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Protein

Replication-associated protein

Gene

C1/C2

Organism
Bean yellow dwarf virus (BeYDV)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Protein inferred from homologyi

Functioni

Essential for the replication of viral ssDNA. The closed circular ssDNA genome is first converted to a superhelical dsDNA. Rep binds a specific region at the genome origin of replication. It introduces an endonucleolytic nick within the conserved sequence 5'-TAATATTAC-3' in the intergenic region of the genome present in all geminiviruses, thereby initiating the rolling circle replication (RCR). Following cleavage, binds covalently to the 5'-phosphate of DNA as a tyrosyl ester. The cleavage gives rise to a free 3'-OH that serves as a primer for the cellular DNA polymerase. The polymerase synthesizes the (+) strand DNA by rolling circle mechanism. After one round of replication, a Rep-catalyzed nucleotidyl transfer reaction releases a circular single-stranded virus genome, thereby terminating the replication. Displays origin-specific DNA cleavage, nucleotidyl transferase, ATPase and helicase activities (By similarity). Acts a an inhibitor of C-sense gene transcription.By similarity2 Publications

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Divalent metal cations, possibly Mg2+ or Mn2+.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi50Divalent metal cationSequence analysis1
Metal bindingi58Divalent metal cationSequence analysis1
Metal bindingi60Divalent metal cationSequence analysis1
Active sitei98For DNA cleavage activityBy similarity1
Metal bindingi102Divalent metal cationSequence analysis1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi213 – 220ATPSequence analysis8

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Helicase, Hydrolase, Nuclease, Nucleotidyltransferase, Repressor, Transferase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

ATP-binding, DNA-binding, Metal-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Replication-associated protein (EC:2.7.7.-, EC:3.1.21.-)
Short name:
Rep
Gene namesi
ORF Names:C1/C2
OrganismiBean yellow dwarf virus (BeYDV)
Taxonomic identifieri57119 [NCBI]
Taxonomic lineageiVirusesssDNA virusesGeminiviridaeMastrevirus
Virus hostiPhaseolus vulgaris (Kidney bean) (French bean) [TaxID: 3885]
Proteomesi
  • UP000007453 Componenti: Genome

Subcellular locationi

  • Host nucleus 1 Publication

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Host nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003187711 – 334Replication-associated proteinAdd BLAST334

Keywords - PTMi

Covalent protein-DNA linkage

Interactioni

Subunit structurei

Homooligomer. Rep binds to repeated DNA motifs (iterons). Forms the O-complex, which is a Rep-DNA complex involved in the initiation of RCR. Part of the C- and V-complexes which are RepA-Rep-DNA complexes involved in the c-sense and v-sense transcription (By similarity).By similarity

Structurei

3D structure databases

ProteinModelPortaliO39522.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni160 – 172OligomerizationBy similarityAdd BLAST13
Regioni236 – 254TransactivationBy similarityAdd BLAST19

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi16 – 20RCR-1By similarity5
Motifi58 – 63RCR-2By similarity6
Motifi98 – 101RCR-3By similarity4
Motifi276 – 286Nuclear localization signalSequence analysisAdd BLAST11

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi279 – 284Poly-Lys6

Domaini

There are 3 rolling circle replication (RCR) motifs. RCR-2 is probably involved in metal coordination. RCR-3 is required for phosphodiester bond cleavage for initiation of RCR.

Sequence similaritiesi

Belongs to the geminiviridae Rep protein family.Curated

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR001301. Gemini_AL1_CLV.
IPR001191. Gemini_AL1_REP.
IPR022690. Gemini_AL1_REP_cat-dom.
IPR022692. Gemini_AL1_REP_central.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF00799. Gemini_AL1. 1 hit.
PF08283. Gemini_AL1_M. 1 hit.
[Graphical view]
PRINTSiPR00227. GEMCOATAL1.
PR00228. GEMCOATCLVL1.
SUPFAMiSSF52540. SSF52540. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform Rep (identifier: O39522-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MPSASKNFRL QSKYVFLTYP KCSSQRDDLF QFLWEKLTPF LIFFLGVASE
60 70 80 90 100
LHQDGTTHYH ALIQLDKKPC IRDPSFFDFE GNHPNIQPAR NSKQVLDYIS
110 120 130 140 150
KDGDIKTRGD FRDHKVSPRK SDARWRTIIQ TATSKEEYLD MIKEEFPHEW
160 170 180 190 200
ATKLQWLEYS ANKLFPPQPE QYVSPFTESD LRCHEDLHNW RETHLYHDEG
210 220 230 240 250
RTGVRHPSLY ICGPTRTGKT TWARSLGRHN YWNGTIDFTN YDEHATYNII
260 270 280 290 300
DDIPFKFVPL WKQLIGCQSD FTVNPKYGKK KKIKGGIPSI ILCNPDEDWM
310 320 330
LSMTSQQKDY FEDNCVTHYM CDGETFFARE SSSH
Length:334
Mass (Da):39,291
Last modified:March 1, 2004 - v2
Checksum:iF6CBAF63A4F10F6C
GO
Isoform RepA (identifier: O39521-1) [UniParc]FASTAAdd to basket
The sequence of this isoform can be found in the external entry O39521.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Note: Produced from the unspliced transcript.
Length:292
Mass (Da):33,354
GO

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural varianti63I → L in strain: Mild. 1
Natural varianti171Q → P in strain: Mild. 1
Natural varianti189N → S in strain: Mild. 1
Natural varianti199E → N in strain: Mild. 1
Natural varianti202 – 204TGV → NGI in strain: Mild. 3
Natural varianti312E → K in strain: Mild. 1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y11023 Genomic DNA. Translation: CAA71908.2.
DQ458791 Genomic DNA. Translation: ABE67102.1.
RefSeqiNP_612221.2. NC_003493.2. [O39522-1]

Genome annotation databases

GeneIDi935292.
KEGGivg:935292.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y11023 Genomic DNA. Translation: CAA71908.2.
DQ458791 Genomic DNA. Translation: ABE67102.1.
RefSeqiNP_612221.2. NC_003493.2. [O39522-1]

3D structure databases

ProteinModelPortaliO39522.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi935292.
KEGGivg:935292.

Family and domain databases

Gene3Di3.40.50.300. 1 hit.
InterProiIPR001301. Gemini_AL1_CLV.
IPR001191. Gemini_AL1_REP.
IPR022690. Gemini_AL1_REP_cat-dom.
IPR022692. Gemini_AL1_REP_central.
IPR027417. P-loop_NTPase.
[Graphical view]
PfamiPF00799. Gemini_AL1. 1 hit.
PF08283. Gemini_AL1_M. 1 hit.
[Graphical view]
PRINTSiPR00227. GEMCOATAL1.
PR00228. GEMCOATCLVL1.
SUPFAMiSSF52540. SSF52540. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiREP_BEYDV
AccessioniPrimary (citable) accession number: O39522
Secondary accession number(s): A4K7Q3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 26, 2008
Last sequence update: March 1, 2004
Last modified: November 30, 2016
This is version 65 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.