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Protein

Replication-associated protein A

Gene

C1

Organism
Bean yellow dwarf virus (BeYDV)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Implicated in enhancement of V-sense gene expression. Acts a an inhibitor of C-sense gene transcription.2 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi50 – 501Divalent metal cationSequence analysis
Metal bindingi58 – 581Divalent metal cationSequence analysis
Metal bindingi60 – 601Divalent metal cationSequence analysis
Active sitei98 – 981For DNA cleavage activityBy similarity
Metal bindingi102 – 1021Divalent metal cationSequence analysis

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Activator, Endonuclease, Hydrolase, Nuclease, Repressor

Keywords - Biological processi

G1/S host cell cycle checkpoint dysregulation by virus, Host-virus interaction, Modulation of host cell cycle by virus

Keywords - Ligandi

DNA-binding, Metal-binding

Names & Taxonomyi

Protein namesi
Recommended name:
Replication-associated protein A (EC:3.1.21.-)
Short name:
RepA
Gene namesi
ORF Names:C1
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
  • Host cytoplasm 1 Publication

  • Note: distributed equally throughout both the nucleus and the cytoplasm.

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Host cytoplasm, Host nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi181 – 1811L → I: 20% loss of ability to bind RBR. 1 Publication
Mutagenesisi183 – 1831C → S: 50% loss of ability to bind RBR. 1 Publication
Mutagenesisi185 – 1851E → Q: 95% loss of ability to bind RBR. Reduced replication efficiency. 2 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 292292Replication-associated protein APRO_0000318770Add
BLAST

Interactioni

Subunit structurei

Homooligomer. Interacts with host retinoblastoma-related protein 1 (RBR1), and may thereby deregulate the host cell cycle. 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

ProteinModelPortaliO39521.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni160 – 17213OligomerizationBy similarityAdd
BLAST
Regioni181 – 1855Binding to RBR1

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi16 – 205RCR-1
Motifi58 – 636RCR-2
Motifi98 – 1014RCR-3

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi282 – 2876Poly-Ser

Domaini

There are three rolling circle replication (RCR) motifs. RCR-2 may be 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

InterProiIPR001146. Gemini_AL1_MSV.
IPR001191. Gemini_AL1_REP.
IPR022690. Gemini_AL1_REP_cat-dom.
IPR022692. Gemini_AL1_REP_central.
[Graphical view]
PfamiPF00799. Gemini_AL1. 1 hit.
PF08283. Gemini_AL1_M. 1 hit.
[Graphical view]
PRINTSiPR00227. GEMCOATAL1.
PR00229. GEMCOATMSVL1.

Sequences (2)i

Sequence statusi: Complete.

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

Isoform RepA (identifier: O39521-1) [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 RETHLYHVSI
210 220 230 240 250
DAYTFIHPVS YDQAQSDLEW MADLTRMREG LGSDTPASTS ADQLVPERPP
260 270 280 290
GLEVSGDTTT GTGPSTSPTT MNTPPIISST TSPSSSSHCG SN
Note: Produced from the unspliced transcript.
Length:292
Mass (Da):33,354
Last modified:January 1, 1998 - v1
Checksum:i31C4DCA03607F3BF
GO
Isoform Rep (identifier: O39522-1) [UniParc]FASTAAdd to basket

The sequence of this isoform can be found in the external entry O39522.
Isoforms of the same protein are often annotated in two different entries if their sequences differ significantly.
Length:334
Mass (Da):39,291
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti63 – 631I → L in strain: Mild.
Natural varianti171 – 1711Q → P in strain: Mild.
Natural varianti189 – 1891N → S in strain: Mild.
Natural varianti205 – 2051F → Y in strain: Mild.
Natural varianti212 – 2121D → Q in strain: Mild.
Natural varianti227 – 2282MR → TM in strain: Mild.
Natural varianti231 – 2322LG → ME in strain: Mild.
Natural varianti256 – 2561G → D in strain: Mild.
Natural varianti260 – 2601T → I in strain: Mild.
Natural varianti263 – 2631G → V in strain: Mild.
Natural varianti266 – 2661T → I in strain: Mild.

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y11023 Genomic DNA. Translation: CAA71907.1.
DQ458791 Genomic DNA. Translation: ABE67103.1.
RefSeqiNP_612222.1. NC_003493.2. [O39521-1]

Genome annotation databases

GeneIDi935291.
KEGGivg:935291.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y11023 Genomic DNA. Translation: CAA71907.1.
DQ458791 Genomic DNA. Translation: ABE67103.1.
RefSeqiNP_612222.1. NC_003493.2. [O39521-1]

3D structure databases

ProteinModelPortaliO39521.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi935291.
KEGGivg:935291.

Family and domain databases

InterProiIPR001146. Gemini_AL1_MSV.
IPR001191. Gemini_AL1_REP.
IPR022690. Gemini_AL1_REP_cat-dom.
IPR022692. Gemini_AL1_REP_central.
[Graphical view]
PfamiPF00799. Gemini_AL1. 1 hit.
PF08283. Gemini_AL1_M. 1 hit.
[Graphical view]
PRINTSiPR00227. GEMCOATAL1.
PR00229. GEMCOATMSVL1.
ProtoNetiSearch...

Publicationsi

  1. "Molecular characterization of a subgroup I geminivirus from a legume."
    Liu L., van Tonder T., Pietersen G., Davies J.W., Stanley J.
    J. Gen. Virol. 78:2113-2117(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "The complete nucleotide sequence of a mild strain of Bean yellow dwarf virus."
    Halley-Stott R.P., Tanzer F., Martin D.P., Rybicki E.P.
    Arch. Virol. 152:1237-1240(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: Mild.
  3. "Bean yellow dwarf virus RepA, but not rep, binds to maize retinoblastoma protein, and the virus tolerates mutations in the consensus binding motif."
    Liu L., Saunders K., Thomas C.L., Davies J.W., Stanley J.
    Virology 256:270-279(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH ZEA MAYS RBR1, MUTAGENESIS OF LEU-181; CYS-183 AND GLU-185.
  4. "Independent expression of Rep and RepA and their roles in regulating bean yellow dwarf virus replication."
    Hefferon K.L., Dugdale B.
    J. Gen. Virol. 84:3465-3472(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH ZEA MAYS RBR1, MUTAGENESIS OF GLU-185.
  5. "Multi-tasking of nonstructural gene products is required for bean yellow dwarf geminivirus transcriptional regulation."
    Hefferon K.L., Moon Y.-S., Fan Y.
    FEBS J. 273:4482-4494(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION.

Entry informationi

Entry nameiREPA_BEYDV
AccessioniPrimary (citable) accession number: O39521
Secondary accession number(s): A4K7Q4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 26, 2008
Last sequence update: January 1, 1998
Last modified: May 27, 2015
This is version 57 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete 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.