3VKW

Crystal Structure of the Superfamily 1 Helicase from Tomato Mosaic Virus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

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Literature

Crystal structure of the superfamily 1 helicase from tomato mosaic virus

Nishikiori, M.Sugiyama, S.Xiang, H.Niiyama, M.Ishibashi, K.Inoue, T.Ishikawa, M.Matsumura, H.Katoh, E.

(2012) J Virol 86: 7565-7576

  • DOI: 10.1128/JVI.00118-12
  • Primary Citation of Related Structures:  
    3VKW

  • PubMed Abstract: 
  • The genomes of the Tomato mosaic virus and many other plant and animal positive-strand RNA viruses of agronomic and medical importance encode superfamily 1 helicases. Although helicases play important roles in viral replication, the crystal structures of viral superfamily 1 helicases have not been determined ...

    The genomes of the Tomato mosaic virus and many other plant and animal positive-strand RNA viruses of agronomic and medical importance encode superfamily 1 helicases. Although helicases play important roles in viral replication, the crystal structures of viral superfamily 1 helicases have not been determined. Here, we report the crystal structure of a fragment (S666 to Q1116) of the replication protein from Tomato mosaic virus. The structure reveals a novel N-terminal domain tightly associated with a helicase core. The helicase core contains two RecA-like α/β domains without any of the accessory domain insertions that are found in other superfamily 1 helicases. The N-terminal domain contains a flexible loop, a long α-helix, and an antiparallel six-stranded β-sheet. On the basis of the structure, we constructed deletion mutants of the S666-to-Q1116 fragment and performed split-ubiquitin-based interaction assays in Saccharomyces cerevisiae with TOM1 and ARL8, host proteins that are essential for tomato mosaic virus RNA replication. The results suggested that both TOM1 and ARL8 interact with the long α-helix in the N-terminal domain and that TOM1 also interacts with the helicase core. Prediction of secondary structures in other viral superfamily 1 helicases and comparison of those structures with the S666-to-Q1116 structure suggested that these helicases have a similar fold. Our results provide a structural basis of viral superfamily 1 helicases.


    Organizational Affiliation

    Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Replicase large subunitA446Tobacco mosaic virus strain tomato/LMutation(s): 0 
EC: 2.1.1 (PDB Primary Data), 2.7.7 (PDB Primary Data), 3.6.4.13 (PDB Primary Data), 2.7.7.48 (UniProt)
Find proteins for P03587 (Tomato mosaic virus (strain L))
Explore P03587 
Go to UniProtKB:  P03587
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.441α = 90
b = 128.817β = 90
c = 40.742γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SHELXSphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-11
    Type: Initial release