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P0CK60

- REP9_FBNY1

UniProt

P0CK60 - REP9_FBNY1

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Protein

Para-Rep C9

Gene

C9

Organism
Faba bean necrotic yellows virus (isolate Egyptian EV1-93) (FBNYV)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi

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 (By similarity).By similarity

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 cationSequence Analysis
Metal bindingi39 – 391Divalent metal cationSequence Analysis
Active sitei78 – 781For DNA cleavage activityBy similarity
Metal bindingi83 – 831Divalent metal cationSequence Analysis

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi178 – 1803ATPBy 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: UniProtKB-KW
  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:
Para-Rep C9 (EC:2.7.7.-, EC:3.1.21.-, EC:3.6.1.3)
Short name:
Rep9
Alternative name(s):
ATP-dependent helicase C9
Replication-associated protein of non-essential DNA C9
Gene namesi
Name:C9
OrganismiFaba bean necrotic yellows virus (isolate Egyptian EV1-93) (FBNYV)
Taxonomic identifieri291603 [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]
ProteomesiUP000008665: 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 – 281281Para-Rep C9PRO_0000222442Add
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

ProteinModelPortaliP0CK60.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

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

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.

P0CK60-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSAVNWVFTL NFAGEVPVLS FDERVQYAVW QHERVNHDHI QGVIQLKKKA
60 70 80 90 100
KMNTVKNIIG GNPHLEKMKG SIEEASAYAQ KEESRVAGPW SYGELLKKGS
110 120 130 140 150
HKRKIMELIK DPENELEEPQ KYRRAMAWSA MDESRKLAEE GGFPYTLYSW
160 170 180 190 200
QETVLGLLEE EPNDRIIIWV YGPNGNEGKS QFGKFLGLKK DYLYLPGGKT
210 220 230 240 250
QDMTYMLMKN PKANVVMDIP RCNSEYLNYQ FMELIKNRTI FSYKYEPVGC
260 270 280
IINNKIHVIV LANVLPDYEK ISQDRIKIIY C
Length:281
Mass (Da):32,568
Last modified:March 21, 2012 - v1
Checksum:iF50CF0C3CFC6E3B2
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AJ132187 Genomic DNA. Translation: CAB44027.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AJ132187 Genomic DNA. Translation: CAB44027.1 .

3D structure databases

ProteinModelPortali P0CK60.
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. "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: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION.
  2. "Nanoviruses: genome organisation and protein function."
    Gronenborn B.
    Vet. Microbiol. 98:103-109(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.

Entry informationi

Entry nameiREP9_FBNY1
AccessioniPrimary (citable) accession number: P0CK60
Secondary accession number(s): O91252, Q9WIK2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 21, 2012
Last sequence update: March 21, 2012
Last modified: October 29, 2014
This is version 11 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.Curated

Keywords - Technical termi

Complete proteome, Multifunctional enzyme

Documents

  1. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3