Magnesium induced structural reorganization in the active site of adenylate kinase

Phosphoryl transfer is a fundamental reaction in cellular signaling and metabolism that requires Mg²⁺ as an essential cofactor. While the primary function of Mg²⁺ is electrostatic activation of substrates, such as ATP, the full spectrum of catalytic mechanisms exerted by Mg²⁺ is not known. In this study, we integrate structural biology methods, molecular dynamic (MD) simulations, phylogeny, and enzymology assays to provide molecular insights into Mg²⁺-dependent structural reorganization in the active site of the metabolic enzyme adenylate kinase. Our results demonstrate that Mg²⁺ induces a conformational rearrangement of the substrates (ATP and ADP), resulting in a 30° adjustment of the angle essential for reversible phosphoryl transfer, thereby optimizing it for catalysis. MD simulations revealed transitions between conformational substates that link the fluctuation of the angle to large-scale enzyme dynamics. The findings contribute detailed insight into Mg²⁺ activation of enzymes and may be relevant for reversible and irreversible phosphoryl transfer reactions.