Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

Master replication protein

Gene

DNA-R

Organism
Faba bean necrotic yellows virus (isolate SV292-88) (FBNYV)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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.

Catalytic activityi

ATP + H2O = ADP + phosphate.

Cofactori

Mg2+1 Publication, Mn2+1 PublicationNote: Divalent metal cations, possibly Mg2+ or Mn2+.1 Publication

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi33Divalent metal cationSequence analysis1
Metal bindingi41Divalent metal cationSequence analysis1
Active sitei79For DNA cleavage activityBy similarity1
Metal bindingi84Divalent metal cationSequence analysis1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi186 – 188ATPBy similarity3

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
Alternative name(s):
ATP-dependent helicase C2
Replication-associated protein 2
Short name:
Rep2
Gene namesi
Name:DNA-R
Synonyms:C2
OrganismiFaba bean necrotic yellows virus (isolate SV292-88) (FBNYV)
Taxonomic identifieri291604 [NCBI]
Taxonomic lineageiVirusesssDNA virusesNanoviridaeNanovirus
Virus hostiCicer arietinum (Chickpea) (Garbanzo) [TaxID: 3827]
Lens culinaris (Lentil) (Cicer lens) [TaxID: 3864]
Phaseolus vulgaris (Kidney bean) (French bean) [TaxID: 3885]
Vicia faba (Broad bean) (Faba vulgaris) [TaxID: 3906]
Proteomesi
  • UP000008666 Componenti: Genome

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Host nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00003187721 – 286Master replication proteinAdd BLAST286

Keywords - PTMi

Covalent protein-DNA linkage

Interactioni

Subunit structurei

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

Structurei

Secondary structure

1286
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi8 – 14Combined sources7
Beta strandi26 – 34Combined sources9
Beta strandi36 – 47Combined sources12
Beta strandi49 – 51Combined sources3
Helixi54 – 60Combined sources7
Beta strandi64 – 67Combined sources4
Turni71 – 74Combined sources4
Helixi75 – 77Combined sources3
Helixi83 – 85Combined sources3
Beta strandi91 – 94Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2HWTNMR-A2-95[»]
ProteinModelPortaliO39828.
SMRiO39828.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO39828.

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi10 – 13RCR-1By similarity4
Motifi41 – 46RCR-2By similarity6
Motifi50 – 70Nuclear localization signalSequence analysisAdd BLAST21
Motifi79 – 82RCR-3By similarity4
Motifi96 – 102Nuclear localization signalSequence analysis7

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi144 – 147Poly-Lys4

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.

O39828-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MARQVICWCF TLNNPLSPLS LHDSMKYLVY QTEQGEAGNI HFQGYIEMKK
60 70 80 90 100
RTSLAGMKKL IPGAHFEKRR GTQGEARAYS MKEDTRLEGP WEYGEFVPTI
110 120 130 140 150
EDKLREVMND MKITGKRPIE YIEECCNTYD KSASTLREFR GELKKKKAIS
160 170 180 190 200
SWELQRKPWM GEVDALLQER DGRRIIWVYG PQGGEGKTSY AKHLVKTRDA
210 220 230 240 250
FYSTGGKTAD IAFAWDHQEL VLFDFPRSFE EYVNYGVIEQ LKNGIIQSGK
260 270 280
YQSVIKYSDY VEVIVFANFT PRSGMFSEDR IVYVYA
Length:286
Mass (Da):33,141
Last modified:January 1, 1998 - v1
Checksum:iFE878BF9336D23CD
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y11405 Genomic DNA. Translation: CAA72209.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
Y11405 Genomic DNA. Translation: CAA72209.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2HWTNMR-A2-95[»]
ProteinModelPortaliO39828.
SMRiO39828.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Miscellaneous databases

EvolutionaryTraceiO39828.

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...

Entry informationi

Entry nameiMREP_FBNY2
AccessioniPrimary (citable) accession number: O39828
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 26, 2008
Last sequence update: January 1, 1998
Last modified: November 30, 2016
This is version 71 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

3D-structure, Complete proteome, Multifunctional enzyme, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families

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 one 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.