1HAV

HEPATITIS A VIRUS 3C PROTEINASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 2436-2448

  • DOI: 10.1128/JVI.71.3.2436-2448.1997
  • Primary Citation of Related Structures:  
    1HAV

  • PubMed Abstract: 
  • The virally encoded 3C proteinases of picornaviruses process the polyprotein produced by the translation of polycistronic viral mRNA. The X-ray crystallographic structure of a catalytically active mutant of the hepatitis A virus (HAV) 3C proteinase (C24S) has been determined ...

    The virally encoded 3C proteinases of picornaviruses process the polyprotein produced by the translation of polycistronic viral mRNA. The X-ray crystallographic structure of a catalytically active mutant of the hepatitis A virus (HAV) 3C proteinase (C24S) has been determined. Crystals of this mutant of HAV 3C are triclinic with unit cell dimensions a = 53.6 A, b = 53.5 A, c = 53.2 A, alpha = 99.1 degrees, beta = 129.0 degrees, and gamma = 103.3 degrees. There are two molecules of HAV 3C in the unit cell of this crystal form. The structure has been refined to an R factor of 0.211 (Rfree = 0.265) at 2.0-A resolution. Both molecules fold into the characteristic two-domain structure of the chymotrypsin-like serine proteinases. The active-site and substrate-binding regions are located in a surface groove between the two beta-barrel domains. The catalytic Cys 172 S(gamma) and His 44 N(epsilon2) are separated by 3.9 A; the oxyanion hole adopts the same conformation as that seen in the serine proteinases. The side chain of Asp 84, the residue expected to form the third member of the catalytic triad, is pointed away from the side chain of His 44 and is locked in an ion pair interaction with the epsilon-amino group of Lys 202. A water molecule is hydrogen bonded to His 44 N(delta1). The side-chain phenolic hydroxyl group of Tyr 143 is close to this water and to His 44 N(delta1) and may be negatively charged. The glutamine specificity for P1 residues of substrate cleavage sites is attributed to the presence of a highly conserved His 191 in the S1 pocket. A very unusual environment of two water molecules and a buried glutamate contribute to the imidazole tautomer believed to be important in the P1 specificity. HAV 3C proteinase has the conserved RNA recognition sequence KFRDI located in the interdomain connection loop on the side of the molecule diametrically opposite the proteolytic site. This segment of polypeptide is located between the N- and C-terminal helices, and its conformation results in the formation of a well-defined surface with a strongly charged electrostatic potential. Presumably, this surface of HAV 3C participates in the recognition of the 5' and 3' nontranslated regions of the RNA genome during viral replication.


    Related Citations: 
    • Hepatitis a Virus Picornain 3C
      Bergmann, E.M.
      () To be published --: --
    • Picornaviral 3C Cysteine Proteinases Have a Fold Similar to Chymotrypsin-Like Serine Proteinases
      Allaire, M., Chernaia, M.M., Malcolm, B.A., James, M.N.
      (1994) Nature 369: 72
    • 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.B., Ralston, R., Rosenberg, S.
      (1992) Biochemistry 31: 3358

    Organizational Affiliation

    Department of Biochemistry, University of Alberta, Edmonton, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEPATITIS A VIRUS 3C PROTEINASEA217Hepatovirus AMutation(s): 1 
Gene Names: 3C
EC: 2.7.7.48 (PDB Primary Data), 3.6.1.15 (UniProt), 3.4.22.28 (UniProt)
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:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HEPATITIS A VIRUS 3C PROTEINASEB217Hepatovirus AMutation(s): 1 
Gene Names: 3C
EC: 2.7.7.48 (PDB Primary Data), 3.6.1.15 (UniProt), 3.4.22.28 (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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OCS
Query on OCS
BL-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.211 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.6α = 99.08
b = 53.55β = 129
c = 53.2γ = 103.31
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
BIOMOLdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-12-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance