Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism

Kumar, Gyanendra; Cuypers, Maxime; Webby, Richard R.; Webb, Thomas R.; White, Stephen W.

doi:10.1093/nar/gkaa1294

Title: Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism

Journal Article · Tue Jan 19 00:00:00 EST 2021 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkaa1294· OSTI ID:1761220

Kumar, Gyanendra ^[1];

^[1]; Webby, Richard R. ^[2]; Webb, Thomas R. ^[3];

^[1]

Department of Structural Biology, Memphis, TN 38105, USA
Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
Wildflower Biopharma, Inc., 8650 Genesee Ave. STE 214, San Diego, CA 92122, USA, Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA 95064, USA

Abstract The endonuclease activity within the influenza virus cap-snatching process is a proven therapeutic target. The anti-influenza drug baloxavir is highly effective, but is associated with resistance mutations that threaten its clinical efficacy. The endonuclease resides within the N-terminal domain of the PA subunit (PAN) of the influenza RNA dependent RNA polymerase, and we report here complexes of PAN with RNA and DNA oligonucleotides to understand its specificity and the structural basis of baloxavir resistance mutations. The RNA and DNA oligonucleotides bind within the substrate binding groove of PAN in a similar fashion, explaining the ability of the enzyme to cleave both substrates. The individual nucleotides occupy adjacent conserved pockets that flank the two-metal active site. However, the 2′ OH of the RNA ribose moieties engage in additional interactions that appear to optimize the binding and cleavage efficiency for the natural substrate. The major baloxavir resistance mutation at position 38 is at the core of the substrate binding site, but structural studies and modeling suggest that it maintains the necessary virus fitness via compensating interactions with RNA. These studies will facilitate the development of new influenza therapeutics that spatially match the substrate and are less likely to elicit resistance mutations.

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Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: USDOE Office of Science (SC); National Institutes of Health (NIH)

Grant/Contract Number:: W-31-109-Eng-38; AI098757

OSTI ID:: 1761220

Alternate ID(s):: OSTI ID: 1772757

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Vol. 49 Journal Issue: 3; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United Kingdom

Language:: English

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