1QA7

CRYSTAL COMPLEX OF THE 3C PROTEINASE FROM HEPATITIS A VIRUS WITH ITS INHIBITOR AND IMPLICATIONS FOR THE POLYPROTEIN PROCESSING IN HAV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.214 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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: 153-163

  • DOI: 10.1006/viro.1999.9968
  • Primary Citation of Related Structures:  
    1QA7

  • PubMed Abstract: 
  • The proteolytic processing of the viral polyprotein is an essential step during the life cycle of hepatitis A virus (HAV), as it is in all positive-sense, single-stranded RNA viruses of animals. In HAV the 3C proteinase is the only proteolytic activity involved in the polyprotein processing ...

    The proteolytic processing of the viral polyprotein is an essential step during the life cycle of hepatitis A virus (HAV), as it is in all positive-sense, single-stranded RNA viruses of animals. In HAV the 3C proteinase is the only proteolytic activity involved in the polyprotein processing. The specific recognition of the cleavage sites by the 3C proteinase depends on the amino acid sequence of the cleavage site. The structure of the complex of the HAV 3C proteinase and a dipeptide inhibitor has been determined by X-ray crystallography. The double-mutant of HAV 3C (C24S, F82A) was inhibited with the specific inhibitor iodoacetyl-valyl-phenylalanyl-amide. The resulting complex had an acetyl-Val-Phe-amide group covalently attached to the S(gamma) atom of the nucleophilic Cys 172 of the enzyme. Crystals of the complex of HAV 3C (C24S, F82A) acetyl-Val-Phe-amide were found to be monoclinic, space group P2(1), having 4 molecules in the asymmetric unit and diffracting to 1.9-A resolution. The final refined structure consists of 4 molecules of HAV 3C (C24S,F82A) acetyl-Val-Phe-amide, 1 molecule of DMSO, 1 molecule of glycerol, and 514 water molecules. There are considerable conformational differences among the four molecules in the asymmetric unit. The final R-factor is 20.4% for all observed reflections between 15.0- and 1.9-A resolution and the corresponding R(free) is 29.8%. The dipeptide inhibitor is bound to the S(1)(') and S(2)(') specificity subsites of the proteinase. The crystal structure reveals that the HAV 3C proteinase possesses a well-defined S(2)(') specificity pocket and suggests that the P(2)(') residue could be an important determinant for the selection of the primary cleavage site during the polyprotein processing in HAV.


    Related Citations: 
    • 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.G.
      (1997) J Virol 71: 2436
    • Hepatitis A virus picornain 3C
      Bergmann, E.M.
      (1998) Handbook Of Proteolytic Enzymes --: 709
    • The 3C proteinases of picornaviruses and other positive-sense, single-stranded RNA viruses
      Bergmann, E.M., James, M.N.G.
      (1999) Handbook Of Exp Pharmacol , Vol Proteases As Targets For Therapy --: --
    • Expression and characterization of recombinant hepatitis A virus 3C proteinase
      Malcolm, B.A., Chin, S.M., Jewell, D.A., Stratton-Thomas, J.R., Thudium, K.
      (1992) Biochemistry 31: 3358

    Organizational Affiliation

    Department of Biochemistry, University of Alberta, Edmonton, Alberta, T6G 2H7, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HAV 3C PROTEINASEA, B, C, D217Hepatovirus AMutation(s): 2 
EC: 3.6.1.15 (UniProt), 3.4.22.28 (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
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IVF (Subject of Investigation/LOI)
Query on IVF

Download Ideal Coordinates CCD File 
E [auth A], F [auth B], G [auth C], H [auth D]N-(iodoacetyl)-L-valyl-L-phenylalaninamide
C16 H22 I N3 O3
IBXSBHDYMGMZJA-JSGCOSHPSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download Ideal Coordinates CCD File 
I [auth D]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.214 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.562α = 90
b = 78.357β = 97.5
c = 105.287γ = 90
Software Package:
Software NamePurpose
AMoREphasing
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-04-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2012-05-16
    Changes: Non-polymer description