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P0CK61

- REP9_FBNY2

UniProt

P0CK61 - REP9_FBNY2

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Protein
Para-Rep C9
Gene
C9
Organism
Faba bean necrotic yellows virus (isolate SV292-88) (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.

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 By similarity
Metal bindingi83 – 831Divalent metal cation Reviewed prediction

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi172 – 1809ATP By similarity

GO - Molecular functioni

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

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 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

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 281281Para-Rep C9
PRO_0000378527Add
BLAST

Keywords - PTMi

Covalent protein-DNA linkage

Interactioni

Subunit structurei

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

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.

P0CK61-1 [UniParc]FASTAAdd to Basket

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MSAVNWVFTL NFAGEVPVLS FDERVQYAVW QHERVNHDHI QGVIQLKKKA    50
KMNTVKNIIG GNPHLEKMKG SIEEASAYAQ KEESRVAGPW SYGELLKKGS 100
HKRKIMELIK DPENELEEPQ KYRRAMAWSA MDESRKLAEE EGFPYMFYSW 150
QETVLGLLEE EPNDRTIIWV YGPNGNEGKS QFGKFLGLKK DYLYLPGGKT 200
QDMTYMLMKN PKANVVMDIP RCNSEYLNYQ FMELIKNRTI YSYKYEPVGC 250
IINNKIHVIV LANVLPDYEK ISQDRIKIIY C 281
Length:281
Mass (Da):32,708
Last modified:March 21, 2012 - v1
Checksum:iBE746CEFB41A8CA9
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AJ005966 Genomic DNA. Translation: CAA06789.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AJ005966 Genomic DNA. Translation: CAA06789.1 .

3D structure databases

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. "Ten distinct circular ssDNA components, four of which encode putative replication-associated proteins, are associated with the faba bean necrotic yellows virus genome."
    Katul L., Timchenko T., Gronenborn B., Vetten H.J.
    J. Gen. Virol. 79:3101-3109(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].

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: April 16, 2014
This is version 6 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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