3KQK

Three Conformational Snapshots of the Hepatitis C Virus NS3 Helicase Reveal a Ratchet Translocation Mechanism

Summary for 3KQK

• Entry DOI: 10.2210/pdb3kqk/pdb
• Related: 3KQH 3KQL 3KQN 3KQU
• Descriptor: Serine protease/NTPase/helicase NS3, 5'-D(*TP*TP*TP*TP*TP*T)-3' (3 entities in total)
• Functional Keywords: helicase-substrate binary complex, hcv, ns3 protein, helicase, dna-binding, hydrolase-dna complex, hydrolase/dna
• Biological source: Hepatitis C virus (HCV)
• Cellular location: Core protein p21: Host endoplasmic reticulum membrane ; Single-pass membrane protein . Core protein p19: Virion . Envelope glycoprotein E1: Virion membrane ; Single-pass type I membrane protein . Envelope glycoprotein E2: Virion membrane ; Single-pass type I membrane protein . p7: Host endoplasmic reticulum membrane ; Multi-pass membrane protein . Protease NS2-3: Host endoplasmic reticulum membrane ; Multi-pass membrane protein . Serine protease NS3: Host endoplasmic reticulum membrane ; Peripheral membrane protein . Non-structural protein 4A: Host endoplasmic reticulum membrane ; Single-pass type I membrane protein . Non-structural protein 4B: Host endoplasmic reticulum membrane ; Multi-pass membrane protein . Non-structural protein 5A: Host endoplasmic reticulum membrane ; Peripheral membrane protein . RNA-directed RNA polymerase: Host endoplasmic reticulum membrane ; Single-pass type I membrane protein : Q9WMX2
• Total number of polymer chains: 4
• Total formula weight: 96902.36

Authors

Gu, M.,Rice, C.M. (deposition date: 2009-11-17, release date: 2010-01-26, Last modification date: 2024-02-21)

Primary citation

Gu, M.,Rice, C.M.
Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism.
Proc.Natl.Acad.Sci.USA, 107:521-528, 2010

PubMed Abstract: A virally encoded superfamily-2 (SF2) helicase (NS3h) is essential for the replication of hepatitis C virus, a leading cause of liver disease worldwide. Efforts to elucidate the function of NS3h and to develop inhibitors against it, however, have been hampered by limited understanding of its molecular mechanism. Here we show x-ray crystal structures for a set of NS3h complexes, including ground-state and transition-state ternary complexes captured with ATP mimics (ADP.BeF(3) and ). These structures provide, for the first time, three conformational snapshots demonstrating the molecular basis of action for a SF2 helicase. Upon nucleotide binding, overall domain rotation along with structural transitions in motif V and the bound DNA leads to the release of one base from the substrate base-stacking row and the loss of several interactions between NS3h and the 3' DNA segment. As nucleotide hydrolysis proceeds into the transition state, stretching of a "spring" helix and another overall conformational change couples rearrangement of the (d)NTPase active site to additional hydrogen-bonding between NS3h and DNA. Together with biochemistry, these results demonstrate a "ratchet" mechanism involved in the unidirectional translocation and define the step size of NS3h as one base per nucleotide hydrolysis cycle. These findings suggest feasible strategies for developing specific inhibitors to block the action of this attractive, yet largely unexplored drug target.

PubMed: 20080715
DOI: 10.1073/pnas.0913380107

Experimental method

X-RAY DIFFRACTION (2.8 Å)