2HAL

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: 1.35 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.184 

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:  

  • 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: 
    • Crystal Structure of an Inhibitor Complex of the 3C Proteinase from Hepatitis A Virus (HAV) and Implications for the Polyprotein Processing in HAV
      Bergmann, E.M.,Cherney, M.M.,Mckendrick, J.,Frormann, S.,Luo, C.,Malcolm, B.A.,Vederas, J.C.,James, M.N.
      (1999) VIROLOGY 265: 153
    • The Refined Crystal Structure of the 3C Gene Product from Hepatitis A Virus: Specific Proteinase Activity and RNA Recognition
      Bergmann, E.M.,Mosimann, S.C.,Chernaia, M.M.,Malcolm, B.A.,James, M.N.
      (1997) J.VIROL. 71: 2436
    • 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.,Cherney, M.M.,Bergmann, E.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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hepatitis A Protease 3C
A
212Human hepatitis A virus genotype IB (isolate HM175)Mutation(s): 1 
Find proteins for P08617 (Human hepatitis A virus genotype IB (isolate HM175))
Go to UniProtKB:  P08617
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
N-ACETYL-LEUCYL-PHENYLALANYL-PHENYLALANYL-GLUTAMATE-FLUOROMETHYLKETONE INHIBITOR
I
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BBL
Query on BBL

Download SDF File 
Download CCD File 
A
N-[(BENZYLOXY)CARBONYL]-L-ALANINE
N-BENZYLOXYCARBONYL-L-SERINE-BETALACTONE
C11 H13 N O4
TYRGLVWXHJRKMT-QMMMGPOBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.584α = 90.00
b = 56.240β = 90.00
c = 81.052γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
MOLREPphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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