Master replication protein - Faba bean necrotic yellows virus (isolate SV292-88) (FBNYV)

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Reviewed, UniProtKB/Swiss-Prot O39828 (MREP_FBNY2)

Last modified July 7, 2009. Version 42. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    Master replication protein
      Short name=M-Rep
    EC=2.7.7.-
    EC=3.1.21.-
    EC=3.6.1.3
Alternative name(s):
    ATP-dependent helicase C2
    Replication-associated protein 2
      Short name=Rep2

Gene names

Name:	DNA-R
Synonyms:	C2

Organism

Faba bean necrotic yellows virus (isolate SV292-88) (FBNYV)

Taxonomic identifier

291604 [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) [TaxID: 3906]

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Protein attributes

Sequence length	286 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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General annotation (Comments)

Function	Essential for the replication of all genomic viral ssDNA (trans-replication). 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 conserved sequence 5'-A[GT]TATTAC-3' in 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.
Catalytic activity	ATP + H₂O = ADP + phosphate.
Cofactor	Divalent metal cations, possibly magnesium or manganese Probable.
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.

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Ontologies

Keywords
Biological process	DNA replication
Cellular component	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	3D-structure Multifunctional enzyme
Gene Ontology (GO)
Biological process	DNA replication Inferred from electronic annotation. Source: UniProtKB-KW protein-DNA covalent cross-linking Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	host cell nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell nucleus Inferred from electronic annotation. Source: UniProtKB-KW
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW ATPase activity, uncoupled Inferred from electronic annotation. Source: EC 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...

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 286

286

Master replication protein

PRO_0000318772

Regions

Nucleotide binding

186 – 188

ATP By similarity

Motif

10 – 13

RCR-1 By similarity

Motif

41 – 46

RCR-2 By similarity

Motif

50 – 70

Nuclear localization signal Potential

Motif

79 – 82

RCR-3 By similarity

Motif

96 – 102

Nuclear localization signal Potential

Compositional bias

144 – 147

Poly-Lys

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

Secondary structure

286

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

O39828-1 [UniParc].

Last modified January 1, 1998. Version 1.
Checksum: FE878BF9336D23CD
Show »

FASTA

286

33,141

        10         20         30         40         50         60 
MARQVICWCF TLNNPLSPLS LHDSMKYLVY QTEQGEAGNI HFQGYIEMKK RTSLAGMKKL 

        70         80         90        100        110        120 
IPGAHFEKRR GTQGEARAYS MKEDTRLEGP WEYGEFVPTI EDKLREVMND MKITGKRPIE 

       130        140        150        160        170        180 
YIEECCNTYD KSASTLREFR GELKKKKAIS SWELQRKPWM GEVDALLQER DGRRIIWVYG 

       190        200        210        220        230        240 
PQGGEGKTSY AKHLVKTRDA FYSTGGKTAD IAFAWDHQEL VLFDFPRSFE EYVNYGVIEQ 

       250        260        270        280 
LKNGIIQSGK YQSVIKYSDY VEVIVFANFT PRSGMFSEDR IVYVYA

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References

[1]

"Analysis of six DNA components of the faba bean necrotic yellows virus genome and their structural affinity to related plant virus genomes."
Katul L., Maiss E., Morozov S.Y., Vetten H.J.
Virology 233:247-259(1997) [PubMed: 9217049] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].

[2]

"Solution structure of the endonuclease domain from the master replication initiator protein of the nanovirus faba bean necrotic yellows virus and comparison with the corresponding geminivirus and circovirus structures."
Vega-Rocha S., Gronenborn B., Gronenborn A.M., Campos-Olivas R.
Biochemistry 46:6201-6212(2007) [PubMed: 17472345] [Abstract]
Cited for: STRUCTURE BY NMR OF 2-95, COFACTOR, CHARACTERIZATION.

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Cross-references

Sequence databases

Y11405 Genomic DNA. Translation: CAA72209.1.

3D structure databases

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2HWT	NMR	-	A	2-95	[»]

ModBase

Search...

Family and domain databases

InterPro

IPR000605. Helicase_SF3_ssDNA/RNA_vir.
IPR013628. Viral_Rep_C.
IPR003365. Viral_rep_N.
[Graphical view]

Pfam

PF00910. RNA_helicase. 1 hit.
PF02407. Viral_Rep. 1 hit.
PF08419. Viral_Rep_C. 1 hit.
[Graphical view]

ProtoNet

Search...

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Entry information

Entry name

MREP_FBNY2

Accession

Primary (citable) accession number: O39828

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 26, 2008
Last sequence update:	January 1, 1998
Last modified:	July 7, 2009
This is version 42 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

Virus (Virus annotation project)

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Relevant documents

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families