3ZFP

Crystal structure of product-like, processed N-terminal protease Npro with internal His-Tag


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structures of the Viral Protease Npro Imply Distinct Roles for the Catalytic Water in Catalysis

Zogg, T.Sponring, M.Schindler, S.Koll, M.Schneider, R.Brandstetter, H.Auer, B.

(2013) Structure 21: 929

  • DOI: 10.1016/j.str.2013.04.003
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Npro is a key effector protein of pestiviruses such as bovine viral diarrhea virus and abolishes host cell antiviral defense mechanisms. Synthesized as the N-terminal part of the viral polyprotein, Npro releases itself via an autoproteolytic cleavage ...

    Npro is a key effector protein of pestiviruses such as bovine viral diarrhea virus and abolishes host cell antiviral defense mechanisms. Synthesized as the N-terminal part of the viral polyprotein, Npro releases itself via an autoproteolytic cleavage, triggering its immunological functions. However, the mechanisms of its proteolytic action and its immune escape were unclear. Here, we present the crystal structures of Npro to 1.25 Å resolution. Structures of pre- and postcleavage intermediates identify three catalytically relevant elements. The trapping of the putative catalytic water reveals its distinct roles as a base, acid, and nucleophile. The presentation of the substrate further explains the enigmatic latency of the protease, ensuring a single in cis cleavage. Additionally, we identified a zinc-free, disulfide-linked conformation of the TRASH motif, an interaction hub of immune factors. The structure opens additional opportunities in utilizing Npro as an autocleaving fusion protein and as a pharmaceutical target.


    Organizational Affiliation

    Department of Molecular Biology, University of Salzburg, Billrothstraße 11, 5020 Salzburg, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-TERMINAL PROTEASE NPRO
A
148Pestivirus strain D32/00_HoBiMutation(s): 6 
Gene Names: Npro
Find proteins for Q5L4B1 (Pestivirus strain D32/00_HoBi)
Go to UniProtKB:  Q5L4B1
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SGM
Query on SGM

Download SDF File 
Download CCD File 
A
MONOTHIOGLYCEROL
C3 H8 O2 S
PJUIMOJAAPLTRJ-GSVOUGTGSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.158 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 42.390α = 90.00
b = 41.040β = 115.31
c = 44.510γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
iMOSFLMdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2013-06-19
    Type: Database references, Refinement description