Protein structure portrait: NMNAT

Summary

Science

Data

Nicotinamide mononucleotide adenylyltransferase (NMNAT) is a nuclear protein that catalyses the reaction NMN + ATP >> NAD + PPi. Three crystal structures of NMNAT were published in 2002 and show different ligand binding states. One represents the apoenzyme (1kku), a second binds NMN (1gzu) and a third NAD (1kqn). The conformational changes between those three structures allow a detailed view on the molecular reaction mechanism and the enzyme behaviour. In the cell, NMNAT occurs as hexamer which plays a role in attracting the ligands in the first place.

status: July 2020

Nicotinamide adenine dinucleotide, NAD+ / NADH, is an important cofactor in the living cell as hydrogen-acceptor or donor, respectively. It is involved in many reactions of the metabolism and serves as oxidising (accepting electrons) or reducing (donating electrons) agent. NAD+ is synthesised from simpler compounds (de novo) or from nucleotides via the so called salvage pathway. Nicotinamide mononucleotide adenylyltransferase (NMNAT) is involved in both pathways and catalyses the last step, the adenylylation (transfer of adenosine mononphosphate, AMP) of nicotinamide mononucleotide (NMN).

Human NMNAT, UniProt ID Q9H2AN9) is a 32 kDa, one domain, globular protein with a length of 279 amino acid. It folds into a beta-sheet surrounded by alpha-helices in a so called Rossman Fold. It is located in the nucleus and occurs as hexamer. The oligomerisation is relevant for attracting the ligands NMN and ATP as it results in a electrostatic potential formed by a cluster of positively charged amino acids from adjacent monomers. Both ligands have phosphate groups with negative charges.

The animation shows the amino acids involved in the cluster as well as those involved in ligand binding. The three crystal structures described (see references under “data”) reveal conformational changes dependent on the ligand binding status that allow a prediction of the reaction mechanism. NMN is bound in the upper part of the deep ligand binding pocket and the ring system of nicotine is bound in stacking interactions while hydrogen bonds stabilise the position near the nicotine and the phosphate sections. The loops formed by amino acids 51 to 60 and 156 to 171 close in on NMN from both sides and narrow the ligand binding pocket at this pre-reaction moment. Also, the C-terminus of NMNAT, unstructured and therefore flexible in the apoenzyme, covers the same section of the pocket.

ATP is bound in the lower part of the ligand binding pocket with minor conformational changes but several hydrogen bonds, especially close to the reaction centre, the phosphates. A nucleophilic attack on the first ATP-Phosphate initiates the reaction that ultimately results in the adenylylation, the transfer of AMP, of NMN, resulting in NAD+ and PPi to dissociate from the enzyme. NMNAT goes back into the apoenzyme state with a widened gap between the moving loops and the C-terminus flexible.

Besides NAD, NMNAT also binds other ligands, including deamido-NAD and tiazofurin adenine dinucleotide (TAD) (crystal structures 1kqo and 1kr2, respectively - see Zhou et al., 2002) and is a target for drug discovery research due to the central role of NAD in the organism. Also it seems to be an important factor in neuronal maintenance.

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Protein structure portrait: NMNAT

Summary

Science

Data