Elucidating the tunability of binding behavior for the MERS-CoV macro domain with NAD metabolites

Abstract

The macro domain is an ADP-ribose (ADPR) binding module, which is considered to act as a sensor to recognize nicotinamide adenine dinucleotide (NAD) metabolites, including poly ADPR (PAR) and other small molecules. The recognition of macro domains with various ligands is important for a variety of biological functions involved in NAD metabolism, including DNA repair, chromatin remodeling, maintenance of genomic stability, and response to viral infection. Nevertheless, how the macro domain binds to moieties with such structural obstacles using a simple cleft remains a puzzle. We systematically investigated the Middle East respiratory syndrome-coronavirus (MERS-CoV) macro domain for its ligand selectivity and binding properties by structural and biophysical approaches. Of interest, NAD, which is considered not to interact with macro domains, was co-crystallized with the MERS-CoV macro domain. Further studies at physiological temperature revealed that NAD has similar binding ability with ADPR because of the accommodation of the thermal-tunable binding pocket. This study provides the biochemical and structural bases of the detailed ligand-binding mode of the MERS-CoV macro domain. In addition, our observation of enhanced binding affinity of the MERS-CoV macro domain to NAD at physiological temperature highlights the need for further study to reveal the biological functions.

NMR study of macro domains (MDs) from betacoronavirus: backbone resonance assignments of SARS–CoV and MERS–CoV MDs in the free and the ADPr-bound state

“…All these missing residues belong to a very conserved loop that is broadened beyond detection in both forms and for this loop this suggests conformational variability and flexibility upon binding. This is comparable with previously assigned MERS–COV macro domain proteins in the free (BMRB_ID 26657) and bound (BMRB_ID 50393) forms even though the previously deposited assignments are reported in different buffer and acquisition conditions (Huang et al 2016 ; Lin et al 2021 ).

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“…Additionally, several structural studies on ADPr-free and ADPr-bound macro domains indicate that despite some similarities of the binding mode, each macro domain may exhibit unique ADPr recognition and binding properties because of the adaptability of the macro polypeptide that might tune its binding mode and the affinity for ADPr molecules (Neuvonen et al 2009 ; Zapata-Pérez et al 2017 ; Ferreira-Ramos et al 2020 ; Lin et al 2021 ). In summary Coronaviruses macro domains have the ability to block the innate immune response of the host and separately to promote in vivo replication (Fehr et al 2016 ).…”