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Protein

Para-Rep C9

Gene

C9

Organism
Faba bean necrotic yellows virus (isolate SV292-88) (FBNYV)
Status
Reviewed-Annotation score: 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

Mg2+By similarity, Mn2+By similarityNote: Divalent metal cations, possibly Mg2+ or Mn2+.By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi33Divalent metal cationSequence analysis1
Metal bindingi39Divalent metal cationSequence analysis1
Active sitei78For DNA cleavage activityBy similarity1
Metal bindingi83Divalent metal cationSequence analysis1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi172 – 180ATPBy similarity9

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:
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 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_00003785271 – 281Para-Rep C9Add BLAST281

Keywords - PTMi

Covalent protein-DNA linkage

Interactioni

Subunit structurei

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

Family & Domainsi

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi8 – 11RCR-1By similarity4
Motifi39 – 44RCR-2By similarity6
Motifi48 – 69Nuclear localization signalSequence analysisAdd BLAST22
Motifi78 – 81RCR-3By similarity4
Motifi95 – 101Nuclear localization signalSequence analysis7

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.

P0CK61-1 [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 EGFPYMFYSW
160 170 180 190 200
QETVLGLLEE EPNDRTIIWV YGPNGNEGKS QFGKFLGLKK DYLYLPGGKT
210 220 230 240 250
QDMTYMLMKN PKANVVMDIP RCNSEYLNYQ FMELIKNRTI YSYKYEPVGC
260 270 280
IINNKIHVIV LANVLPDYEK ISQDRIKIIY C
Length:281
Mass (Da):32,708
Last modified:March 21, 2012 - v1
Checksum:iBE746CEFB41A8CA9
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ005966 Genomic DNA. Translation: CAA06789.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ005966 Genomic DNA. Translation: CAA06789.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

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 nameiREP9_FBNY2
AccessioniPrimary (citable) accession number: P0CK61
Secondary accession number(s): O91252, P0CAX6, Q9WIK2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 21, 2012
Last sequence update: March 21, 2012
Last modified: November 30, 2016
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, Reference proteome

Documents

  1. 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.