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Q87009

- REP2_SCSVF

UniProt

Q87009 - REP2_SCSVF

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Protein

Para-Rep C2

Gene

C2

Organism
Subterranean clover stunt virus (strain F) (SCSV)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi

Functioni

Initiates and terminates the replication only of its own subviral DNA molecule. The closed circular ssDNA genome is first converted to a superhelical dsDNA. Rep binds a specific hairpin at the genome origin of replication. Introduces an endonucleolytic nick within the intergenic region of the genome, 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).By similarity

Catalytic activityi

ATP + H2O = ADP + phosphate.

Cofactori

Mg2+By similarity, Mn2+By similarityNote: Divalent metal cations, possibly Mg(2+) or Mn(2+).By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi37 – 371Divalent metal cationSequence Analysis
Metal bindingi45 – 451Divalent metal cationSequence Analysis
Active sitei84 – 841For DNA cleavage activityBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi172 – 1809ATPBy similarity

GO - Molecular functioni

  1. ATPase activity, uncoupled Source: InterPro
  2. ATP binding Source: UniProtKB-KW
  3. DNA binding Source: UniProtKB-KW
  4. endodeoxyribonuclease activity, producing 5'-phosphomonoesters Source: InterPro
  5. metal ion binding Source: UniProtKB-KW
  6. nucleotidyltransferase activity Source: UniProtKB-KW
  7. RNA binding Source: InterPro
  8. RNA helicase activity Source: InterPro

GO - Biological processi

  1. DNA replication Source: UniProtKB-KW
  2. protein-DNA covalent cross-linking Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Endonuclease, Helicase, Hydrolase, Nuclease, Nucleotidyltransferase, Transferase

Keywords - Biological processi

DNA replication

Keywords - Ligandi

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

Names & Taxonomyi

Protein namesi
Recommended name:
Para-Rep C2 (EC:2.7.7.-, EC:3.1.21.-, EC:3.6.1.3)
Short name:
Rep2
Alternative name(s):
Replication-associated protein of non-essential DNA C2
Gene namesi
Name:C2
OrganismiSubterranean clover stunt virus (strain F) (SCSV)
Taxonomic identifieri291607 [NCBI]
Taxonomic lineageiVirusesssDNA virusesNanoviridaeNanovirus
Virus hostiMedicago arabica [TaxID: 70936]
Medicago lupulina [TaxID: 47085]
Medicago minima [TaxID: 70957]
Phaseolus vulgaris (Kidney bean) (French bean) [TaxID: 3885]
Pisum sativum (Garden pea) [TaxID: 3888]
Trifolium cernuum [TaxID: 74509]
Trifolium dubium (Suckling clover) (Lesser trefoil) [TaxID: 97021]
Trifolium glomeratum [TaxID: 74514]
Trifolium pratense (Red clover) [TaxID: 57577]
Trifolium repens (Creeping white clover) [TaxID: 3899]
Trifolium subterraneum (Subterranean clover) [TaxID: 3900]
Vicia faba (Broad bean) (Faba vulgaris) [TaxID: 3906]
Wisteria sinensis [TaxID: 20997]
ProteomesiUP000006543: Genome

Subcellular locationi

Host nucleus Curated

GO - Cellular componenti

  1. host cell nucleus Source: UniProtKB-KW
Complete GO annotation...

Keywords - Cellular componenti

Host nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 280280Para-Rep C2PRO_0000378523Add
BLAST

Keywords - PTMi

Covalent protein-DNA linkage

Interactioni

Subunit structurei

Homooligomer (Potential). Rep binds to repeated DNA motifs (iterons) (By similarity).By similarityCurated

Structurei

3D structure databases

ProteinModelPortaliQ87009.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi7 – 104RCR-1By similarity
Motifi45 – 506RCR-2By similarity
Motifi54 – 7522Nuclear localization signalSequence AnalysisAdd
BLAST
Motifi84 – 874RCR-3By similarity
Motifi97 – 1037Nuclear localization signalSequence Analysis

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

Family and domain databases

InterProiIPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR003365. Viral_rep_N.
[Graphical view]
PfamiPF00910. RNA_helicase. 1 hit.
PF02407. Viral_Rep. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q87009-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MARRYCFTLN YATEIERETF LSLFSQDELN YFVVGDETAT TGQKHLQGFV
60 70 80 90 100
SFKNKIRLGG LKKKFGNRAH WEIARGSDSQ NRDYCCKETL ISEIGIPVMK
110 120 130 140 150
GSNKRKTMEI YEEDPEEMQL KDPDTALRCK AKKLKEEYCS CYDFQKLRPW
160 170 180 190 200
QIELHAALMA EPDDRSIIWV YGSDGGEGKT SFAKELIRYG WFYTAGGKTQ
210 220 230 240 250
DVLYMYAQDP ERNIAFDVPR CSSEMMNYQA MEMLKNRVFA STKYRPVDLC
260 270 280
IRKLVHLIVF ANVAPDPTRI SEDRLVIINC
Length:280
Mass (Da):32,473
Last modified:November 1, 1996 - v1
Checksum:iBAE273C64B04D6E3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U16731 Genomic DNA. Translation: AAA68018.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U16731 Genomic DNA. Translation: AAA68018.1 .

3D structure databases

ProteinModelPortali Q87009.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Family and domain databases

InterProi IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR003365. Viral_rep_N.
[Graphical view ]
Pfami PF00910. RNA_helicase. 1 hit.
PF02407. Viral_Rep. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  1. "Sequence of subterranean clover stunt virus DNA: affinities with the geminiviruses."
    Boevink P.C., Chu P.W.G., Keese P.K.
    Virology 207:354-361(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].

Entry informationi

Entry nameiREP2_SCSVF
AccessioniPrimary (citable) accession number: Q87009
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 7, 2009
Last sequence update: November 1, 1996
Last modified: November 26, 2014
This is version 53 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programViral Protein Annotation Program

Miscellaneousi

Miscellaneous

The genome of nanoviruses is composed of six to eight segments. In addition, some isolates contain subviral DNAs.

Caution

This protein is encoded by a subviral DNA that is not present in all isolates of the virus.Curated

Keywords - Technical termi

Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3