2W5E

Structural and biochemical analysis of human pathogenic astrovirus serine protease at 2.0 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.234 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural and Biochemical Analysis of Human Pathogenic Astrovirus Serine Protease at 2.0 A Resolution.

Speroni, S.Rohayem, J.Nenci, S.Bonivento, D.Robel, I.Barthel, J.Luzhkov, V.B.Coutard, B.Canard, B.Mattevi, A.

(2009) J.Mol.Biol. 387: 1137

  • DOI: 10.1016/j.jmb.2009.02.044

  • PubMed Abstract: 
  • Astroviruses are single-stranded RNA viruses with a replication strategy based on the proteolytic processing of a polyprotein precursor and subsequent release of the viral enzymes of replication. So far, the catalytic properties of the astrovirus pro ...

    Astroviruses are single-stranded RNA viruses with a replication strategy based on the proteolytic processing of a polyprotein precursor and subsequent release of the viral enzymes of replication. So far, the catalytic properties of the astrovirus protease as well as its structure have remained uncharacterized. In this study, the three-dimensional crystal structure of the predicted protease of human pathogenic astrovirus has been solved to 2.0 A resolution. The protein displays the typical properties of trypsin-like enzymes but also several characteristic features: (i) a catalytic Asp-His-Ser triad in which the aspartate side chain is oriented away from the histidine, being replaced by a water molecule; (ii) a non-common conformation and composition of the S1 pocket; and (iii) the lack of the typical surface beta-ribbons together with a "featureless" shape of the substrate-binding site. Hydrolytic activity assays indicate that the S1 pocket recognises Glu and Asp side chains specifically, which, therefore, are predicted to occupy the P1 position on the substrate cleavage site. The positive electrostatic potential featured by the S1 region underlies this specificity. The comparative structural analysis highlights the peculiarity of the astrovirus protease, and differentiates it from the human and viral serine proteases.


    Organizational Affiliation

    Department of Genetics and Microbiology, University of Pavia, via Ferrata 1, Pavia, 27100 Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PUTATIVE SERINE PROTEASE
A, B, C, D, E, F
163Human astrovirus-1Mutation(s): 0 
Find proteins for Q3ZN04 (Human astrovirus-1)
Go to UniProtKB:  Q3ZN04
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B, C, D, E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A, B, C, D, E, F
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.234 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 135.047α = 90.00
b = 135.047β = 90.00
c = 189.955γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SHARPphasing
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance