title: Complex of NS3 protease and NS4A peptide of BK strain hepatitis C virus: a 2.2 A resolution structure in a hexagonal crystal form.
abstract: The crystal structure of the NS3 protease of the hepatitis C virus (BK strain) has been determined in the space group P6(3)22 to a resolution of 2.2 A. This protease is bound with a 14-mer peptide representing the central region of the NS4A protein. There are two molecules of the NS3(1-180)-NS4A(21'-34') complex per asymmetric unit. Each displays a familiar chymotrypsin-like fold that includes two beta-barrel domains and four short alpha-helices. The catalytic triad (Ser-139, His-57, and Asp-81) is located in the crevice between the beta-barrel domains. The NS4A peptide forms an almost completely enclosed peptide surface association with the protease. In contrast to the reported H strain complex of NS3 protease-NS4A peptide in a trigonal crystal form (Kim JL et al., 1996, Cell 87:343-355), the N-terminus of the NS3 protease is well-ordered in both molecules in the asymmetric unit of our hexagonal crystal form. The folding of the N-terminal region of the NS3 protease is due to the formation of a three-helix bundle as a result of crystal packing. When compared with the unbound structure (Love RA et al., 1996, Cell 87:331-342), the binding of the NS4A peptide leads to the ordering of the N-terminal 28 residues of the NS3 protease into a beta-strand and an alpha-helix and also causes local rearrangements important for a catalytically favorable conformation at the active site. Our analysis provides experimental support for the proposal that binding of an NS4A-mimicking peptide, which increases catalytic rates, is necessary but not sufficient for formation of a well-ordered, compact and, hence, highly active protease molecule.
authors.affiliation: Department of Antiviral Research, Merck Research Laboratories, West Point, Pennsylvania 19486, USA.
authors.forename: Y
authors.initials: Y
authors.lastname: Yan
authors.forename: Y
authors.initials: Y
authors.lastname: Li
authors.forename: S
authors.initials: S
authors.lastname: Munshi
authors.forename: V
authors.initials: V
authors.lastname: Sardana
authors.forename: J L
authors.initials: JL
authors.lastname: Cole
authors.forename: M
authors.initials: M
authors.lastname: Sardana
authors.forename: C
authors.initials: C
authors.lastname: Steinkuehler
authors.forename: L
authors.initials: L
authors.lastname: Tomei
authors.forename: R
authors.initials: R
authors.lastname: De Francesco
authors.forename: L C
authors.initials: LC
authors.lastname: Kuo
authors.forename: Z
authors.initials: Z
authors.lastname: Chen
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites / Q000502:physiology; D002918:Chymotrypsin / Q000737:chemistry; D018360:Crystallography, X-Ray; D016174:Hepacivirus / Q000201:enzymology; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010455:Peptides / Q000737:chemistry; D011485:Protein Binding / Q000502:physiology; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017361:Viral Nonstructural Proteins / Q000737:chemistry*; D014764:Viral Proteins / Q000737:chemistry; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D002918:Chymotrypsin; D010455:Peptides; D017361:Viral Nonstructural Proteins; D014764:Viral Proteins; C084422:NS3 protein, hepatitis C virus; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases; C093542:NS4 protein, hepatitis C virus