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  • The EMBO Journal (2008) 27, 3209 - 3219
  • doi:10.1038/emboj.2008.232

Published online: 13 November 2008

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

  1. Structural & Computational Biology Division, School of Biological Sciences, Nanyang Technological University, Singapore
  2. Dengue Unit, Novartis Institute for Tropical Diseases, Singapore
  3. Novartis Institutes for BioMedical Research, Discovery Technologies, Basel, Switzerland
  4. Burnham Institute, La Jolla, CA, USA
  5. 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

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 beta-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