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Protein

Para-Rep C2

Gene

C2

Organism
Milk vetch dwarf virus (isolate N) (MDV)
Status
Reviewed-Annotation score: 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 Mn2+.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi38 – 381Divalent metal cationSequence Analysis
Metal bindingi47 – 471Divalent metal cationSequence Analysis
Active sitei86 – 861For DNA cleavage activityBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi174 – 1829ATPBy 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
OrganismiMilk vetch dwarf virus (isolate N) (MDV)
Taxonomic identifieri291605 [NCBI]
Taxonomic lineageiVirusesssDNA virusesNanoviridaeNanovirus
Virus hostiAstragalus sinicus (Chinese milk vetch) [TaxID: 47065]
Glycine max (Soybean) (Glycine hispida) [TaxID: 3847]
Phaseolus vulgaris (Kidney bean) (French bean) [TaxID: 3885]
Pisum sativum (Garden pea) [TaxID: 3888]
Vicia faba (Broad bean) (Faba vulgaris) [TaxID: 3906]
ProteomesiUP000008236 Componenti: Genome

Subcellular locationi

Host nucleus Curated

GO - Cellular componenti

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

Keywords - Cellular componenti

Host nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 282282Para-Rep C2PRO_0000378522Add
BLAST

Keywords - PTMi

Covalent protein-DNA linkage

Interactioni

Subunit structurei

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

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi8 – 114RCR-1By similarity
Motifi47 – 526RCR-2By similarity
Motifi56 – 7722Nuclear localization signalSequence AnalysisAdd
BLAST
Motifi86 – 894RCR-3By similarity
Motifi99 – 1057Nuclear 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.

Q9Z0D4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MASKRWCFTL NYKTALERET FISLFSRDEL NYFVCGDEIA PTTGQKHLQG
60 70 80 90 100
YVSMKKLIRL GGLKKKFGSI AHWEIAKGDD FQNRDYCTKE TLIAEIGAPV
110 120 130 140 150
KKGSNRRKIM EIYEEDPEEM KLRDPDTALR CKAKKLREEY CSEVSVFSLR
160 170 180 190 200
PWQIELHRAL MEVPDDRTII WAYGPDGGEG KSTFAKELIK YGWFYTAGGK
210 220 230 240 250
TQDILYMYAQ DPERNIAFDV PRCSSEMMNY QAMEMMKNRV FASTKYRPVD
260 270 280
LCIRKKVHLI VFANVAPDPT KLSEDRIVII NC
Length:282
Mass (Da):32,682
Last modified:May 1, 1999 - v1
Checksum:i6E8CE00C0BB7462E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB000921 Genomic DNA. Translation: BAA33981.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB000921 Genomic DNA. Translation: BAA33981.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

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]
ProtoNetiSearch...

Publicationsi

  1. "Sequences of ten circular ssDNA components associated with the milk vetch dwarf virus genome."
    Sano Y., Wada M., Hashimoto Y., Matsumoto T., Kojima M.
    J. Gen. Virol. 79:3111-3118(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].

Entry informationi

Entry nameiREP2_MDV1
AccessioniPrimary (citable) accession number: Q9Z0D4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 7, 2009
Last sequence update: May 1, 1999
Last modified: April 1, 2015
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

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.