ID   REP_TLCVA               Reviewed;         362 AA.
AC   P36279;
DT   01-JUN-1994, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-1994, sequence version 1.
DT   03-AUG-2022, entry version 75.
DE   RecName: Full=Replication-associated protein;
DE            Short=Rep;
DE            EC=2.7.7.-;
DE            EC=3.1.21.-;
DE   AltName: Full=Protein C1;
GN   ORFNames=C1;
OS   Tomato leaf curl virus (strain Australia) (ToLCV).
OC   Viruses; Monodnaviria; Shotokuvirae; Cressdnaviricota; Repensiviricetes;
OC   Geplafuvirales; Geminiviridae; Begomovirus.
OX   NCBI_TaxID=223353;
OH   NCBI_TaxID=185024; Cynanchum acutum.
OH   NCBI_TaxID=145753; Malva parviflora (Little mallow) (Cheeseweed mallow).
OH   NCBI_TaxID=4081; Solanum lycopersicum (Tomato) (Lycopersicon esculentum).
RN   [1]
RP   NUCLEOTIDE SEQUENCE.
RX   PubMed=8423446; DOI=10.1099/0022-1317-74-1-147;
RA   Dry I.B., Rigden J.E., Krake L.R., Mullineaux P.M., Rezaian M.A.;
RT   "Nucleotide sequence and genome organization of tomato leaf curl
RT   geminivirus.";
RL   J. Gen. Virol. 74:147-151(1993).
RN   [2]
RP   FUNCTION, AND INTERACTION WITH THE HOST RAD54 PROTEIN.
RX   PubMed=22171001; DOI=10.1096/fj.11-188508;
RA   Kaliappan K., Choudhury N.R., Suyal G., Mukherjee S.K.;
RT   "A novel role for RAD54: this host protein modulates geminiviral DNA
RT   replication.";
RL   FASEB J. 26:1142-1160(2012).
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.
CC       {ECO:0000269|PubMed:22171001}.
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). Binds to host RAD54
CC       protein to ensure geminiviral replication. {ECO:0000250,
CC       ECO:0000269|PubMed:22171001}.
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   PIR; JQ1887; JQ1887.
DR   SMR; P36279; -.
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:0051701; P:biological process involved in interaction with host; IPI:UniProtKB.
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; Transferase.
FT   CHAIN           1..362
FT                   /note="Replication-associated protein"
FT                   /id="PRO_0000222217"
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   REGION          341..362
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
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         221..228
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255"
SQ   SEQUENCE   362 AA;  41197 MW;  343E7184B4704098 CRC64;
     MTRPKSFRIN AKNYFLTYPK CSLTKEEALS QLNNLETPTS KKYIKVCREL HENGEPHLHV
     LIQFEGKFQC KNQRFFDLVS PTRSAHFHPN IQGAKSSSDV KSYLEKDGDT LEWGEFQIDG
     RSARGGQQSA NDAYAQALNT GSKSEALNVL RELAPKDYVL QFHNLNSNLD RIFTPPLEVY
     VSPFLSSSFD RVPEELEEWV AENVKDAAAR PLRPISIVIE GESRTGKTVW ARSLGPHNYL
     CGHLDLSPKV YSNDAWYNVI DDVDPHYLKH FKEFMGAQRD WQSNTKYGKP VQIKGGIPTI
     FLCNPGPNSS YKEYLDEEKN SALKAWALKN AEFITLNEPL YSGTYQGPTQ NSEEEVHPEE
     EN