PDBsum entry 2k1q

Viral protein

PDB id: 2k1q

Contents

Protein chain

165 a.a.

Ligands

IBU-GLU-LEU-OBF-FE3

Metals

_ZN

PDB id:

2k1q

Name:

Viral protein

Title:

Nmr structure of hepatitis c virus ns3 serine protease complexed with the non-covalently bound phenethylamide inhibitor

Structure:

Ns3 protease. Chain: a. Fragment: residues 1048-1206. Engineered: yes. Phenethylamide. Chain: b. Engineered: yes

Source:

Hepatitis c virus. Organism_taxid: 11103. Strain: 1b. Expressed in: escherichia coli. Expression_system_variant: de3. Synthetic: yes

NMR struc:

20 models

Authors:

T.Eliseo,M.Gallo,M.Pennestri,R.Bazzo,D.O.Cicero

Key ref:

M.Gallo et al. (2009). Binding of a Noncovalent Inhibitor Exploiting the S' region Stabilizes the Hepatitis C virus NS3 Protease Conformation in the Absence of Cofactor. J Mol Biol, 385, 1142-1155. PubMed id: 19061898 DOI: 10.1016/j.jmb.2008.11.017

Date:

13-Mar-08 Release date: 03-Feb-09

Protein chain

P90191  (P90191_9HEPC) -  Genome polyprotein from Hepacivirus hominis

Seq: 3010 a.a.

Struc: 165 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.3.4.21.98 - hepacivirin.
• Reaction: Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1'.
• Enzyme class 2: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺
• Enzyme class 3: E.C.3.6.4.13 - Rna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2008.11.017

J Mol Biol 385:1142-1155 (2009)

PubMed id: 19061898

Binding of a Noncovalent Inhibitor Exploiting the S' region Stabilizes the Hepatitis C virus NS3 Protease Conformation in the Absence of Cofactor.

M.Gallo, M.Pennestri, M.J.Bottomley, G.Barbato, T.Eliseo, M.Paci, F.Narjes, R.De Francesco, V.Summa, U.Koch, R.Bazzo, D.O.Cicero.

ABSTRACT

We present the first structure of a noncovalent inhibitor bound to the protease domain of hepatitis C virus NS3 protein (NS3p), solved by NMR. The inhibitor exploits interactions with the S' region of NS3p to form a long-lived complex, although the absence of negative charges strongly reduces the association rate. The inhibitor stabilizes the N-terminal domain of NS3p and the substrate-binding site, and correctly aligns catalytic His-Asp residues. These actions were previously attributed exclusively to the cofactor NS4A, which interacts with the N-terminal domain of the NS3p and functions as an activator in vivo. The structure of the inhibitor/NS3p complex is very similar to that of the NS3p-NS4A complex, showing that binding of the NS4A cofactor is not the only event leading to a stable active-site conformation.

Selected figure(s)

Figure 1.
Fig. 1. Inhibitors of NS3–NS4A serine protease and titration experiments. (a) Chemical structures of phenethylamide (compound 1) and hexapeptide DEDifEChaC-OH (compound 2) inhibitors. (b and c) Selected region of the HSQC spectra of NS3p showing the well-resolved R123 NH signal after the addition of different amounts of compounds 1 and 2, respectively.

Figure 2.
Fig. 2. High-resolution structure of the NS3p/compound 1 complex derived by NMR. (a) Stereoview of the superposition of the 20 lowest-energy structures and (b) a ribbon model of the structure. Compound 1 backbone is shown in green. Only residues 22–186 are included, since residues 1–21 are not assigned. (c) The intermolecular interface is color-coded to indicate electrostatic potential (negative charge: red; positive charge: blue). (d) Schematic representations of the N-terminal domain in the NS3–NS4A (left) and the NS3/compound 1 (right) complexes are shown to illustrate the change in topology caused by the insertion of the cofactor NS4A.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 385, 1142-1155) copyright 2009.

Figures were selected by an automated process.