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 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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 beyond 1 ...

    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., 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
    • 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

    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 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)
UniProt
Find proteins for P08617 (Human hepatitis A virus genotype IB (isolate HM175))
Explore P08617 
Go to UniProtKB:  P08617
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
N-ACETYL-LEUCYL-PHENYLALANYL-PHENYLALANYL-GLUTAMATE-FLUOROMETHYLKETONE INHIBITORB [auth I]6N/AMutation(s): 1 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BBL (Subject of Investigation/LOI)
Query on BBL

Download Ideal Coordinates CCD File 
C [auth A]N-[(BENZYLOXY)CARBONYL]-L-ALANINE
C11 H13 N O4
TYRGLVWXHJRKMT-QMMMGPOBSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
GLK
Query on GLK
B [auth I]PEPTIDE-LIKEC5 H11 N O4GLU
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.584α = 90
b = 56.24β = 90
c = 81.052γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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