4V0Q

Dengue Virus Full Length NS5 Complexed with SAH

Summary for 4V0Q

• Entry DOI: 10.2210/pdb4v0q/pdb
• Related: 4V0R
• Descriptor: NS5 POLYMERASE, ZINC ION, S-ADENOSYL-L-HOMOCYSTEINE, ... (6 entities in total)
• Functional Keywords: transferase, methyltransferase, rna-dependent rna polymerase
• Biological source: DENGUE VIRUS 3
• Total number of polymer chains: 1
• Total formula weight: 103792.22

Authors

Zhao, Y.,Soh, S.,Zheng, J.,Phoo, W.W.,Swaminathan, K.,Cornvik, T.C.,Lim, S.P.,Shi, P.-Y.,Lescar, J.,Vasudevan, S.G.,Luo, D. (deposition date: 2014-09-18, release date: 2015-01-28, Last modification date: 2024-01-10)

Primary citation

Zhao, Y.,Soh, T.S.,Zheng, J.,Chan, K.W.K.,Phoo, W.W.,Lee, C.C.,Tay, M.Y.F.,Swaminathan, K.,Cornvik, T.C.,Lim, S.P.,Shi, P.,Lescar, J.,Vasudevan, S.G.,Luo, D.
A Crystal Structure of the Dengue Virus Ns5 Protein Reveals a Novel Inter-Domain Interface Essential for Protein Flexibility and Virus Replication.
Plos Pathog., 11:04682-, 2015

PubMed Abstract: Flavivirus RNA replication occurs within a replication complex (RC) that assembles on ER membranes and comprises both non-structural (NS) viral proteins and host cofactors. As the largest protein component within the flavivirus RC, NS5 plays key enzymatic roles through its N-terminal methyltransferase (MTase) and C-terminal RNA-dependent-RNA polymerase (RdRp) domains, and constitutes a major target for antivirals. We determined a crystal structure of the full-length NS5 protein from Dengue virus serotype 3 (DENV3) at a resolution of 2.3 Å in the presence of bound SAH and GTP. Although the overall molecular shape of NS5 from DENV3 resembles that of NS5 from Japanese Encephalitis Virus (JEV), the relative orientation between the MTase and RdRp domains differs between the two structures, providing direct evidence for the existence of a set of discrete stable molecular conformations that may be required for its function. While the inter-domain region is mostly disordered in NS5 from JEV, the NS5 structure from DENV3 reveals a well-ordered linker region comprising a short 310 helix that may act as a swivel. Solution Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) analysis reveals an increased mobility of the thumb subdomain of RdRp in the context of the full length NS5 protein which correlates well with the analysis of the crystallographic temperature factors. Site-directed mutagenesis targeting the mostly polar interface between the MTase and RdRp domains identified several evolutionarily conserved residues that are important for viral replication, suggesting that inter-domain cross-talk in NS5 regulates virus replication. Collectively, a picture for the molecular origin of NS5 flexibility is emerging with profound implications for flavivirus replication and for the development of therapeutics targeting NS5.

PubMed: 25775415
DOI: 10.1371/JOURNAL.PPAT.1004682

Experimental method

X-RAY DIFFRACTION (2.3 Å)