PDBsum entry 3p8o

Hydrolase/hydrolase inhibitor

PDB id: 3p8o

Contents

Protein chains

182 a.a.

13 a.a.

Ligands

L5T ×2

Metals

_NA ×2

Waters ×66

PDB id:

3p8o

Name:

Hydrolase/hydrolase inhibitor

Title:

Crystal structure of hcv ns3/ns4a protease complexed with des-bromine analogue of bi 201335

Structure:

Hcv serine protease ns3. Chain: a, b. Engineered: yes. Hcv non-structural protein 4a. Chain: c, d. Fragment: ns3 interacting peptide. Engineered: yes

Source:

Hepatitis c virus. Hcv. Organism_taxid: 11116. Strain: isolate japanese. Gene: polg_hcvja. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes

Resolution:

2.30Å R-factor: 0.208 R-free: 0.255

Authors:

C.T.Lemke

Key ref:

C.T.Lemke et al. (2011). Combined X-ray, NMR, and kinetic analyses reveal uncommon binding characteristics of the hepatitis C virus NS3-NS4A protease inhibitor BI 201335. J Biol Chem, 286, 11434-11443. PubMed id: 21270126 DOI: 10.1074/jbc.M110.211417

Date:

14-Oct-10 Release date: 26-Jan-11

Protein chains

P26662  (POLG_HCVJA) -  Genome polyprotein from Hepatitis C virus genotype 1b (isolate Japanese)

Seq: 3010 a.a.

Struc: 182 a.a.*

Protein chains

P26662  (POLG_HCVJA) -  Genome polyprotein from Hepatitis C virus genotype 1b (isolate Japanese)

Seq: 3010 a.a.

Struc: 13 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chains A, B, C, D: E.C.2.7.7.48 - RNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 2: Chains A, B, C, D: 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 3: Chains A, B, C, D: E.C.3.4.22.- - ?????
• Enzyme class 4: Chains A, B, C, D: E.C.3.6.1.15 - nucleoside-triphosphate phosphatase.
• Reaction: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H⁺
• Enzyme class 5: Chains A, B, C, D: 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: 10.1074/jbc.M110.211417

J Biol Chem 286:11434-11443 (2011)

PubMed id: 21270126

Combined X-ray, NMR, and kinetic analyses reveal uncommon binding characteristics of the hepatitis C virus NS3-NS4A protease inhibitor BI 201335.

C.T.Lemke, N.Goudreau, S.Zhao, O.Hucke, D.Thibeault, M.Llinàs-Brunet, P.W.White.

ABSTRACT

Hepatitis C virus infection, a major cause of liver disease worldwide, is curable, but currently approved therapies have suboptimal efficacy. Supplementing these therapies with direct-acting antiviral agents has the potential to considerably improve treatment prospects for hepatitis C virus-infected patients. The critical role played by the viral NS3 protease makes it an attractive target, and despite its shallow, solvent-exposed active site, several potent NS3 protease inhibitors are currently in the clinic. BI 201335, which is progressing through Phase IIb trials, contains a unique C-terminal carboxylic acid that binds noncovalently to the active site and a bromo-quinoline substitution on its proline residue that provides significant potency. In this work we have used stopped flow kinetics, x-ray crystallography, and NMR to characterize these distinctive features. Key findings include: slow association and dissociation rates within a single-step binding mechanism; the critical involvement of water molecules in acid binding; and protein side chain rearrangements, a bromine-oxygen halogen bond, and profound pK(a) changes within the catalytic triad associated with binding of the bromo-quinoline moiety.