2J7W

Dengue virus NS5 RNA dependent RNA polymerase domain complexed with 3' dGTP

Summary for 2J7W

• Entry DOI: 10.2210/pdb2j7w/pdb
• Descriptor: POLYPROTEIN, ZINC ION, GUANOSINE-5'-TRIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: nucleoside binding site, rna-dependent rna polymerase, dengue, flavivirus, high-throughput assay, viral protein
• Biological source: DENGUE VIRUS
• Cellular location: Envelope protein E: Virion membrane; Multi- pass membrane protein: Q6DLV0
• Total number of polymer chains: 1
• Total formula weight: 74356.93

Authors

Yap, T.L.,Xu, T.,Chen, Y.L.,Malet, H.,Egloff, M.P.,Canard, B.,Vasudevan, S.G.,Lescar, J. (deposition date: 2006-10-17, release date: 2007-03-13, Last modification date: 2023-12-13)

Primary citation

Yap, T.L.,Xu, T.,Chen, Y.L.,Malet, H.,Egloff, M.P.,Canard, B.,Vasudevan, S.G.,Lescar, J.
Crystal Structure of the Dengue Virus RNA- Dependent RNA Polymerase Catalytic Domain at 1.85 Angstrom Resolution.
J.Virol., 81:4753-, 2007

PubMed Abstract: Dengue fever, a neglected emerging disease for which no vaccine or antiviral agents exist at present, is caused by dengue virus, a member of the Flavivirus genus, which includes several important human pathogens, such as yellow fever and West Nile viruses. The NS5 protein from dengue virus is bifunctional and contains 900 amino acids. The S-adenosyl methionine transferase activity resides within its N-terminal domain, and residues 270 to 900 form the RNA-dependent RNA polymerase (RdRp) catalytic domain. Viral replication begins with the synthesis of minus-strand RNA from the dengue virus positive-strand RNA genome, which is subsequently used as a template for synthesizing additional plus-strand RNA genomes. This essential function for the production of new viral particles is catalyzed by the NS5 RdRp. Here we present a high-throughput in vitro assay partly recapitulating this activity and the crystallographic structure of an enzymatically active fragment of the dengue virus RdRp refined at 1.85-A resolution. The NS5 nuclear localization sequences, previously thought to fold into a separate domain, form an integral part of the polymerase subdomains. The structure also reveals the presence of two zinc ion binding motifs. In the absence of a template strand, a chain-terminating nucleoside analogue binds to the priming loop site. These results should inform and accelerate the structure-based design of antiviral compounds against dengue virus.

PubMed: 17301146
DOI: 10.1128/JVI.02283-06

Experimental method

X-RAY DIFFRACTION (2.6 Å)