A locking mechanism regulates RNA synthesis and host protein interaction by the hepatitis C virus polymerase

Mutational analysis of the hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp) template channel identified two residues, Trp³⁹⁷ and His⁴²⁸, which are required for de novo initiation but not for extension from a primer. These two residues interact with the Δ1 loop on the surface of the RdRp. A deletion within the Δ1 loop also resulted in comparable activities. The mutant proteins exhibit increased double-stranded RNA binding compared with the wild type, suggesting that the Δ1 loop serves as a flexible locking mechanism to regulate the conformations needed for de novo initiation and for elongative RNA synthesis. A similar locking motif can be found in other viral RdRps. Products associated with the open conformation of the HCV RdRp were inhibited by interaction with the retinoblastoma protein but not cyclophilin A. Different conformations of the HCV RdRp can thus affect RNA synthesis and interaction with cellular proteins.