Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN Domain

Small, G. I.; Federova, O.; Olinares, P. D. B.; Chandanani, J.; Banerjee, A.; Choi, Y. J.; Molina, H.; Chait, B.; Darst, S. A.; Campbell, E. A.

doi:10.1101/2023.09.25.558837

bioRxiv · 10.1101/2023.09.25.558837

Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN Domain

Small, G. I.·Federova, O.·Olinares, P. D. B.·Chandanani, J.·Banerjee, A.·Choi, Y. J.·Molina, H.·Chait, B.·Darst, S. A.·Campbell, E. A.

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Abstract

The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with modification of the nsp9 N-terminus, NMPylation, RNAylation, and deRNAylation/capping via a GDP-polyribonucleotidyltransferase reaction. The latter two activities comprise an unconventional mechanism for initiating viral RNA 5-cap formation, while the role of NMPylation is unclear. The structural mechanisms for these diverse enzymatic activities have not been properly delineated. Here we determine high-resolution cryo-electron microscopy structures of catalytic intermediates for the NMPylation and deRNAylation/capping reactions, revealing diverse nucleotide binding poses and divalent metal ion coordination sites to promote its repertoire of activities. The deRNAylation/capping structure explains why GDP is a preferred substrate for the capping reaction over GTP. Altogether, these findings enhance our understanding of the promiscuous coronaviral NiRAN domain, a therapeutic target, and provide an accurate structural platform for drug development.

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Small, G. I., Federova, O., Olinares, P. D. B., Chandanani, J., Banerjee, A., Choi, Y. J., Molina, H., Chait, B., Darst, S. A., Campbell, E. A.. 2023-09-26. Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN Domain. https://doi.org/10.1101/2023.09.25.558837

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