2H9H

An episulfide cation (thiiranium ring) trapped in the active site of HAV 3C proteinase inactivated by peptide-based ketone inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

An Episulfide Cation (Thiiranium Ring) Trapped in the Active Site of HAV 3C Proteinase Inactivated by Peptide-based Ketone Inhibitors.

Yin, J.Cherney, M.M.Bergmann, E.M.Zhang, J.Huitema, C.Pettersson, H.Eltis, L.D.Vederas, J.C.James, M.N.

(2006) J Mol Biol 361: 673-686

  • DOI: 10.1016/j.jmb.2006.06.047
  • Primary Citation of Related Structures:  
    2H6M, 2H9H, 2HAL

  • PubMed Abstract: 
  • We have solved the crystal and molecular structures of hepatitis A viral (HAV) 3C proteinase, a cysteine peptidase having a chymotrypsin-like protein fold, in complex with each of three tetrapeptidyl-based methyl ketone inhibitors to resolutions beyo ...

    We have solved the crystal and molecular structures of hepatitis A viral (HAV) 3C proteinase, a cysteine peptidase having a chymotrypsin-like protein fold, in complex with each of three tetrapeptidyl-based methyl ketone inhibitors to resolutions beyond 1.4 A, the highest resolution to date for a 3C or a 3C-Like (e.g. SARS viral main proteinase) peptidase. The residues of the beta-hairpin motif (residues 138-158), an extension of two beta-strands of the C-terminal beta-barrel of HAV 3C are critical for the interactions between the enzyme and the tetrapeptide portion of these inhibitors that are analogous to the residues at the P4 to P1 positions in the natural substrates of picornaviral 3C proteinases. Unexpectedly, the Sgamma of Cys172 forms two covalent bonds with each inhibitor, yielding an unusual episulfide cation (thiiranium ring) stabilized by a nearby oxyanion. This result suggests a mechanism of inactivation of 3C peptidases by methyl ketone inhibitors that is distinct from that occurring in the structurally related serine proteinases or in the papain-like cysteine peptidases. It also provides insight into the mechanisms underlying both the inactivation of HAV 3C by these inhibitors and on the proteolysis of natural substrates by this viral cysteine peptidase.


    Related Citations: 
    • Dual modes of modification of Hepatitis A virus 3C protease by a Serine-derived beta-lactone: selective crystallization and formation of a functional catalytic triad in the active site
      Yin, J., Bergmann, E.M., Cherney, M.M., Lall, M.S., Jain, R.P., Vederas, J.C., James, M.N.G.
      (2005) J Mol Biol 354: 854

    Organizational Affiliation

    Group in Protein Structure and Function, Department of Biochemistry, University of Alberta, Edmonton, AB, Canada T6G 2H7.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Hepatitis A virus protease 3CA212Hepatovirus AMutation(s): 1 
Gene Names: 3C
EC: 3.4.22.28 (PDB Primary Data), 3.6.1.15 (UniProt), 2.7.7.48 (UniProt)
Find proteins for P08617 (Human hepatitis A virus genotype IB (isolate HM175))
Explore P08617 
Go to UniProtKB:  P08617
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Three residue peptideI6N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BBL
Query on BBL

Download CCD File 
A
N-[(BENZYLOXY)CARBONYL]-L-ALANINE
C11 H13 N O4
TYRGLVWXHJRKMT-QMMMGPOBSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
QMM
Query on QMM
IL-PEPTIDE LINKINGC7 H14 N2 O3GLN
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.39 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.672α = 90
b = 56.055β = 90
c = 80.974γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-08
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other