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O39828

- MREP_FBNY2

UniProt

O39828 - MREP_FBNY2

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
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    • History
      Entry version 60 (01 Oct 2014)
      Sequence version 1 (01 Jan 1998)
      Previous versions | rss
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    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

    Divalent metal cations, possibly magnesium or manganese.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

    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-SubCell

    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 – 147
    Beta strandi26 – 349
    Beta strandi36 – 4712
    Beta strandi49 – 513
    Helixi54 – 607
    Beta strandi64 – 674
    Turni71 – 744
    Helixi75 – 773
    Helixi83 – 853
    Beta strandi91 – 944

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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

    MARQVICWCF TLNNPLSPLS LHDSMKYLVY QTEQGEAGNI HFQGYIEMKK    50
    RTSLAGMKKL IPGAHFEKRR GTQGEARAYS MKEDTRLEGP WEYGEFVPTI 100
    EDKLREVMND MKITGKRPIE YIEECCNTYD KSASTLREFR GELKKKKAIS 150
    SWELQRKPWM GEVDALLQER DGRRIIWVYG PQGGEGKTSY AKHLVKTRDA 200
    FYSTGGKTAD IAFAWDHQEL VLFDFPRSFE EYVNYGVIEQ LKNGIIQSGK 250
    YQSVIKYSDY VEVIVFANFT PRSGMFSEDR IVYVYA 286
    Length:286
    Mass (Da):33,141
    Last modified:January 1, 1998 - v1
    Checksum:iFE878BF9336D23CD
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y11405 Genomic DNA. Translation: CAA72209.1.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    Y11405 Genomic DNA. Translation: CAA72209.1 .

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    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: October 1, 2014
    This is version 60 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