
FT   BINDING         49
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         57
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         59
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         107
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         220..227
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255"
SQ   SEQUENCE   351 AA;  40058 MW;  708C8C8AAEA1820E CRC64;
     MSPPKRFQIN AKNYFLTYPR CSLTKEEALS QIRNFQTPTN PKFIKICREL HENGEPHLHV
     LIQFEGKYKC QNQRFFDLVS PTRSAHFHPN IQGAKSSSDV KSYIDKDGDT WRWGTFQIDG
     RSARGGQQSA NDAYAAALNS GSKSEALKIL RELAPRDYLR DFHHISSNLD RIFTKPPPPY
     ENPFPLSSFD RVPEELDEWF HENVMGRARP LRPKSIVIEG DSRTGKTMWS RALGPHNYLC
     GHLDLSPKVY NNDAWYNVID DVDPHYLKHF KRIHGGPEDW QSNTKYGKPV QIKGGIPTIF
     LCNPGPNSSY KEFLDEEKNS ALKAWALKNA TFISLEGPLY SGTNQGPTQS C