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Q9Z0D3

- REP3_MDV1

UniProt

Q9Z0D3 - REP3_MDV1

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Protein
Para-Rep C3
Gene
C3
Organism
Milk vetch dwarf virus (isolate N) (MDV)
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.

Catalytic activityi

ATP + H2O = ADP + phosphate.

Cofactori

Divalent metal cations, possibly magnesium or manganese By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi36 – 361Divalent metal cation Reviewed prediction
Metal bindingi42 – 421Divalent metal cation Reviewed prediction
Active sitei81 – 811For DNA cleavage activity By similarity
Metal bindingi86 – 861Divalent metal cation Reviewed prediction

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi174 – 1829ATP By similarity

GO - Molecular functioni

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

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 C3 (EC:2.7.7.-, EC:3.1.21.-, EC:3.6.1.3)
Short name:
Rep3
Alternative name(s):
Replication-associated protein of non-essential DNA C3
Gene namesi
Name:C3
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: Genome

Subcellular locationi

Host nucleus Reviewed prediction

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 – 284284Para-Rep C3
PRO_0000378524Add
BLAST

Keywords - PTMi

Covalent protein-DNA linkage

Interactioni

Subunit structurei

Homooligomer Reviewed prediction. Rep binds to repeated DNA motifs (iterons) By similarity.

Structurei

3D structure databases

ProteinModelPortaliQ9Z0D3.

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi11 – 144RCR-1 By similarity
Motifi42 – 476RCR-2 By similarity
Motifi51 – 7121Nuclear localization signal Reviewed prediction
Add
BLAST
Motifi81 – 844RCR-3 By similarity
Motifi98 – 1047Nuclear localization signal Reviewed prediction

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.

Q9Z0D3-1 [UniParc]FASTAAdd to Basket

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MPTVQSTCWV FTLNFKGEIP ILPFNERVQY ACWQHERVGH DHLQGFIQMK    50
AQQSLGQMKA IIPGAHFEKM RALNSDQAKA YAMKEDTRIE GPWEYGKYIK 100
KGSHKRKIME RFEDDPEEMK IEDPSLYRRC LSRKMTEEQR STAEWNYDMK 150
PWQDQVIQEI EETPDYRKII WVYGPKGGEG KSTFARYLSL KQGWGYLPGG 200
PTHDMLHIIS GEPKNNWVFD IPRVASEYVN YGVLEQVKNR VMVNTKYEPI 250
VIRDDNHPVH VIVFANCMPD FTKISEDRMK IVHC 284
Length:284
Mass (Da):33,349
Last modified:May 1, 1999 - v1
Checksum:iC9C880B8459B3355
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB000922 Genomic DNA. Translation: BAA33982.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB000922 Genomic DNA. Translation: BAA33982.1 .

3D structure databases

ProteinModelPortali Q9Z0D3.
ModBasei 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. "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(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].

Entry informationi

Entry nameiREP3_MDV1
AccessioniPrimary (citable) accession number: Q9Z0D3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 7, 2009
Last sequence update: May 1, 1999
Last modified: April 16, 2014
This is version 47 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.

Keywords - Technical termi

Complete proteome, Multifunctional enzyme

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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