title: Inhibitor binding induces active site stabilization of the HCV NS3 protein serine protease domain.
abstract: Few structures of viral serine proteases, those encoded by the Sindbis and Semliki Forest viruses, hepatitis C virus (HCV) and cytomegalovirus, have been reported. In the life cycle of HCV a crucial role is played by a chymotrypsin-like serine protease encoded at the N-terminus of the viral NS3 protein, the solution structure of which we present here complexed with a covalently bound reversible inhibitor. Unexpectedly, the residue in the P2 position of the inhibitor induces an effective stabilization of the catalytic His-Asp hydrogen bond, by shielding that region of the protease from the solvent. This interaction appears crucial in the activation of the enzyme catalytic machinery and represents an unprecedented observation for this family of enzymes. Our data suggest that natural substrates of this serine protease could contribute to the enzyme activation by a similar induced-fit mechanism. The high degree of similarity at the His-Asp catalytic site region between HCV NS3 and other viral serine proteases suggests that this behaviour could be a more general feature for this category of viral enzymes.
authors.affiliation: Department of Biochemistry, IRBM 'P.Angeletti', Via Pontina km 30. 600, 00040 Pomezia, Roma, Italy. Barbato@irbm.it
authors.forename: G
authors.initials: G
authors.lastname: Barbato
authors.forename: D O
authors.initials: DO
authors.lastname: Cicero
authors.forename: F
authors.initials: F
authors.lastname: Cordier
authors.forename: F
authors.initials: F
authors.lastname: Narjes
authors.forename: B
authors.initials: B
authors.lastname: Gerlach
authors.forename: S
authors.initials: S
authors.lastname: Sambucini
authors.forename: S
authors.initials: S
authors.lastname: Grzesiek
authors.forename: V G
authors.initials: VG
authors.lastname: Matassa
authors.forename: R
authors.initials: R
authors.lastname: De Francesco
authors.forename: R
authors.initials: R
authors.lastname: Bazzo
mesh_terms: D000613:Aminobutyrates / Q000737:chemistry / Q000378:metabolism*; D001665:Binding Sites; D002384:Catalysis; D020134:Catalytic Domain; D004151:Dipeptides / Q000737:chemistry / Q000378:metabolism*; D004789:Enzyme Activation; D004795:Enzyme Stability; D016174:Hepacivirus / Q000201:enzymology*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid; D012697:Serine Endopeptidases / Q000737:chemistry / Q000378:metabolism*; D015842:Serine Proteinase Inhibitors / Q000737:chemistry / Q000378:metabolism*; D012997:Solvents; D013329:Structure-Activity Relationship; D017361:Viral Nonstructural Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D000613:Aminobutyrates; D004151:Dipeptides; D012697:Serine Endopeptidases; D015842:Serine Proteinase Inhibitors; D012997:Solvents; D017361:Viral Nonstructural Proteins; C084422:NS3 protein, hepatitis C virus; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases; C406864:butyloxycarbonyl-glutamyl-leucyl-(difluoro)aminobutyric acid