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O39828

- MREP_FBNY2

UniProt

O39828 - MREP_FBNY2

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Protein

Master replication protein

Gene

DNA-R

Organism
Faba bean necrotic yellows virus (isolate SV292-88) (FBNYV)
Status
Reviewed - 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 Mg(2+) or Mn(2+).1 Publication

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 bindingi186 – 1883ATPBy 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: CACAO
  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:
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]
ProteomesiUP000008666: 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 – 286286Master replication proteinPRO_0000318772Add
BLAST

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

1
286
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi8 – 147Combined sources
Beta strandi26 – 349Combined sources
Beta strandi36 – 4712Combined sources
Beta strandi49 – 513Combined sources
Helixi54 – 607Combined sources
Beta strandi64 – 674Combined sources
Turni71 – 744Combined sources
Helixi75 – 773Combined sources
Helixi83 – 853Combined sources
Beta strandi91 – 944Combined sources

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiO39828.

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.

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
Entry Method Resolution (Å) Chain Positions PDBsum
2HWT NMR - A 2-95 [» ]
ProteinModelPortali O39828.
SMRi O39828. Positions 2-95.
ModBasei Search...
MobiDBi Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Miscellaneous databases

EvolutionaryTracei O39828.

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. "Analysis of six DNA components of the faba bean necrotic yellows virus genome and their structural affinity to related plant virus genomes."
    Katul L., Maiss E., Morozov S.Y., Vetten H.J.
    Virology 233:247-259(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Solution structure of the endonuclease domain from the master replication initiator protein of the nanovirus faba bean necrotic yellows virus and comparison with the corresponding geminivirus and circovirus structures."
    Vega-Rocha S., Gronenborn B., Gronenborn A.M., Campos-Olivas R.
    Biochemistry 46:6201-6212(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 2-95, COFACTOR, CHARACTERIZATION.

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 26, 2014
This is version 62 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

Documents

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

External Data

Dasty 3