Complex of NS3 protease and NS4A peptide of BK strain hepatitis C virus: A 2.2 Å resolution structure in a hexagonal crystal form

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Abstract
The crystal structure of the NS3 protease of the hepatitis C virus (BK strain) has been determined in the space group P6322 to a resolution of 2.2 Å. This protease is bound with a 14‐mer peptide representing the central region of the NS4A protein. There are two molecules of the NS31_180‐NS4A21′‐34′ complex per asymmetric unit. Each displays a familiar chymotrypsin‐like fold that includes two β‐barrel domains and four short α‐helices. The catalytic triad (Ser‐139, His‐57, and Asp‐81) is located in the crevice between the β‐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 β‐strand and an α‐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.