title: A locking mechanism regulates RNA synthesis and host protein interaction by the hepatitis C virus polymerase.
abstract: Mutational analysis of the hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp) template channel identified two residues, Trp(397) and His(428), which are required for de novo initiation but not for extension from a primer. These two residues interact with the Delta1 loop on the surface of the RdRp. A deletion within the Delta1 loop also resulted in comparable activities. The mutant proteins exhibit increased double-stranded RNA binding compared with the wild type, suggesting that the Delta1 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.
authors.affiliation: Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.
authors.forename: Sreedhar
authors.initials: S
authors.lastname: Chinnaswamy
authors.forename: Ian
authors.initials: I
authors.lastname: Yarbrough
authors.forename: Satheesh
authors.initials: S
authors.lastname: Palaninathan
authors.forename: C T Ranjith
authors.initials: CT
authors.lastname: Kumar
authors.forename: Vinodhini
authors.initials: V
authors.lastname: Vijayaraghavan
authors.forename: Borries
authors.initials: B
authors.lastname: Demeler
authors.forename: Stanley M
authors.initials: SM
authors.lastname: Lemon
authors.forename: James C
authors.initials: JC
authors.lastname: Sacchettini
authors.forename: C Cheng
authors.initials: CC
authors.lastname: Kao
mesh_terms: D001483:Base Sequence; D021983:Cyclophilins / Q000737:chemistry / Q000378:metabolism; D016174:Hepacivirus / Q000201:enzymology* / Q000235:genetics* / Q000378:metabolism; D008958:Models, Molecular; D009154:Mutation / Q000235:genetics; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D012367:RNA, Viral / Q000096:biosynthesis* / Q000737:chemistry / Q000378:metabolism*; D012324:RNA-Dependent RNA Polymerase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012175:Retinoblastoma / Q000737:chemistry / Q000378:metabolism; D040681:Structural Homology, Protein
chemical_list: D012367:RNA, Viral; D012324:RNA-Dependent RNA Polymerase; D021983:Cyclophilins