title: Visualizing ATP-dependent RNA translocation by the NS3 helicase from HCV.
abstract: The structural mechanism by which nonstructural protein 3 (NS3) from the hepatitis C virus (HCV) translocates along RNA is currently unknown. HCV NS3 is an ATP-dependent motor protein essential for viral replication and a member of the superfamily 2 helicases. Crystallographic analysis using a labeled RNA oligonucleotide allowed us to unambiguously track the positional changes of RNA bound to full-length HCV NS3 during two discrete steps of the ATP hydrolytic cycle. The crystal structures of HCV NS3, NS3 bound to bromine-labeled RNA, and a tertiary complex of NS3 bound to labeled RNA and a non-hydrolyzable ATP analog provide a direct view of how large domain movements resulting from ATP binding and hydrolysis allow the enzyme to translocate along the phosphodiester backbone. While directional translocation of HCV NS3 by a single base pair per ATP hydrolyzed is observed, the 3' end of the RNA does not shift register with respect to a conserved tryptophan residue, supporting a "spring-loading" mechanism that leads to larger steps by the enzyme as it moves along a nucleic acid substrate.
authors.affiliation: Department of Structural Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA. todd.appleby@gilead.com
authors.forename: Todd C
authors.initials: TC
authors.lastname: Appleby
authors.forename: Robert
authors.initials: R
authors.lastname: Anderson
authors.forename: Olga
authors.initials: O
authors.lastname: Fedorova
authors.forename: Anna M
authors.initials: AM
authors.lastname: Pyle
authors.forename: Ruth
authors.initials: R
authors.lastname: Wang
authors.forename: Xiaohong
authors.initials: X
authors.lastname: Liu
authors.forename: Katherine M
authors.initials: KM
authors.lastname: Brendza
authors.forename: John R
authors.initials: JR
authors.lastname: Somoza
mesh_terms: D000251:Adenosine Triphosphatases / Q000737:chemistry; D000255:Adenosine Triphosphate / Q000737:chemistry; D003461:Crystallography; D016174:Hepacivirus / Q000201:enzymology*; D006801:Humans; D017434:Protein Structure, Tertiary; D020365:RNA Helicases / Q000737:chemistry*; D034443:RNA Transport; D013379:Substrate Specificity; D017361:Viral Nonstructural Proteins / Q000737:chemistry*; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases
chemical_list: D000251:Adenosine Triphosphatases; D000255:Adenosine Triphosphate; D020365:RNA Helicases; D017361:Viral Nonstructural Proteins; C084422:NS3 protein, hepatitis C virus; D012697:Serine Endopeptidases; D043583:Nucleoside-Triphosphatase; D053487:DEAD-box RNA Helicases; D000085242:Viral Proteases