Para-Rep C9 - Faba bean necrotic yellows virus (isolate Egyptian EV1-93) (FBNYV)

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P0CK60 (REP9_FBNY1) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 6. History...

Clusters with 100%, 90%, 50% identity |

Documents (1) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Para-Rep C9
Short name=Rep9
EC=2.7.7.-
EC=3.1.21.-
EC=3.6.1.3

Alternative name(s):
ATP-dependent helicase C9
Replication-associated protein of non-essential DNA C9

Gene names

Name:

Organism

Faba bean necrotic yellows virus (isolate Egyptian EV1-93) (FBNYV) [Complete proteome]

Taxonomic identifier

291603 [NCBI]

Taxonomic lineage

Viruses › ssDNA viruses › Nanoviridae › Nanovirus ›

Virus host

Cicer 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]

Protein attributes

Sequence length	281 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	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. Ref.1
Catalytic activity	ATP + H₂O = ADP + phosphate.
Cofactor	Divalent metal cations, possibly magnesium or manganese By similarity.
Subunit structure	Homooligomer Potential. Rep binds to repeated DNA motifs (iterons) By similarity.
Subcellular location	Host nucleus Potential.
Domain	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.
Miscellaneous	The genome of nanoviruses is composed of six to eight segments. In addition, some isolates contain subviral DNAs.
Sequence similarities	Belongs to the nanoviridea/circoviridae replication-associated protein family.
Caution	This protein is encoded by a subviral DNA that is not present in all isolates of the virus.

Ontologies

Keywords
Biological process	DNA replication
Cellular component	Host nucleus
Ligand	ATP-binding DNA-binding Metal-binding Nucleotide-binding
Molecular function	Endonuclease Helicase Hydrolase Nuclease Nucleotidyltransferase Transferase
PTM	Covalent protein-DNA linkage
Technical term	Complete proteome Multifunctional enzyme
Gene Ontology (GO)
Biological_process	ATP catabolic process Inferred from electronic annotation. Source: GOC DNA replication Inferred from electronic annotation. Source: UniProtKB-KW nucleic acid phosphodiester bond hydrolysis Inferred from electronic annotation. Source: GOC protein-DNA covalent cross-linking Inferred from electronic annotation. Source: InterPro
Cellular_component	host cell nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATPase activity, uncoupled Inferred from electronic annotation. Source: InterPro DNA binding Inferred from electronic annotation. Source: UniProtKB-KW RNA binding Inferred from electronic annotation. Source: InterPro RNA helicase activity Inferred from electronic annotation. Source: InterPro endodeoxyribonuclease activity, producing 5'-phosphomonoesters Inferred from electronic annotation. Source: InterPro metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW nucleotidyltransferase activity Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 281

281

Para-Rep C9

PRO_0000222442

Regions

Nucleotide binding

178 – 180

ATP By similarity

Motif

8 – 11

RCR-1 By similarity

Motif

39 – 44

RCR-2 By similarity

Motif

48 – 69

Nuclear localization signal Potential

Motif

78 – 81

RCR-3 By similarity

Motif

95 – 101

Nuclear localization signal Potential

Sites

Active site

For DNA cleavage activity By similarity

Metal binding

Divalent metal cation Potential

Metal binding

Divalent metal cation Potential

Metal binding

Divalent metal cation Potential

Sequences

Sequence

Length

Mass (Da)

Tools

P0CK60 [UniParc].

Last modified March 21, 2012. Version 1.
Checksum: F50CF0C3CFC6E3B2
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FASTA

281

32,568

        10         20         30         40         50         60 
MSAVNWVFTL NFAGEVPVLS FDERVQYAVW QHERVNHDHI QGVIQLKKKA KMNTVKNIIG 

        70         80         90        100        110        120 
GNPHLEKMKG SIEEASAYAQ KEESRVAGPW SYGELLKKGS HKRKIMELIK DPENELEEPQ 

       130        140        150        160        170        180 
KYRRAMAWSA MDESRKLAEE GGFPYTLYSW QETVLGLLEE EPNDRIIIWV YGPNGNEGKS 

       190        200        210        220        230        240 
QFGKFLGLKK DYLYLPGGKT QDMTYMLMKN PKANVVMDIP RCNSEYLNYQ FMELIKNRTI 

       250        260        270        280 
FSYKYEPVGC IINNKIHVIV LANVLPDYEK ISQDRIKIIY C

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References

[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.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AJ132187 Genomic DNA. Translation: CAB44027.1.
RefSeq	NP_619574.1. NC_003567.1.
3D structure databases
ProteinModelPortal	P0CK60.
ModBase	Search...
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	993380.
Family and domain databases
InterPro	IPR000605. Helicase_SF3_ssDNA/RNA_vir. IPR003365. Viral_rep_N. [Graphical view]
Pfam	PF00910. RNA_helicase. 1 hit. PF02407. Viral_Rep. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

REP9_FBNY1

Accession

Primary (citable) accession number: P0CK60
Secondary accession number(s): O91252, Q9WIK2

Entry history

Integrated into UniProtKB/Swiss-Prot:	March 21, 2012
Last sequence update:	March 21, 2012
Last modified:	April 3, 2013
This is version 6 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protocols and materials databases

Genome annotation databases

Family and domain databases

Entry information

Relevant documents