Hepacivirin

 

Hepatitis C virus has an RNA genome encoding a single polyprotein. This polyprotein includes a serine protease, NS3, which is required for processing of part of the polyprotein. Specifically, NS3 catalyses cleavage of the NS3/NS4A, NS4A/NS4B, NS4B/NS5A, and NS5A/NS5B segment junctions; NS3/NS4A cleavage probably occurs in cis with the remaining cleavages occurring in trans. The NS3 protease associates with the NS4A polypeptide which functions to activate the protease activity.

 

Reference Protein and Structure

Sequences
P27958 UniProt (2.7.7.48, 3.4.21.98, 3.4.22.-, 3.6.1.15, 3.6.4.13)
O39914 UniProt IPR004109 (Sequence Homologues) (PDB Homologues)
Biological species
Hepatitis C virus (isolate H77) Uniprot
PDB
1rgq - M9A HCV Protease complex with pentapeptide keto-amide inhibitor (2.9 Å) PDBe PDBsum 1rgq
Catalytic CATH Domains
2.40.10.10 CATHdb 2.40.10.120 CATHdb (see all for 1rgq)
Click To Show Structure

Enzyme Reaction (EC:3.4.21.98)

water
CHEBI:15377ChEBI
+
dipeptide zwitterion
CHEBI:90799ChEBI
→
L-alpha-amino acid zwitterion
CHEBI:59869ChEBI
Alternative enzyme names: Cpro-2, NS3-4A serine proteinase complex, Hepatitis C virus NS3 serine proteinase,

Enzyme Mechanism

Introduction

Hepatitis C virus NS3 protease employs a classical serine protease mechanism. Ser 142 acts as a nucleophile to attack the peptide bond and form a tetrahedral intermediate that is stabilised by the backbone NH of Ser 142 and Gly 140. His 60 promotes the nucleophilic attack by deprotonating Ser 142, while Asp 84 functions to modify the pKa of His 60. Collapse of the tetrahedral intermediate with protonation of the departing amine leaving group by His 60 generates an acyl-enzyme intermediate. This is then hydrolysed by a water molecule that is deprotonated by His 60.

Catalytic Residues Roles

UniProt PDB* (1rgq)
His1083 His60(68)A Deprotonates Ser 142 as Ser 142 attacks the peptide bond. Protonates the departing amine leaving group. Deprotonates the water molecule that attacks the acyl-enzyme intermediate. proton shuttle (general acid/base)
Asp1107 Asp84(92)A Modifies the pKa of His 60, allowing it to deprotonate Ser 142. electrostatic stabiliser
Ser1165 Ser142(150)A Side chain OH acts as a nucleophile to attack the peptide carbonyl. Backbone NH forms part of the oxyanion hole that stabilises the tetrahedral intermediate and associated transition state. covalently attached, electrostatic stabiliser
Gly1163 (main-N) Gly140(148)A (main-N) Backbone NH forms part of oxyanion hole that stabilises the tetrahedral intermediate and associated transition state. electrostatic stabiliser
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

References

  1. Di Marco S et al. (2000), J Biol Chem, 275, 7152-7157. Inhibition of the Hepatitis C Virus NS3/4A Protease: THE CRYSTAL STRUCTURES OF TWO PROTEASE-INHIBITOR COMPLEXES. DOI:10.1074/jbc.275.10.7152. PMID:10702283.
  2. Liu Y et al. (2004), Arch Biochem Biophys, 421, 207-216. Hepatitis C NS3 protease inhibition by peptidyl-α-ketoamide inhibitors: kinetic mechanism and structure. DOI:10.1016/j.abb.2003.11.013. PMID:14984200.
  3. Kim JL et al. (1996), Cell, 87, 343-355. Crystal Structure of the Hepatitis C Virus NS3 Protease Domain Complexed with a Synthetic NS4A Cofactor Peptide. DOI:10.1016/s0092-8674(00)81351-3. PMID:8861917.

Step 1.

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Catalytic Residues Roles

Residue Roles
Ser142(150)A covalently attached, electrostatic stabiliser
Gly140(148)A (main-N) electrostatic stabiliser
His60(68)A proton shuttle (general acid/base)
Asp84(92)A electrostatic stabiliser

Chemical Components

Step 1.

Contributors

Steven Smith, Gemma L. Holliday