O39828 (MREP_FBNY2) Reviewed, UniProtKB/Swiss-Prot

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) [Complete proteome]

Taxonomic identifier

291604 [NCBI]

Taxonomic lineage

Viruses › ssDNA viruses › Nanoviridae › Nanovirus › Faba bean necrotic yellows virus

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	286 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

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. Ref.2
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.

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	3D-structure 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 – 286

286

Master replication protein

PRO_0000318772

Regions

Nucleotide binding

186 – 188

3

ATP By similarity

Motif

10 – 13

4

RCR-1 By similarity

Motif

41 – 46

6

RCR-2 By similarity

Motif

50 – 70

21

Nuclear localization signal Potential

Motif

79 – 82

4

RCR-3 By similarity

Motif

96 – 102

7

Nuclear localization signal Potential

Compositional bias

144 – 147

4

Poly-Lys

Sites

Active site

79

1

For DNA cleavage activity By similarity

Metal binding

33

1

Divalent metal cation Potential

Metal binding

41

1

Divalent metal cation Potential

Metal binding

84

1

Divalent metal cation Potential

Secondary structure

1

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286

Helix Strand Turn

Details...

Beta strand

8 – 14

7

Beta strand

26 – 34

9

Beta strand

36 – 47

12

Beta strand

49 – 51

3

Helix

54 – 60

7

Beta strand

64 – 67

4

Turn

71 – 74

4

Helix

75 – 77

3

Helix

83 – 85

3

Beta strand

91 – 94

4

Sequences

	Sequence		Length	Mass (Da)
	O39828 [UniParc]. Last modified January 1, 1998. Version 1. Checksum: FE878BF9336D23CD	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

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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: STRUCTURE BY NMR OF 2-95, COFACTOR, CHARACTERIZATION.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

Y11405 Genomic DNA. Translation: CAA72209.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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

ProteinModelPortal

O39828.

SMR

O39828. Positions 2-95.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

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...

Other

EvolutionaryTrace

O39828.

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:	April 3, 2013
This is version 56 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Viral Protein Annotation Program