Venezuelan Equine Encephalitis Virus (VEEV) Nonstructural Protein 2 (nsP2) Cysteine Protease Inhibited by E64d

Experimental Data Snapshot

  • Resolution: 2.16 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Kinetic, Mutational, and Structural Studies of the Venezuelan Equine Encephalitis Virus Nonstructural Protein 2 Cysteine Protease.

Hu, X.Compton, J.R.Leary, D.H.Olson, M.A.Lee, M.S.Cheung, J.Ye, W.Ferrer, M.Southall, N.Jadhav, A.Morazzani, E.M.Glass, P.J.Marugan, J.Legler, P.M.

(2016) Biochemistry 55: 3007-3019

  • DOI: https://doi.org/10.1021/acs.biochem.5b00992
  • Primary Citation of Related Structures:  
    5EZQ, 5EZS

  • PubMed Abstract: 

    The Venezuelan equine encephalitis virus (VEEV) nonstructural protein 2 (nsP2) cysteine protease (EC 3.4.22.-) is essential for viral replication and is involved in the cytopathic effects (CPE) of the virus. The VEEV nsP2 protease is a member of MEROPS Clan CN and characteristically contains a papain-like protease linked to an S-adenosyl-l-methionine-dependent RNA methyltransferase (SAM MTase) domain. The protease contains an alternative active site motif, (475)NVCWAK(480), which differs from papain's (CGS(25)CWAFS), and the enzyme lacks a transition state-stabilizing residue homologous to Gln-19 in papain. To understand the roles of conserved residues in catalysis, we determined the structure of the free enzyme and the first structure of an inhibitor-bound alphaviral protease. The peptide-like E64d inhibitor was found to bind beneath a β-hairpin at the interface of the SAM MTase and protease domains. His-546 adopted a conformation that differed from that found in the free enzyme; one or both of the conformers may assist in leaving group departure of either the amine or Cys thiolate during the catalytic cycle. Interestingly, E64c (200 μM), the carboxylic acid form of the E64d ester, did not inhibit the nsP2 protease. To identify key residues involved in substrate binding, a number of mutants were analyzed. Mutation of the motif residue, N475A, led to a 24-fold reduction in kcat/Km, and the conformation of this residue did not change after inhibition. N475 forms a hydrogen bond with R662 in the SAM MTase domain, and the R662A and R662K mutations both led to 16-fold decreases in kcat/Km. N475 forms the base of the P1 binding site and likely orients the substrate for nucleophilic attack or plays a role in product release. An Asn homologous to N475 is similarly found in coronaviral papain-like proteases (PLpro) of the Severe Acute Respiratory Syndrome (SARS) virus and Middle East Respiratory Syndrome (MERS) virus. Mutation of another motif residue, K480A, led to a 9-fold decrease in kcat and kcat/Km. K480 likely enhances the nucleophilicity of the Cys. Consistent with our substrate-bound models, the SAM MTase domain K706A mutation increased Km 4.5-fold to 500 μM. Within the β-hairpin, the N545A mutation slightly but not significantly increased kcat and Km. The structures and identified active site residues may facilitate the discovery of protease inhibitors with antiviral activity.

  • Organizational Affiliation

    Center for Bio/molecular Science and Engineering, U.S. Naval Research Laboratory , Washington, D.C. 20375, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Non-structural Protein 2 Cysteine Protease338Venezuelan equine encephalitis virus (strain Trinidad donkey)Mutation(s): 0 
EC: 3.4.22 (PDB Primary Data), 2.1.1 (UniProt), 2.7.7 (UniProt), (UniProt), (UniProt), (UniProt), (UniProt), (UniProt), (UniProt)
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on E6D

Download Ideal Coordinates CCD File 
B [auth A]ethyl (3S)-3-hydroxy-4-({(2S)-4-methyl-1-[(3-methylbutyl)amino]-1-oxopentan-2-yl}amino)-4-oxobutanoate
C17 H32 N2 O5
Experimental Data & Validation

Experimental Data

  • Resolution: 2.16 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.89α = 90
b = 63.63β = 90
c = 86.75γ = 90
Software Package:
Software NamePurpose
SAINTdata reduction
SADABSdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

  • Released Date: 2016-04-13 
  • Deposition Author(s): Legler, P.M.

Funding OrganizationLocationGrant Number
Defense Threat Reduction Agency (DTRA)United StatesCBCall4-CBM-05-2-0019

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-06-08
    Changes: Database references
  • Version 1.2: 2016-10-26
    Changes: Non-polymer description
  • Version 1.3: 2018-01-17
    Changes: Advisory, Author supporting evidence, Derived calculations
  • Version 1.4: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Advisory, Data collection, Database references, Refinement description