FIGURE 1.

a, location of the NS3-coding sequence in the HCV genome. The cis-acting elements in the NTRs are shown. The asterisk indicates the microRNA-122-binding site. Full-length NS3 protein is located from amino acids 1027 to 1658 of the polyprotein of the genotype 1b consensus sequence (NCBI accession number AJ238799) (2). IRES, internal ribosome entry site. b, structure of the NS3 protease domain in complex with the NS4A cofactor and substrate peptide. The crystal structure (Protein Data Bank code 1A1R) of the N-terminal protease domain (red) in complex with the NS4A peptide cofactor (purple) is rendered as a ribbon (28). The polypeptide containing the NS3/NS4A junction, corresponding to positions P4–P2′, was modeled into the active site of the NS3 protease and shown as surface (gray); the sequence of the peptide is shown next to the structure. The polypeptide model, starting with its primary sequence, was constructed in-house. The expanded views highlight the catalytic triad, the oxyanion hole, and the zinc-binding site. The lower left expanded view displays the interactions of the catalytic triad (His-57, Asp-81, and Ser-139), rendered as ball-and-stick, with the modeled peptide; black dashed lines represent the hydrogen bonds. The lower right expanded view shows the oxyanion loop (positions 135–139), whose backbone nitrogen atoms play a role in stabilizing the developing negative charge on the Oγ of Ser-139 during the peptide cleavage; the side chains are drawn as sticks, and the oxyanion hole is highlighted by the blue shadow. The top expanded view shows the side chains of the key residues (Cys-97, Cys-99, Cys-145, and His-149), depicted as sticks, that interact with the metal ion (purple sphere). c, structure of the NS3 helicase domain in complex with ssDNA and ADP·AlF₄⁻. Coordinates are from Protein Data Bank code 3KQL (89). The conserved motifs of RNA helicases are colored and indentified by established Roman numeral designations (62, 89). The expanded view shows the ATP transition state analog in the NTP-binding/catalytic site of the enzyme.