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Q66862

- REP1_FBNY2

UniProt

Q66862 - REP1_FBNY2

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Protein
Para-Rep C1
Gene
C1, ORF1
Organism
Faba bean necrotic yellows virus (isolate SV292-88) (FBNYV)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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.1 Publication

Catalytic activityi

ATP + H2O = ADP + phosphate.

Cofactori

Divalent metal cations, possibly magnesium or manganese By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi33 – 331Divalent metal cation Reviewed prediction
Metal bindingi39 – 391Divalent metal cation Reviewed prediction
Active sitei78 – 781For DNA cleavage activity
Metal bindingi83 – 831Divalent metal cation Reviewed prediction

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi176 – 1783ATP Inferred

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. ATPase activity Source: CACAO
  3. ATPase activity, uncoupled Source: InterPro
  4. DNA binding Source: UniProtKB-KW
  5. RNA binding Source: InterPro
  6. RNA helicase activity Source: InterPro
  7. endodeoxyribonuclease activity, producing 5'-phosphomonoesters Source: InterPro
  8. metal ion binding Source: UniProtKB-KW
  9. nucleotidyltransferase activity Source: CACAO

GO - Biological processi

  1. ATP catabolic process Source: GOC
  2. DNA replication Source: UniProtKB-KW
  3. protein-DNA covalent cross-linking Source: InterPro
  4. viral DNA cleavage involved in viral genome maturation Source: CACAO
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):
ATP-dependent helicase C1
Replication-associated protein of non-essential DNA C1
Gene namesi
Name:C1
ORF Names:ORF1
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 Reviewed prediction

GO - Cellular componenti

  1. host cell nucleus Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Host nucleus

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi78 – 781Y → F: Complete loss of DNA cleavage and nucleotidyl transfer activity. 1 Publication
Mutagenesisi177 – 1771K → A: Complete loss of ATPase activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 278278Para-Rep C1
PRO_0000222439Add
BLAST

Keywords - PTMi

Covalent protein-DNA linkage

Interactioni

Subunit structurei

Homooligomer Reviewed prediction. Rep binds to repeated DNA motifs (iterons) By similarity.

Structurei

3D structure databases

ProteinModelPortaliQ66862.

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi8 – 114RCR-1 By similarity
Motifi39 – 446RCR-2 By similarity
Motifi48 – 6922Nuclear localization signal Reviewed prediction
Add
BLAST
Motifi78 – 814RCR-3 By similarity
Motifi95 – 1017Nuclear localization signal Reviewed prediction

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.

Q66862-1 [UniParc]FASTAAdd to Basket

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MACSNWVFTR NFQGALPLLS FDERVQYAVW QHERGTHDHI QGVIQLKKKA    50
RFSTVKEIIG GNPHVEKMKG TIEEASAYVQ KEETRVAGPW SYGDLLKRGS 100
HRRKTMERYL EDPEEMQLKD PDTALRCNAK RLKEDFMKEK TKLQLRPWQK 150
ELHDLILTEP DDRTIIWVYG PDGGEGKSMF AKELIKYGWF YTAGGKTQDI 200
LYMYAQDPER NIAFDVPRCS SEMMNYQAME MMKNRCFAST KYRSVDLCCN 250
KNVHLVVFAN VAYDPTKISE DRIVIINC 278
Length:278
Mass (Da):32,382
Last modified:November 1, 1996 - v1
Checksum:i4D9F4451F4EA2DED
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X80879 Genomic DNA. Translation: CAA56847.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X80879 Genomic DNA. Translation: CAA56847.1 .

3D structure databases

ProteinModelPortali Q66862.
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. "Sequence analysis of a faba bean necrotic yellows virus DNA component containing a putative replicase gene."
    Katul L., Maiss E., Vetten V.J.
    J. Gen. Virol. 76:475-479(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "A single Rep protein initiates replication of multiple genome components of faba bean necrotic yellows virus, a single-stranded DNA virus of plants."
    Timchenko T., de Kouchkovsky F., Katul L., David C., Vetten H.J., Gronenborn B.
    J. Virol. 73:10173-10182(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, MUTAGENESIS OF TYR-78 AND LYS-177.
  3. "Nanoviruses: genome organisation and protein function."
    Gronenborn B.
    Vet. Microbiol. 98:103-109(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.

Entry informationi

Entry nameiREP1_FBNY2
AccessioniPrimary (citable) accession number: Q66862
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 25, 2005
Last sequence update: November 1, 1996
Last modified: April 16, 2014
This is version 63 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.

Keywords - Technical termi

Complete proteome, Multifunctional enzyme

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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