New insights into the mechanism of the Schiff base hydrolysis catalyzed by type I dehydroquinate dehydratase from S. enterica: a theoretical study

Abstract

The reaction pathway of Schiff base hydrolysis catalyzed by type I dehydroquinate dehydratase (DHQD) from S. enterica has been studied by performing molecular dynamics (MD) simulations and density functional theory (DFT) calculations and the corresponding potential energy profile has also been identified. On the basis of the results, the catalytic hydrolysis process for the wild-type enzyme consists of three major reaction steps, including nucleophilic attack on the carbon atom involved in the carbon-nitrogen double bond of the Schiff base intermediate by a water molecule, deprotonation of the His143 residue, and dissociation between the product and the Lys170 residue of the enzyme. The remarkable difference between this and the previously proposed reaction mechanism is that the second step here, absent in the previously proposed reaction mechanism, plays an important role in facilitating the reaction through a key proton transfer by the His143 residue, resulting in a lower energy barrier. Comparison with our recently reported results on the Schiff base formation and dehydration processes clearly shows that the Schiff base hydrolysis is rate-determining in the overall reaction catalyzed by type I DHQD, consistent with the experimental prediction, and the calculated energy barrier of ∼16.0 kcal mol(-1) is in good agreement with the experimentally derived activation free energy of ∼14.3 kcal mol(-1). When the imidazole group of His143 residue is missing, the Schiff base hydrolysis is initiated by a hydroxide ion in the solution, rather than a water molecule, and both the reaction mechanism and the kinetics of Schiff base hydrolysis have been remarkably changed, clearly elucidating the catalytic role of the His143 residue in the reaction. The new mechanistic insights obtained here will be valuable for the rational design of high-activity inhibitors of type I DHQD as non-toxic antimicrobials, anti-fungals, and herbicides.

Reassessing the type I dehydroquinate dehydratase catalytic triad: Kinetic and structural studies of Glu86 mutants

“…1(A)] 8. Within this triad, Lys170 forms the covalent Schiff base with the substrate and His143 acts as the general acid and general base that catalyzes multiple proton transfer events within the formation and hydrolysis of the Schiff base and the catalytic dehydration event 9–12. The final member of the triad, Glu86, hydrogen bonds with His143 but its role in catalysis remains unclear.…”

Synergistic Redox Reaction for Value-Added Organic Transformation via Dual-Functional Photocatalytic Systems

“…Generally, the presence of aldehydes and amines in one reactor leads to the formation of Schiff bases through the amide condensation reaction. Schiff bases are important chemicals in the fabrication of pharmaceuticals; 55,56 however they were not generated or detected in these works mentioned above. Recently, Zhang and co-workers fabricated CdS nanorods modified with the ultra-low amounts (0.03%) of Pt nanoparticles (Pt/CdS) composite for the selective reduction of NB to AL and oxidation of p-MBA to p-MBAD in one reaction system.…”

Stereochemistry of enzymatic water addition to C = C bonds

“…The OH − for the first step of the hydration originates from water, and the remaining proton comes from the same water molecule, resulting in synaddition. Release of the Schiff base is facilitated by His143, in which the H bound to the His is given to Lys and not the free proton as formerly thought (Yao and Li, 2012;Light et al, 2014).…”