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J Biol Chem
. 2023 May 4;104787.
doi: 10.1016/j.jbc.2023.104787. Online ahead of print. Kinetic analysis of RNA cleavage by coronavirus Nsp15 endonuclease: Evidence for acid base catalysis and substrate dependent metal ion activation
Tong Huang 1 , Kimberly C Snell 1 , Nidhi Kalia 1 , Shahbaz Gardezi 1 , Lily Guo 1 , Michael E Harris 2
Affiliations
Understanding the functional properties of SARS-CoV-2 nonstructural proteins is essential for defining their roles in the viral life cycle, developing improved therapeutics and diagnostics, and countering future variants. Coronavirus nonstructural protein Nsp15 is a hexameric U-specific endonuclease whose functions, substrate specificity, mechanism, and dynamics have not been fully defined. Previous studies report SARS-CoV-2 Nsp15 requires Mn2+ ions for optimal activity; however, the effects of divalent ions on Nsp15 reaction kinetics have not been investigated in detail. Here, we analyzed the single and multiple turnover kinetics for model single-stranded RNA substrates. Our data confirm that divalent ions are dispensable for catalysis and show that Mn2+ activates Nsp15 cleavage of two different ssRNA oligonucleotide substrates, but not a dinucleotide. Furthermore, biphasic kinetics of ssRNA substrates demonstrates that Mn2+ stabilizes alternative enzyme states that have faster substrate cleavage on the enzyme. However, we did not detect Mn2+-induced conformational changes using CD and fluorescence spectroscopy. The pH-rate profiles in the presence and absence of Mn2+ are consistent with active site ionizable groups with similar pKas of ca. 4.8-5.2. We found the Rp stereoisomer phosphorothioate modification at the scissile phosphate had minimal effect on catalysis, which supports a mechanism involving an anionic transition state. In contrast, the Sp stereoisomer is inactive due to weak binding, consistent with models that position the non-bridging phosphoryl oxygen deep in the active site. Together, these kinetic data demonstrate that Nsp15 employs a conventional acid-base catalytic mechanism passing through an anionic transition state, and that divalent ion activation is substrate-dependent.
Keywords: Endonuclease; RNA; enzyme catalysis; enzyme kinetics; nucleic acid enzymology; ribonuclease.
. 2023 May 4;104787.
doi: 10.1016/j.jbc.2023.104787. Online ahead of print. Kinetic analysis of RNA cleavage by coronavirus Nsp15 endonuclease: Evidence for acid base catalysis and substrate dependent metal ion activation
Tong Huang 1 , Kimberly C Snell 1 , Nidhi Kalia 1 , Shahbaz Gardezi 1 , Lily Guo 1 , Michael E Harris 2
Affiliations
- PMID: 37149147
- DOI: 10.1016/j.jbc.2023.104787
Understanding the functional properties of SARS-CoV-2 nonstructural proteins is essential for defining their roles in the viral life cycle, developing improved therapeutics and diagnostics, and countering future variants. Coronavirus nonstructural protein Nsp15 is a hexameric U-specific endonuclease whose functions, substrate specificity, mechanism, and dynamics have not been fully defined. Previous studies report SARS-CoV-2 Nsp15 requires Mn2+ ions for optimal activity; however, the effects of divalent ions on Nsp15 reaction kinetics have not been investigated in detail. Here, we analyzed the single and multiple turnover kinetics for model single-stranded RNA substrates. Our data confirm that divalent ions are dispensable for catalysis and show that Mn2+ activates Nsp15 cleavage of two different ssRNA oligonucleotide substrates, but not a dinucleotide. Furthermore, biphasic kinetics of ssRNA substrates demonstrates that Mn2+ stabilizes alternative enzyme states that have faster substrate cleavage on the enzyme. However, we did not detect Mn2+-induced conformational changes using CD and fluorescence spectroscopy. The pH-rate profiles in the presence and absence of Mn2+ are consistent with active site ionizable groups with similar pKas of ca. 4.8-5.2. We found the Rp stereoisomer phosphorothioate modification at the scissile phosphate had minimal effect on catalysis, which supports a mechanism involving an anionic transition state. In contrast, the Sp stereoisomer is inactive due to weak binding, consistent with models that position the non-bridging phosphoryl oxygen deep in the active site. Together, these kinetic data demonstrate that Nsp15 employs a conventional acid-base catalytic mechanism passing through an anionic transition state, and that divalent ion activation is substrate-dependent.
Keywords: Endonuclease; RNA; enzyme catalysis; enzyme kinetics; nucleic acid enzymology; ribonuclease.