Crystal structure of Venezuelan Equine Encephalitis alphavirus (VEEV) nonstructural protein 2 (nsp2) (K741A/K767A) protease domain

Experimental Data Snapshot

  • Resolution: 1.46 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.156 

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Self-inhibited State of Venezuelan Equine Encephalitis Virus (VEEV) nsP2 Cysteine Protease: A Crystallographic and Molecular Dynamics Analysis.

Hoffka, G.Lountos, G.T.Needle, D.Wlodawer, A.Waugh, D.S.Tozser, J.Motyan, J.A.

(2023) J Mol Biol 435: 168012-168012

  • DOI: https://doi.org/10.1016/j.jmb.2023.168012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The Venezuelan equine encephalitis virus (VEEV) belongs to the Togaviridae family and is pathogenic to both humans and equines. The VEEV non-structural protein 2 (nsP2) is a cysteine protease (nsP2pro) that processes the polyprotein and thus it is a drug target for inhibitor discovery. The atomic structure of the VEEV nsP2 catalytic domain was previously characterized by both X-ray crystallography and computational studies. A modified nsP2pro harboring a N475A mutation in the N terminus was observed to exhibit an unexpected conformation: the N-terminal residues bind to the active site, mimicking binding of a substrate. The large conformational change of the N terminus was assumed to be induced by the N475A mutation, as N475 has an important role in stabilization of the N terminus and the active site. This conformation was first observed in the N475A mutant, but we also found it while determining a crystal structure of the catalytically active nsP2pro containing the wild-type N475 active site residue and K741A/K767A surface entropy reduction mutations. This suggests that the N475A mutation is not a prerequisite for self-inhibition. Here, we describe a high resolution (1.46 Å) crystal structure of a truncated nsP2pro (residues 463-785, K741A/K767A) and analyze the structure further by molecular dynamics to study the active and self-inhibited conformations of nsP2pro and its N475A mutant. A comparison of the different conformations of the N-terminal residues sheds a light on the interactions that play an important role in the stabilization of the enzyme.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Hungary; Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Debrecen, Hungary.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
nsp2 protease domain323Venezuelan equine encephalitis virusMutation(s): 2 
Gene Names: NSPWQI_35787gpNSPWQI_36543gpNSP
Find proteins for P27282 (Venezuelan equine encephalitis virus (strain Trinidad donkey))
Explore P27282 
Go to UniProtKB:  P27282
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP27282
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.46 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.156 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.186α = 90
b = 46.165β = 90
c = 175.945γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-15
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description