Crystal Structure of the Dengue Virus RNA-Dependent RNA Polymerase Catalytic Domain at 1.85-Angstrom Resolution

TLDR

Dengue fever, caused by a Flavivirus lacking current vaccines or antivirals, relies on the NS5 protein’s RNA‑dependent RNA polymerase domain (residues 270‑900) to synthesize viral RNA strands. The study aims to provide a high‑throughput in‑vitro assay and crystal structure of an active dengue RdRp fragment. An enzymatically active RdRp fragment was crystallized at 1.85‑Å resolution and characterized using a high‑throughput in‑vitro assay that mimics polymerase activity. The structure shows that the NS5 nuclear localization sequences integrate into polymerase subdomains, reveals two zinc‑binding motifs, and demonstrates that a chain‑terminating nucleoside analogue occupies the priming loop, providing a framework for antiviral development.

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.