(1)H, (13)C, and (15)N backbone chemical shift assignments of the apo and the ADP-ribose bound forms of the macrodomain of SARS-CoV-2 non-structural protein 3b

Cantini, F.; Banci, L.; Altincekic, N.; Bains, J. K.; Dhamotharan, K.; Fuks, C.; Fürtig, B.; Gande, S. L.; Hargittay, B.; Hengesbach, M.; Hutchison, M. T.; Korn, S. M.; Kubatova, N.; Kutz, F.; Linhard, V.; Löhr, F.; Meiser, N.; Pyper, D. J.; Qureshi, N. S.; Richter, C.; Saxena, K.; Schlundt, A.; Schwalbe, H.; Sreeramulu, S.; Tants, J.-N.; Wacker, A.; Weigand, J. E.; Wöhnert, J.; Tsika, A. C.; Fourkiotis, N. K.; Spyroulias, G. A.

The SARS-CoV-2 genome encodes for approximately 30 proteins. Within the international project COVID19-NMR, we distribute the spectroscopic analysis of the viral proteins and RNA. Here, we report NMR chemical shift assignments for the protein Nsp3b, a domain of Nsp3. The 217-kDa large Nsp3 protein contains multiple structurally independent, yet functionally related domains including the viral papain-like protease and Nsp3b, a macrodomain (MD). In general, the MDs of SARS-CoV and MERS-CoV were suggested to play a key role in viral replication by modulating the immune response of the host. The MDs are structurally conserved. They most likely remove ADP-ribose, a common posttranslational modification, from protein side chains. This de-ADP ribosylating function has potentially evolved to protect the virus from the anti-viral ADP-ribosylation catalyzed by poly-ADP-ribose polymerases (PARPs), which in turn are triggered by pathogen-associated sensing of the host immune system. This renders the SARS-CoV-2 Nsp3b a highly relevant drug target in the viral replication process. We here report the near-complete NMR backbone resonance assignment ((1)H, (13)C, (15)N) of the putative Nsp3b MD in its apo form and in complex with ADP-ribose. Furthermore, we derive the secondary structure of Nsp3b in solution. In addition, (15)N-relaxation data suggest an ordered, rigid core of the MD structure. These data will provide a basis for NMR investigations targeted at obtaining small-molecule inhibitors interfering with the catalytic activity of Nsp3b.