Structural biology of SARS-CoV-2 endoribonuclease NendoU (nsp15)

Abstract

The SARS-CoV-2’s endoribonuclease (NendoU) nsp15, is an Mn²⁺ dependent endoribonuclease specific to uridylate that SARS-CoV-2 uses to avoid the innate immune response by managing the stray RNA generated during replication. As of the writing of this review 20 structures of SARS-CoV-2 nsp15 have been deposited into the PDB, largely solved using X-ray crystallography and some through Cryo-EM. These structures show that an nsp15 monomer consist of three conserved domains, the N-terminal oligomerization domain, the middle domain, and the catalytic NendoU domain. Enzymatically active nsp15 forms a hexamer through a dimer of trimers (point group 32), whose assembly is facilitated by the oligomerization domain. This review summarises the structural and functional information gained from SARs-CoV-2, SARs-CoV and MERS-CoV nsp15 structures, compiles the current structure-based drug design efforts, and complementary knowledge with a view to provide a clear starting point for downstream structure users interested in studying nsp15 as a novel drug target to treat COVID-19.

Keyword:

• COVID-19
• SARS-CoV-2
• nsp15
• endoribonuclease
• RNA
• computational drug design
• structure based drug design

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 copyright for the text and the figures.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Subjects index

assembly 4, 7

Benzopurpurin 11, 12

docking 11, 12

endoribonuclease 5, 16

Fragment 11, 12

immune response 5, 6, 11, 16

in-silico 11, 12, 13

NendoU domain 6, 7

Oligomerisation domain 6, 7, 9, 12

Subgenomic RNA 5

Tipiracil 12, 16

Uracil specificity 9

viral replication 5, 11, 14

Additional information

Funding

This work was supported by Bundesministerium für Bildung und Forschung: [Grant Number 05K19WWA]; Deutsche Forschungsgemeinschaft: [Grant Number TH2135/2-1].

Notes on contributors

Sam Horrell

Sam Horrell is a beamline scientist at Diamond Light Source Beamline I24. His research interests are focused on method development around time-resolved serial crystallography at synchrotrons and XFELs. He is interested in bridging the gap between ultrafast time-resolved structural biology at XFELs and what can be offered at synchrotrons. Sam has a particular interest in radiation damage in X-ray crystallography and how it can be minimised, mitigated, or used to drive reactions in crystals, such as in metalloproteins where a redox reaction can be kicked off by the electrons generated from X-rays hitting the sample. Sam was the president of the Young Crystallographers Group of the British Crystallographic Association and a member of the BCA Spring meeting organising committee (2016-2018).

Gianluca Santoni

Gianluca Santoni is a scientist at the European Synchrotron radiation facility. His 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

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 started and leads the Coronavirus Structural Task Force.