REP_BEYDV
ID REP_BEYDV Reviewed; 334 AA.
AC O39522; A4K7Q3;
DT 26-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2004, sequence version 2.
DT 03-AUG-2022, entry version 85.
DE RecName: Full=Replication-associated protein;
DE Short=Rep;
DE EC=2.7.7.-;
DE EC=3.1.21.-;
GN ORFNames=C1/C2;
OS Bean yellow dwarf virus (BeYDV).
OC Viruses; Monodnaviria; Shotokuvirae; Cressdnaviricota; Repensiviricetes;
OC Geplafuvirales; Geminiviridae; Mastrevirus.
OX NCBI_TaxID=57119;
OH NCBI_TaxID=3885; Phaseolus vulgaris (Kidney bean) (French bean).
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=9267015; DOI=10.1099/0022-1317-78-8-2113;
RA Liu L., van Tonder T., Pietersen G., Davies J.W., Stanley J.;
RT "Molecular characterization of a subgroup I geminivirus from a legume.";
RL J. Gen. Virol. 78:2113-2117(1997).
RN [2]
RP SEQUENCE REVISION.
RA Stanley J.;
RL Submitted (DEC-2003) to the EMBL/GenBank/DDBJ databases.
RN [3]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=Mild;
RX PubMed=17347772; DOI=10.1007/s00705-006-0933-6;
RA Halley-Stott R.P., Tanzer F., Martin D.P., Rybicki E.P.;
RT "The complete nucleotide sequence of a mild strain of Bean yellow dwarf
RT virus.";
RL Arch. Virol. 152:1237-1240(2007).
RN [4]
RP FUNCTION.
RX PubMed=14645928; DOI=10.1099/vir.0.19494-0;
RA Hefferon K.L., Dugdale B.;
RT "Independent expression of Rep and RepA and their roles in regulating bean
RT yellow dwarf virus replication.";
RL J. Gen. Virol. 84:3465-3472(2003).
RN [5]
RP FUNCTION, SUBCELLULAR LOCATION, AND NUCLEAR LOCALIZATION SIGNAL.
RX PubMed=16972938; DOI=10.1111/j.1742-4658.2006.05454.x;
RA Hefferon K.L., Moon Y.-S., Fan Y.;
RT "Multi-tasking of nonstructural gene products is required for bean yellow
RT dwarf geminivirus transcriptional regulation.";
RL FEBS J. 273:4482-4494(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). Acts a an
CC inhibitor of C-sense gene transcription. {ECO:0000250,
CC ECO:0000269|PubMed:14645928, ECO:0000269|PubMed:16972938}.
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. Rep binds to repeated DNA motifs (iterons).
CC Forms the O-complex, which is a Rep-DNA complex involved in the
CC initiation of RCR. Part of the C- and V-complexes which are RepA-Rep-
CC DNA complexes involved in the c-sense and v-sense transcription (By
CC similarity). {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Host nucleus {ECO:0000269|PubMed:16972938}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=Rep;
CC IsoId=O39522-1; Sequence=Displayed;
CC Name=RepA;
CC IsoId=O39521-1; Sequence=External;
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 -!- SIMILARITY: Belongs to the geminiviridae Rep protein family.
CC {ECO:0000305}.
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DR EMBL; Y11023; CAA71908.2; -; Genomic_DNA.
DR EMBL; DQ458791; ABE67102.1; -; Genomic_DNA.
DR RefSeq; NP_612221.2; NC_003493.2. [O39522-1]
DR SMR; O39522; -.
DR GeneID; 935292; -.
DR KEGG; vg:935292; -.
DR Proteomes; UP000007453; 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 InterPro; IPR027417; P-loop_NTPase.
DR Pfam; PF00799; Gemini_AL1; 1.
DR Pfam; PF08283; Gemini_AL1_M; 1.
DR PRINTS; PR00227; GEMCOATAL1.
DR PRINTS; PR00228; GEMCOATCLVL1.
DR SUPFAM; SSF52540; SSF52540; 1.
PE 3: Inferred from homology;
KW Alternative splicing; ATP-binding; Covalent protein-DNA linkage;
KW DNA replication; DNA-binding; Endonuclease; Helicase; Host nucleus;
KW Hydrolase; Metal-binding; Multifunctional enzyme; Nuclease;
KW Nucleotide-binding; Nucleotidyltransferase; Reference proteome; Repressor;
KW Transferase.
FT CHAIN 1..334
FT /note="Replication-associated protein"
FT /id="PRO_0000318771"
FT REGION 160..172
FT /note="Oligomerization"
FT /evidence="ECO:0000250"
FT REGION 236..254
FT /note="Transactivation"
FT /evidence="ECO:0000250"
FT MOTIF 16..20
FT /note="RCR-1"
FT /evidence="ECO:0000250"
FT MOTIF 58..63
FT /note="RCR-2"
FT /evidence="ECO:0000250"
FT MOTIF 98..101
FT /note="RCR-3"
FT /evidence="ECO:0000250"
FT MOTIF 276..286
FT /note="Nuclear localization signal"
FT /evidence="ECO:0000255"
FT ACT_SITE 98
FT /note="For DNA cleavage activity"
FT /evidence="ECO:0000250"
FT BINDING 50
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255"
FT BINDING 58
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255"
FT BINDING 60
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255"
FT BINDING 102
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000255"
FT BINDING 213..220
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255"
FT VARIANT 63
FT /note="I -> L (in strain: Mild)"
FT VARIANT 171
FT /note="Q -> P (in strain: Mild)"
FT VARIANT 189
FT /note="N -> S (in strain: Mild)"
FT VARIANT 199
FT /note="E -> N (in strain: Mild)"
FT VARIANT 202..204
FT /note="TGV -> NGI (in strain: Mild)"
FT VARIANT 312
FT /note="E -> K (in strain: Mild)"
SQ SEQUENCE 334 AA; 39291 MW; F6CBAF63A4F10F6C CRC64;
MPSASKNFRL QSKYVFLTYP KCSSQRDDLF QFLWEKLTPF LIFFLGVASE LHQDGTTHYH
ALIQLDKKPC IRDPSFFDFE GNHPNIQPAR NSKQVLDYIS KDGDIKTRGD FRDHKVSPRK
SDARWRTIIQ TATSKEEYLD MIKEEFPHEW ATKLQWLEYS ANKLFPPQPE QYVSPFTESD
LRCHEDLHNW RETHLYHDEG RTGVRHPSLY ICGPTRTGKT TWARSLGRHN YWNGTIDFTN
YDEHATYNII DDIPFKFVPL WKQLIGCQSD FTVNPKYGKK KKIKGGIPSI ILCNPDEDWM
LSMTSQQKDY FEDNCVTHYM CDGETFFARE SSSH
