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Journal of Virology, January 2008, p. 173-183, Vol. 82, No. 1
0022-538X/08/$08.00+0     doi:10.1128/JVI.01788-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Crystal Structure of the NS3 Protease-Helicase from Dengue Virus

Dahai Luo,^1,2, Ting Xu,^2, Cornelia Hunke,³ Gerhard Grüber,³ Subhash G. Vasudevan,² and Julien Lescar^1,2*

School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore,¹ Novartis Institute for Tropical Diseases, 10 Biopolis Road, Chromos Building, Singapore 138670, Republic of Singapore,² School of Biological Sciences, Section of Structure and Function of Molecular Motors, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore³

Received 15 August 2007/ Accepted 3 October 2007

Several flaviviruses are important human pathogens, including dengue virus, a disease against which neither a vaccine nor specific antiviral therapies currently exist. During infection, the flavivirus RNA genome is translated into a polyprotein, which is cleaved into several components. Nonstructural protein 3 (NS3) carries out enzymatic reactions essential for viral replication, including proteolysis of the polyprotein through its serine protease N-terminal domain, with a segment of 40 residues from the NS2B protein acting as a cofactor. The ATPase/helicase domain is located at the C terminus of NS3. Atomic structures are available for these domains separately, but a molecular view of the full-length flavivirus NS3 polypeptide is still lacking. We report a crystallographic structure of a complete NS3 molecule fused to 18 residues of the NS2B cofactor at a resolution of 3.15 Å. The relative orientation between the protease and helicase domains is drastically different than the single-chain NS3-NS4A molecule from hepatitis C virus, which was caught in the act of cis cleavage at the NS3-NS4A junction. Here, the protease domain sits beneath the ATP binding site, giving the molecule an elongated shape. The domain arrangement found in the crystal structure fits nicely into an envelope determined ab initio using small-angle X-ray scattering experiments in solution, suggesting a stable molecular conformation. We propose that a basic patch located at the surface of the protease domain increases the affinity for nucleotides and could also participate in RNA binding, explaining the higher unwinding activity of the full-length enzyme compared to that of the isolated helicase domain.

Published ahead of print on 17 October 2007.

D.L. and T.X. contributed equally to this work.

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