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Protein

Master replication protein

Gene

DNA-R

Organism
Milk vetch dwarf virus (isolate N) (MDV)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

Essential for the replication of all genomic viral ssDNA (trans-replication). 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 conserved sequence 5'-A[GT]TATTAC-3' in 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 bindingi33 – 331Divalent metal cationSequence Analysis
Metal bindingi41 – 411Divalent metal cationSequence Analysis
Active sitei79 – 791For DNA cleavage activityBy similarity
Metal bindingi84 – 841Divalent metal cationSequence Analysis

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi180 – 1889ATPBy similarity

GO - Molecular functioni

GO - Biological processi

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:
Master replication protein (EC:2.7.7.-, EC:3.1.21.-, EC:3.6.1.3)
Short name:
M-Rep
Gene namesi
Name:DNA-R
Synonyms:C11
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

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Host nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 286286Master replication proteinPRO_0000378520Add
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

ProteinModelPortaliQ9IR51.
SMRiQ9IR51. Positions 2-95.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi10 – 134RCR-1By similarity
Motifi41 – 466RCR-2By similarity
Motifi50 – 7021Nuclear localization signalSequence AnalysisAdd
BLAST
Motifi79 – 824RCR-3By similarity
Motifi96 – 1027Nuclear localization signalSequence Analysis

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi144 – 1474Poly-Lys

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 (By similarity).By similarity

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.

Q9IR51-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARQVICWCF TLNNPLSPLS LHELMKYLVY QREQGEAGNI HFQGYIEMKK
60 70 80 90 100
RTSLAGMKKL IPGAHFEKRR GTQGEARAYA MKEDTRLEGP WEYGEFIPTI
110 120 130 140 150
EDKLREVMND MKITGKRPIE YIEECCNTYD KSASTLREFR GELKKKKAII
160 170 180 190 200
SWELQRKPWM DEVDTLLQER DGRRIIWVYG PQGGEGKTSY AKHLVKTRDA
210 220 230 240 250
FYSTGGKTAD IAFAWDHQEL VLFDFPRSFE EYVNYGVIEQ LKNGIIQSGK
260 270 280
YQSVIKYSDY VEVIVFANFT PRSGMFSDDR IVYVYA
Length:286
Mass (Da):33,334
Last modified:October 1, 2000 - v1
Checksum:iFC8854716C7F6C6B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB027511 Genomic DNA. Translation: BAA97561.1.
RefSeqiNP_619769.1. NC_003648.1.

Genome annotation databases

GeneIDi995288.
KEGGivg:995288.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB027511 Genomic DNA. Translation: BAA97561.1.
RefSeqiNP_619769.1. NC_003648.1.

3D structure databases

ProteinModelPortaliQ9IR51.
SMRiQ9IR51. Positions 2-95.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi995288.
KEGGivg:995288.

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

Entry informationi

Entry nameiMREP_MDV1
AccessioniPrimary (citable) accession number: Q9IR51
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 7, 2009
Last sequence update: October 1, 2000
Last modified: April 1, 2015
This is version 46 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.

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.