Article
- The EMBO Journal (2008) 27, 3209 - 3219
- doi:10.1038/emboj.2008.232
Published online: 13 November 2008
Subject Categories:
Insights into RNA unwinding and ATP hydrolysis by the flavivirus NS3 protein
Dahai Luo1,a, Ting Xu2,a, Randall P Watson3,a, Daniella Scherer-Becker3, Aruna Sampath2, Wolfgang Jahnke3, Sui Sum Yeong1, Chern Hoe Wang1, Siew Pheng Lim2, Alex Strongin4, Subhash G Vasudevan5 and Julien Lescar1,2
- Structural & Computational Biology Division, School of Biological Sciences, Nanyang Technological University, Singapore
- Dengue Unit, Novartis Institute for Tropical Diseases, Singapore
- Novartis Institutes for BioMedical Research, Discovery Technologies, Basel, Switzerland
- Burnham Institute, La Jolla, CA, USA
- Program for Emerging Infectious Diseases, Duke-NUS Graduate Medical School Singapore, Singapore
Correspondence to:
Subhash G Vasudevan, Program for Emerging Infectious diseases, Duke-NUS Graduate Medical School Singapore, Singapore. Tel.: +65 6516 6718; Fax: +65 6534 8632; E-mail: gmsvsg@nus.edu.sg or
Julien Lescar, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore. Tel.: +65 6316 2859; Fax: +65 6791 3856; E-mail: Julien@ntu.edu.sg
aThese authors contributed equally to this work
Received 16 June 2008; Accepted 10 October 2008
Abstract
Together with the NS5 polymerase, the NS3 helicase has a pivotal function in flavivirus RNA replication and constitutes an important drug target. We captured the dengue virus NS3 helicase at several stages along the catalytic pathway including bound to single-stranded (ss) RNA, to an ATP analogue, to a transition-state analogue and to ATP hydrolysis products. RNA recognition appears largely sequence independent in a way remarkably similar to eukaryotic DEAD box proteins Vasa and eIF4AIII. On ssRNA binding, the NS3 enzyme switches to a catalytic-competent state imparted by an inward movement of the P-loop, interdomain closure and a change in the divalent metal coordination shell, providing a structural basis for RNA-stimulated ATP hydrolysis. These structures demonstrate for the first time large quaternary changes in the flaviviridae helicase, identify the catalytic water molecule and point to a 
-hairpin that protrudes from subdomain 2, as a critical element for dsRNA unwinding. They also suggest how NS3 could exert an effect as an RNA-anchoring device and thus participate both in flavivirus RNA replication and assembly.
Keywords:
- ATP analogues,
- dengue virus,
- flaviviruses,
- NS3 helicase structure,
- RNA complex
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