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 
  • R-Value Observed: 0.161 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1016/j.str.2013.04.003
  • Primary Citation of Related Structures:  
    3ZFN, 3ZFO, 3ZFP, 3ZFQ, 3ZFR, 3ZFT, 3ZFU

  • 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, 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-TERMINAL PROTEASE NPRO148Pestivirus strain D32/00_HoBiMutation(s): 6 
EC: 3.4.22
UniProt
Find proteins for Q5L4B1 (Pestivirus strain D32/00_HoBi)
Explore Q5L4B1 
Go to UniProtKB:  Q5L4B1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5L4B1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.39α = 90
b = 41.04β = 115.31
c = 44.51γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-05-15
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references, Refinement description
  • Version 1.2: 2019-07-17
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2023-12-20
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description