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Q9Z0D5

- REP1_MDV1

UniProt

Q9Z0D5 - REP1_MDV1

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Protein

Para-Rep C1

Gene

C1

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).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 cationSequence Analysis
Metal bindingi42 – 421Divalent metal cationSequence Analysis
Active sitei80 – 801For DNA cleavage activityBy similarity
Metal bindingi85 – 851Divalent metal cationSequence Analysis

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi173 – 1819ATPBy 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 C1 (EC:2.7.7.-, EC:3.1.21.-, EC:3.6.1.3)
Short name:
Rep1
Alternative name(s):
Replication-associated protein of non-essential DNA C1
Gene namesi
Name:C1
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 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 – 281281Para-Rep C1PRO_0000378519Add
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

ProteinModelPortaliQ9Z0D5.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi11 – 144RCR-1By similarity
Motifi42 – 476RCR-2By similarity
Motifi51 – 7121Nuclear localization signalSequence AnalysisAdd
BLAST
Motifi80 – 834RCR-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.

Q9Z0D5-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MPTLQGTFWC FTLNFSGDAP SLSFNERVQY ACWQHERVSH DHLQGYIQMK
60 70 80 90 100
KRSTLKMMKE LLPGAHLEVS KGTPEEASDY AMKEETRVAG PWTYGELLKK
110 120 130 140 150
GSNKRKLLDR YKENPEDMEL EDPAKARRCR AKIDKEKFIA EFKVEDDEQE
160 170 180 190 200
WKKILEKEIE KIASPRSILW VYGPQGGEGK TSKAKELITR GWFYTRGGKK
210 220 230 240 250
DDVAYSYVED PTRHVVFDIP RDMQEYCNYS LIEMLKDRII ISNKYEPITN
260 270 280
CQVYNIHVIV MANFLPDVTK ISEDRIKIIY C
Length:281
Mass (Da):32,870
Last modified:May 1, 1999 - v1
Checksum:i3D3AAE74F3A38A06
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB000920 Genomic DNA. Translation: BAA33980.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AB000920 Genomic DNA. Translation: BAA33980.1 .

3D structure databases

ProteinModelPortali Q9Z0D5.
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. "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 nameiREP1_MDV1
AccessioniPrimary (citable) accession number: Q9Z0D5
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 7, 2009
Last sequence update: May 1, 1999
Last modified: October 29, 2014
This is version 50 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