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

• DOI: 10.1007/s12104-020-09973-4
• Publication Date: 2020-08-14T19:02:46Z
• Authors: F. Cantini; L. Banci; N. Altincekic; J. K. Bains; K. Dhamotharan; C. Fuks; B. Fürtig; S. L. Gande; B. Hargittay; M. Hengesbach; M. T. Hutchison; S. M. Korn; N. Kubatova; F. Kutz; V. Linhard; F. Löhr; N. Meiser; D. J. Pyper; N. S. Qureshi; C. Richter; K. Saxena; A. Schlundt; H. Schwalbe; S. Sreeramulu; J.-N. Tants; A. Wacker; J. E. Weigand; J. Wöhnert; A. C. Tsika; N. K. Fourkiotis; G. A. Spyroulias
• Keywords: 0301 basic medicine; 570; Adenosine Diphosphate Ribose; Nitrogen Isotopes; SARS-CoV-2; ddc:540; Proton Magnetic Resonance Spectroscopy; Viral Nonstructural Proteins; 540; Biochemistry; Article; Protein Structure, Secondary; 3. Good health; Betacoronavirus; 03 medical and health sciences; COVID19-NMR; Macrodomain; Non-structural protein; Protein drugability; SARS-CoV-2; Solution NMR-spectroscopy; Adenosine Diphosphate Ribose; Amino Acid Sequence; Apoproteins; Betacoronavirus; Nitrogen Isotopes; Protein Domains; Protein Structure, Secondary; Viral Nonstructural Proteins; Carbon-13 Magnetic Resonance Spectroscopy; Proton Magnetic Resonance Spectroscopy; Protein Domains; Structural Biology; ddc:570; ddc:540; ddc:570; Amino Acid Sequence; Carbon-13 Magnetic Resonance Spectroscopy; Apoproteins

AbstractThe 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 (1H, 13C, 15N) 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, 15N-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.