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.
Highlights
The macro domain is an adenosine diphosphate (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 thermal melting profiles of the MERS-CoV macro domain monitored at 220 nm using circular dichroism (CD) were greatly affected by the presence of these NAD metabolites
isothermal titration calorimetry (ITC) experiments and nuclear magnetic resonance (NMR) titrations revealed that the MERS-CoV macro domain could interact with ADPR, ADP, adenosine monophosphate (AMP), and adenosine triphosphate (ATP), but the affinity to NAD was extremely weak at 298 K
Summary
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. 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. The first discovered antiviral ADP-ribosylation enzyme was ARTD13, which was found to bind viral RNA, inhibit viral replication, induce transcription of viral defensing interferons, activate proteasome degradation, and promote apoptosis[10,13,14,15,16]. By transcriptome and protein interactome analyses, several mono-ADP-ribosyltransferase, diphtheria toxinlike enzymes (ARTD 10, 12, 14) were found to inhibit viral replication[18,19]. ARTD11 was found upregulated after virus infection and promoted IFN-I antiviral response by mono-ADP-ribosylating ubiquitin E3 ligase[22]. Viruses might have developed mechanisms to regulate the ADP-ribosylation-related conflict between viral replication and host immunity
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