4A5U

Turnip yellow mosaic virus proteinase and Escherichia coli 30S ribosomal S15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Compact Viral Processing Proteinase/Ubiquitin Hydrolase from the Otu Family.

Lombardi, C.Ayach, M.Beaurepaire, L.Chenon, M.Andreani, J.Guerois, R.Jupin, I.Bressanelli, S.

(2013) Plos Pathog. 9: 3560

  • DOI: 10.1371/journal.ppat.1003560

  • PubMed Abstract: 
  • Turnip yellow mosaic virus (TYMV)--a member of the alphavirus-like supergroup of viruses--serves as a model system for positive-stranded RNA virus membrane-bound replication. TYMV encodes a precursor replication polyprotein that is processed by the e ...

    Turnip yellow mosaic virus (TYMV)--a member of the alphavirus-like supergroup of viruses--serves as a model system for positive-stranded RNA virus membrane-bound replication. TYMV encodes a precursor replication polyprotein that is processed by the endoproteolytic activity of its internal cysteine proteinase domain (PRO). We recently reported that PRO is actually a multifunctional enzyme with a specific ubiquitin hydrolase (DUB) activity that contributes to viral infectivity. Here, we report the crystal structure of the 150-residue PRO. Strikingly, PRO displays no homology to other processing proteinases from positive-stranded RNA viruses, including that of alphaviruses. Instead, the closest structural homologs of PRO are DUBs from the Ovarian tumor (OTU) family. In the crystal, one molecule's C-terminus inserts into the catalytic cleft of the next, providing a view of the N-terminal product complex in replication polyprotein processing. This allows us to locate the specificity determinants of PRO for its proteinase substrates. In addition to the catalytic cleft, at the exit of which the active site is unusually pared down and solvent-exposed, a key element in molecular recognition by PRO is a lobe N-terminal to the catalytic domain. Docking models and the activities of PRO and PRO mutants in a deubiquitylating assay suggest that this N-terminal lobe is also likely involved in PRO's DUB function. Our data thus establish that DUBs can evolve to specifically hydrolyze both iso- and endopeptide bonds with different sequences. This is achieved by the use of multiple specificity determinants, as recognition of substrate patches distant from the cleavage sites allows a relaxed specificity of PRO at the sites themselves. Our results thus shed light on how such a compact protein achieves a diversity of key functions in viral genome replication and host-pathogen interaction.


    Related Citations: 
    • In Praise of Impurity: 30S Ribosomal S15 Protein-Assisted Crystallization of Turnip Yellow Mosaic Virus Proteinase.
      Robin, C.,Beaurepaire, L.,Chenon, M.,Jupin, I.,Bressanelli, S.
      (2012) Acta Crystallogr.,Sect.F 68: 486


    Organizational Affiliation

    The Laboratoire de Virologie Mol├ęculaire et Structurale, Centre de Recherche de Gif, CNRS (UPR 3296), Gif sur Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA REPLICASE POLYPROTEIN
A
160Turnip yellow mosaic virusEC: 3.6.4.-, 3.4.22.-, 2.1.1.-, 2.7.7.48
Find proteins for P10358 (Turnip yellow mosaic virus)
Go to UniProtKB:  P10358
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S15
B
88N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.168 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 135.200α = 90.00
b = 135.200β = 90.00
c = 41.900γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
autoSHARPphasing
SHELXCDphasing
PHENIXrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2013-11-13
    Type: Database references