Structural biology of SARS-CoV-2 exoribonuclease/N7–methyltransferase (nsp14), 2′–O–methyltransferase (nsp16) and their enhancing protein (nsp10)

ABSTRACT

Coronaviruses have a very large genome of up to 32 kb in length, almost two thirds of which encode for proteins involved in the production of the virus’s own RNA. Due to the inherent mutations that occur during RNA polymerization, and the large genome size of members of the Coronaviridae family, a proofreading exoribonuclease (ExoN domain within nsp14) has evolved within these viruses to maintain high fidelity of their RNA. This proofreading exoribonuclease not only requires an enhancing protein (nsp10) to function but also performs a secondary methyltransferase of the 5′ end of produced RNA. A further 2’O-methyltransferase (nsp16) also requires the enhancing protein (nsp10) to perform the further final methylation that protects the viral RNA from the host immune system. The structural investigation of these enzymes from SARS-CoV-2 has led to a better understanding of their role in the fidelity regulation and finalization of RNA production and has enabled the development of new drugs to treat COVID-19.

KEYWORDS:

• SARS-CoV-2
• COVID-19
• exoribonuclease
• methyltransferase
• RNA-synthesis
• proofreading

Acknowledgements

The authors would also like to thank Johannes Kaub and Rosemary Wilson for support and discussion. All figures are courtesy of the Coronavirus Structural Task Force (insidecorona.net), who retains the rights for text and figures. All three-dimensional depictions of Molecules were made with 3D Protein Imager [12].

Additional information

Funding

This work was supported by Bundesministerium für Bildung und Forschung [grant numbers 05K22GU5 and 05K19WWA]; Deutsche Forschungsgemeinschaft [grant number TH2135/2-1].

Notes on contributors

Cameron Fyfe

Cameron Fyfe is a research scientist based in Paris since 2016, with a rich academic and industrial background. He has had a multidisciplinary career path, beginning his science education in a BSc Hons in Immunology & Pharmacology going on to work as an analytical chemist while as a study director in the pharmaceutical industry. He then returned to education to obtain a masters in cell and proteomics technologies which lead him to his PhD in Microbiology and Biochemistry. During his PhD and subsequent research, he has become an expert in protein biophysics in particular crystallography and the atomic structure of proteins. In his time with the taskforce, he has used his skills to help evaluate structures and expand the understanding of the structures of proteins and RNA from SARS-CoV-2.

Lea C. von Soosten

Lea C. von Soosten is a M.Sc. physics student at the University of Hamburg with a focus on biophysics. She has a great interest in everything that is related to biology and proteins in particular. Even though she comes from a different field, she joined the team as a student assistant to expand her knowledge in biochemistry and help the Coronavirus Structural Task Force with a main focus on literature research. Besides she is interested in art with a growing enthusiasm for scientific illustrations.

Gianluca Santoni

Gianluca Santoni's work is focused on the development of methods for synchrotron serial crystallography, from the comparison of datasets for multi-crystal data collection methods to the implementation of new measurement techniques at synchrotron beamlines. He got his PhD in structural biology studying the structure of acetylcholinesterase in complex with organophosphate nerve agents, applying a mixture of crystallography and computational methods. More recently he has been involved in the data strategies implementation for open science, participating in activities concerning the storage of experimental metadata, the distribution of raw data along with publication according to FAIR principle, and the definition of the gold standard format for protein diffraction data. His work with the coronavirus structural taskforce has been focused on the implementation of routines to evaluate the quality of both deposited datasets and models.

Andrea Thorn

Dr. Andrea Thorn is a specialist for structure solution by crystallography and Cryo-EM, having contributed to programs like SHELX, ANODE and PHASER in the past. Her group at the University of Hamburg develops AI-based methods in crystallography such as the diffraction diagnostics tool AUSPEX and a neural network for secondary structure annotation of Cryo-EM maps (HARUSPEX). Her methods enable other scientists to solve new structures and to answer challenging biological questions. Andrea is very passionate about structural biology and good at bringing people together. She founded and leads the Coronavirus Structural Task Force.