ID   REPA_TYDVA              Reviewed;         295 AA.
AC   P31617;
DT   01-JUL-1993, integrated into UniProtKB/Swiss-Prot.
DT   01-JUL-1993, sequence version 1.
DT   03-AUG-2022, entry version 73.
DE   RecName: Full=Replication-associated protein A;
DE            Short=RepA;
DE            EC=3.1.21.-;
GN   ORFNames=C1;
OS   Tobacco yellow dwarf virus (strain Australia) (TYDV).
OC   Viruses; Monodnaviria; Shotokuvirae; Cressdnaviricota; Repensiviricetes;
OC   Geplafuvirales; Geminiviridae; Mastrevirus.
OX   NCBI_TaxID=31599;
OH   NCBI_TaxID=4076; Datura stramonium (Jimsonweed) (Common thornapple).
OH   NCBI_TaxID=239686; Datura stramonium var. tatula.
OH   NCBI_TaxID=4097; Nicotiana tabacum (Common tobacco).
OH   NCBI_TaxID=4081; Solanum lycopersicum (Tomato) (Lycopersicon esculentum).
RN   [1]
RP   NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX   PubMed=1546458; DOI=10.1016/0042-6822(92)90466-3;
RA   Morris B.A.M., Richardson K.A., Haley A., Zhan X., Thomas J.E.;
RT   "The nucleotide sequence of the infectious cloned DNA component of tobacco
RT   yellow dwarf virus reveals features of geminiviruses infecting
RT   monocotyledonous plants.";
RL   Virology 187:633-642(1992).
CC   -!- FUNCTION: Implicated in enhancement of V-sense gene expression. Acts a
CC       an inhibitor of C-sense gene transcription (By similarity).
CC       {ECO:0000250}.
CC   -!- SUBUNIT: Homooligomer. Interacts (via LXCXE domain) with host
CC       retinoblastoma-related protein 1 (RBR1), and may thereby deregulate the
CC       host cell cycle. Part of the C- and V-complexes which are RepA-Rep-DNA
CC       complexes involved in the c-sense and v-sense transcription (By
CC       similarity). {ECO:0000250}.
CC   -!- SUBCELLULAR LOCATION: Host nucleus {ECO:0000250}. Host cytoplasm
CC       {ECO:0000250}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=RepA;
CC         IsoId=P31617-1; Sequence=Displayed;
CC       Name=Rep;
CC         IsoId=P31618-1; Sequence=External;
CC   -!- DOMAIN: There are 3 rolling circle replication (RCR) motifs. RCR-2 may
CC       be involved in metal coordination. RCR-3 is required for phosphodiester
CC       bond cleavage for initiation of RCR.
CC   -!- DOMAIN: The LXCXE motif specifically binds to host RBR1. {ECO:0000250}.
CC   -!- MISCELLANEOUS: [Isoform RepA]: Produced from the unspliced transcript.
CC   -!- SIMILARITY: Belongs to the geminiviridae Rep protein family.
CC       {ECO:0000305}.
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DR   EMBL; M81103; AAA47950.1; -; Genomic_DNA.
DR   PIR; D42452; D42452.
DR   SMR; P31617; -.
DR   Proteomes; UP000007548; Genome.
DR   GO; GO:0030430; C:host cell cytoplasm; IEA:UniProtKB-SubCell.
DR   GO; GO:0042025; C:host cell nucleus; IEA:UniProtKB-SubCell.
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:0005198; F:structural molecule activity; IEA:InterPro.
DR   GO; GO:0006260; P:DNA replication; IEA:InterPro.
DR   GO; GO:0039645; P:modulation by virus of host G1/S transition checkpoint; IEA:UniProtKB-KW.
DR   InterPro; IPR001146; Gemini_AL1_MSV.
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; PR00229; GEMCOATMSVL1.
PE   3: Inferred from homology;
KW   Activator; Alternative splicing; DNA-binding; Endonuclease;
KW   G1/S host cell cycle checkpoint dysregulation by virus; Host cytoplasm;
KW   Host nucleus; Host-virus interaction; Hydrolase; Metal-binding;
KW   Modulation of host cell cycle by virus; Nuclease; Repressor.
FT   CHAIN           1..295
FT                   /note="Replication-associated protein A"
FT                   /id="PRO_0000222215"
FT   REGION          163..175
FT                   /note="Oligomerization"
FT                   /evidence="ECO:0000250"
FT   REGION          232..295
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOTIF           19..23
FT                   /note="RCR-1"
FT   MOTIF           61..66
FT                   /note="RCR-2"
FT   MOTIF           101..104
FT                   /note="RCR-3"
FT   MOTIF           184..188
FT                   /note="LXCXE motif, interaction with host RBR1"
FT                   /evidence="ECO:0000250"
FT   COMPBIAS        262..295
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        101
FT                   /note="For DNA cleavage activity"
FT                   /evidence="ECO:0000250"
FT   BINDING         53
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         61
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         63
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
SQ   SEQUENCE   295 AA;  33652 MW;  FBAE447F89DBCFDF CRC64;
     MPSAPQKTKS FRLQTKYVFL TYPRCSSSAE NLRDFLWDKL SRFAIFFIAI ATELHQDGTP
     HLHCLIQLDK RSNIRDPSFF DLEGNHPNIQ PAKNSEQVLE YISKDGNVIT KGEFKKHRVS
     PSKSDERWRT IIQTATSKEE YLDMIKDEFP HEWATKLQWL EYSANKLFPP QPEIYQATFT
     EEDLQCHEDL QLWRDQHLYH VSVDAYRLVH NVTLVEAHSD LVWMDDISRN LEGLEPGSPP
     STSADQVVPE RQHGPEASEG TITGMGPSTS LSMMTTRPTT SSTTSPSNSS HSGSN