Magnesium-induced nucleophile activation in the guanylyltransferase mRNA capping enzyme

The mRNA guanylyltransferase, or mRNA capping enzyme, cotranscriptionally caps the 5'-end of nascent mRNA with GMP during the second reaction in a set of three enzymatic reactions that result in the formation of an N7-methylguanosine cap during mRNA maturation. The mRNA capping enzyme is characterized, in part, by a conserved lysine nucleophile that attacks the α-phosphorus atom of GTP, forming a lysine-GMP intermediate. Experiments have firmly established that magnesium is required for efficient intermediate formation but have provided little insight into the requirement's molecular origins. Using empirical and thermodynamic integration pK(a) estimates, along with conventional molecular dynamics simulations, we show that magnesium binding likely activates the lysine nucleophile by increasing its acidity and by biasing the deprotonated nucleophile into conformations conducive to intermediate formation. These results provide additional functional understanding of an important enzyme in the mRNA transcript life cycle and allow functional analogies to be drawn that affect our understanding of the metal dependence of related superfamily members.