ID   REPE_ONYPE              Reviewed;         434 AA.
AC   P60470;
DT   16-FEB-2004, integrated into UniProtKB/Swiss-Prot.
DT   16-FEB-2004, sequence version 1.
DT   03-AUG-2022, entry version 57.
DE   RecName: Full=Geminivirus-like replication protein;
DE            EC=3.1.21.-;
GN   Name=rep; OrderedLocusNames=PAM_780;
OS   Onion yellows phytoplasma (strain OY-M).
OG   Plasmid EcOYM.
OC   Bacteria; Tenericutes; Mollicutes; Acholeplasmatales; Acholeplasmataceae;
OC   Candidatus Phytoplasma; Candidatus Phytoplasma asteris.
OX   NCBI_TaxID=262768;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=OY-M;
RX   PubMed=11988512; DOI=10.1099/00221287-148-5-1389;
RA   Nishigawa H., Oshima K., Kakizawa S., Jung H.Y., Kuboyama T., Miyata S.,
RA   Ugaki M., Namba S.;
RT   "Evidence of intermolecular recombination between extrachromosomal DNAs in
RT   phytoplasma: a trigger for the biological diversity of phytoplasma?";
RL   Microbiology 148:1389-1396(2002).
CC   -!- FUNCTION: Introduces an endonucleolytic nick, thereby initiating the
CC       rolling circle replication (RCR). {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   -!- 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   -!- SIMILARITY: Belongs to the geminiviridae Rep protein family.
CC       {ECO:0000305}.
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DR   EMBL; AB076263; BAD04084.1; -; Genomic_DNA.
DR   RefSeq; YP_006959585.1; NC_019167.1.
DR   RefSeq; YP_006959591.1; NC_019168.1.
DR   RefSeq; YP_006959597.1; NC_019169.1.
DR   AlphaFoldDB; P60470; -.
DR   OMA; TITHYEY; -.
DR   Proteomes; UP000002523; Plasmid EcOYM.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0004519; F:endonuclease activity; IEA:UniProtKB-KW.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR   InterPro; IPR022690; Gemini_AL1_REP_cat-dom.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   Pfam; PF00799; Gemini_AL1; 1.
DR   SUPFAM; SSF52540; SSF52540; 1.
PE   3: Inferred from homology;
KW   ATP-binding; DNA replication; DNA-binding; Endonuclease; Hydrolase;
KW   Metal-binding; Nuclease; Nucleotide-binding; Plasmid; Reference proteome.
FT   CHAIN           1..434
FT                   /note="Geminivirus-like replication protein"
FT                   /id="PRO_0000222221"
FT   MOTIF           19..23
FT                   /note="RCR-1"
FT                   /evidence="ECO:0000250"
FT   MOTIF           64..69
FT                   /note="RCR-2"
FT                   /evidence="ECO:0000250"
FT   MOTIF           128..131
FT                   /note="RCR-3"
FT                   /evidence="ECO:0000250"
FT   ACT_SITE        128
FT                   /note="For DNA cleavage activity"
FT                   /evidence="ECO:0000250"
FT   BINDING         55
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         64
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         66
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         132
FT                   /ligand="a divalent metal cation"
FT                   /ligand_id="ChEBI:CHEBI:60240"
FT                   /evidence="ECO:0000255"
FT   BINDING         269..276
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255"
SQ   SEQUENCE   434 AA;  51992 MW;  5E02EA3F9DEBF000 CRC64;
     MKKTNNIKKE TMFQAQNIFL TYSQCDLSKE EIKTFIINLC NEKKLQINYL IIGIENHQDH
     KGKHHHVFFQ LNKQFRTRDL TIFNIPKNIK EKKLIDHENI KIKDFFYSPH IEPRPGNPIK
     DTTDVRNYVK KDGDFIEEGT FKHVRYIKLS KNEKPTELES LTNNYFLKLR KEYQQKEINI
     SKTKNEIFKK LKLYAESLEP NYAFKNAKRF KNMVFEYIFE SDIKELPIFD FCTFKKIPIL
     ISIYDILETQ KEQLSNSISK RFKTLIVEGN SKSGKTQFFK SVLTNLELPF NYIKDDVDFS
     DENYDEDKCV NIYDDIDIYD IQARNLTKVV IGNQKDSIVN MKYKPRTKIK GTDISIMLVN
     EDTSIEKYCF DNFKRGRKEY KYIRENAIFI NLDKHTITHY EYQKYENEQA VIQHFEMPKN
     WDGLLYFLDQ ENES