4IZJ

Crystal structure of yellowtail ascites virus VP4 protease with a wild-type active site reveals acyl-enzyme complexes and product complexes.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structures of Yellowtail Ascites Virus VP4 Protease: TRAPPING AN INTERNAL CLEAVAGE SITE TRANS ACYL-ENZYME COMPLEX IN A NATIVE SER/LYS DYAD ACTIVE SITE.

Chung, I.Y.Paetzel, M.

(2013) J.Biol.Chem. 288: 13068-13081

  • DOI: 10.1074/jbc.M112.386953
  • Primary Citation of Related Structures:  4IZK

  • PubMed Abstract: 
  • Yellowtail ascites virus (YAV) is an aquabirnavirus that causes ascites in yellowtail, a fish often used in sushi. Segment A of the YAV genome codes for a polyprotein (pVP2-VP4-VP3), where processing by its own VP4 protease yields the capsid protein ...

    Yellowtail ascites virus (YAV) is an aquabirnavirus that causes ascites in yellowtail, a fish often used in sushi. Segment A of the YAV genome codes for a polyprotein (pVP2-VP4-VP3), where processing by its own VP4 protease yields the capsid protein precursor pVP2, the ribonucleoprotein-forming VP3, and free VP4. VP4 protease utilizes the rarely observed serine-lysine catalytic dyad mechanism. Here we have confirmed the existence of an internal cleavage site, preceding the VP4/VP3 cleavage site. The resulting C-terminally truncated enzyme (ending at Ala(716)) is active, as shown by a trans full-length VP4 cleavage assay and a fluorometric peptide cleavage assay. We present a crystal structure of a native active site YAV VP4 with the internal cleavage site trapped as trans product complexes and trans acyl-enzyme complexes. The acyl-enzyme complexes confirm directly the role of Ser(633) as the nucleophile. A crystal structure of the lysine general base mutant (K674A) reveals the acyl-enzyme and empty binding site states of VP4, which allows for the observation of structural changes upon substrate or product binding. These snapshots of three different stages in the VP4 protease reaction mechanism will aid in the design of anti-birnavirus compounds, provide insight into previous site-directed mutagenesis results, and contribute to understanding of the serine-lysine dyad protease mechanism. In addition, we have discovered that this protease contains a channel that leads from the enzyme surface (adjacent to the substrate binding groove) to the active site and the deacylating water.


    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
Yellowtail Ascites Virus (YAV) VP4 protease
A, E
210Yellowtail ascites virus - Y-6N/A
Find proteins for P89521 (Yellowtail ascites virus - Y-6)
Go to UniProtKB:  P89521
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Yellowtail Ascites Virus (YAV) VP4 protease
B, C
210Yellowtail ascites virus - Y-6N/A
Find proteins for P89521 (Yellowtail ascites virus - Y-6)
Go to UniProtKB:  P89521
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Yellowtail Ascites Virus (YAV) VP4 protease
D
210Yellowtail ascites virus - Y-6N/A
Find proteins for P89521 (Yellowtail ascites virus - Y-6)
Go to UniProtKB:  P89521
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

Download SDF File 
Download CCD File 
A, B, C, D, E
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A, B, C, D, E
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.610α = 90.00
b = 64.330β = 95.80
c = 187.740γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
CrystalCleardata collection
MOSFLMdata reduction
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-27
    Type: Initial release
  • Version 1.1: 2013-04-03
    Type: Database references
  • Version 1.2: 2013-05-22
    Type: Database references