2PNL

Crystal structure of VP4 protease from infectious pancreatic necrosis virus (IPNV) in space group P1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the VP4 protease from infectious pancreatic necrosis virus reveals the acyl-enzyme complex for an intermolecular self-cleavage reaction.

Lee, J.Feldman, A.R.Delmas, B.Paetzel, M.

(2007) J.Biol.Chem. 282: 24928-24937

  • DOI: 10.1074/jbc.M701551200
  • Primary Citation of Related Structures:  2PNM

  • PubMed Abstract: 
  • Infectious pancreatic necrosis virus (IPNV), an aquatic birnavirus that infects salmonid fish, encodes a large polyprotein (NH(2)-pVP2-VP4-VP3-COOH) that is processed through the proteolytic activity of its own protease, VP4, to release the proteins ...

    Infectious pancreatic necrosis virus (IPNV), an aquatic birnavirus that infects salmonid fish, encodes a large polyprotein (NH(2)-pVP2-VP4-VP3-COOH) that is processed through the proteolytic activity of its own protease, VP4, to release the proteins pVP2 and VP3. pVP2 is further processed to give rise to the capsid protein VP2 and three peptides that are incorporated into the virion. Reported here are two crystal structures of the IPNV VP4 protease solved from two different crystal symmetries. The electron density at the active site in the triclinic crystal form, refined to 2.2-A resolution, reveals the acyl-enzyme complex formed with an internal VP4 cleavage site. The complex was generated using a truncated enzyme in which the general base lysine was substituted. Inside the complex, the nucleophilic Ser(633)Ogamma forms an ester bond with the main-chain carbonyl of the C-terminal residue, Ala(716), of a neighboring VP4. The structure of this substrate-VP4 complex allows us to identify the S1, S3, S5, and S6 substrate binding pockets as well as other substrate-VP4 interactions and therefore provides structural insights into the substrate specificity of this enzyme. The structure from the hexagonal crystal form, refined to 2.3-A resolution, reveals the free-binding site of the protease. Three-dimensional alignment with the VP4 of blotched snakehead virus, another birnavirus, shows that the overall structure of VP4 is conserved despite a low level of sequence identity ( approximately 19%). The structure determinations of IPNV VP4, the first of an acyl-enzyme complex for a Ser/Lys dyad protease, provide insights into the catalytic mechanism and substrate recognition of this type of protease.


    Related Citations: 
    • Purification, crystallization and preliminary X-ray analysis of truncated and mutant forms of VP4 protease from infectious pancreatic necrosis virus.
      Lee, J.,Feldman, A.R.,Chiu, E.,Chan, C.,Kim, Y.-N.,Delmas, B.,Paetzel, M.
      (2006) Acta Crystallogr.,Sect.F F62: 1235


    Organizational Affiliation

    Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease VP4
A, B, C, D, E, F, G, H, I, J
203Infectious pancreatic necrosis virusN/A
Find proteins for A1XQQ8 (Infectious pancreatic necrosis virus)
Go to UniProtKB:  A1XQQ8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GAI
Query on GAI

Download SDF File 
Download CCD File 
A, B, C, D, E, F, H, I, J
GUANIDINE
C H5 N3
ZRALSGWEFCBTJO-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H, I, J
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.190 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 41.703α = 93.06
b = 69.262β = 95.03
c = 191.388γ = 97.56
Software Package:
Software NamePurpose
HKL-2000data reduction
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-06-05
    Type: Initial release
  • Version 1.1: 2007-10-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance