Insights into RNA unwinding and ATP hydrolysis by the flavivirus NS3 protein
- 13 November 2008
- journal article
- Published by Springer Science and Business Media LLC in The EMBO Journal
- Vol. 27 (23), 3209-3219
- https://doi.org/10.1038/emboj.2008.232
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 β‐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
This publication has 39 references indexed in Scilit:
- NS3 helicase actively separates RNA strands and senses sequence barriers ahead of the opening forkProceedings of the National Academy of Sciences of the United States of America, 2007
- Structural basis for DNA duplex separation by a superfamily-2 helicaseNature Structural & Molecular Biology, 2007
- Solving structures of protein complexes by molecular replacement with PhaserActa Crystallographica Section D-Biological Crystallography, 2006
- UvrD Helicase Unwinds DNA One Base Pair at a Time by a Two-Part Power StrokeCell, 2006
- A 5′ RNA element promotes dengue virus RNA synthesis on a circular genomeGenes & Development, 2006
- Opening of nucleic-acid double strands by helicases: Active versus passive openingPhysical Review E, 2005
- Coot: model-building tools for molecular graphicsActa Crystallographica Section D-Biological Crystallography, 2004
- The hepatitis C viral NS3 protein is a processive DNA helicase with cofactor enhanced RNA unwindingThe EMBO Journal, 2002
- Refinement of Macromolecular Structures by the Maximum-Likelihood MethodActa Crystallographica Section D-Biological Crystallography, 1997
- The CCP4 suite: programs for protein crystallographyActa Crystallographica Section D-Biological Crystallography, 1994