Escherichia coli dihydrofolate reductase catalyzed proton and hydride transfers: Temporal order and the roles of Asp27 and Tyr100

Significance Dihydrofolate reductase is a classic drug target because it promotes the NADPH-dependent reduction of 7,8-dihydrofolate (DHF) to yield 5,6,7,8-tetrahydrofolate (THF), which is involved in the biosynthesis of purines, thymidylate, and several amino acids. It is also a popular model system for various biochemical/biophysical studies. However, there are many unresolved mechanistic issues regarding the mechanism of catalysis. We combined primary, solvent, and multiple kinetic isotope effects; their temperature dependence; theoretical calculations; and site-specific mutagenesis to elucidate the reaction mechanism, which involves stepwise protonation of DHF by a water molecule prior to the hydride transfer. These two events are facilitated by two active site residues (D27 and Y100) that operate synergistically to ensure catalysis and to enable efficient DHF protonation over a wide pH range. The reaction catalyzed by Escherichia coli dihydrofolate reductase (ecDHFR) has become a model for understanding enzyme catalysis, and yet several details of its mechanism are still unresolved. Specifically, the mechanism of the chemical step, the hydride transfer reaction, is not fully resolved. We found, unexpectedly, the presence of two reactive ternary complexes [enzyme:NADPH:7,8-dihydrofolate (E:NADPH:DHF)] separated by one ionization event. Furthermore, multiple kinetic isotope effect (KIE) studies revealed a stepwise mechanism in which protonation of the DHF precedes the hydride transfer from the nicotinamide cofactor (NADPH) for both reactive ternary complexes of the WT enzyme. This mechanism was supported by the pH- and temperature-independent intrinsic KIEs for the C-H→C hydride transfer between NADPH and the preprotonated DHF. Moreover, we showed that active site residues D27 and Y100 play a synergistic role in facilitating both the proton transfer and subsequent hydride transfer steps. Although D27 appears to have a greater effect on the overall rate of conversion of DHF to tetrahydrofolate, Y100 plays an important electrostatic role in modulating the pKa of the N5 of DHF to enable the preprotonation of DHF by an active site water molecule.

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