Theoretical study of the reaction mechanism of Mycobacterium tuberculosis type II dehydroquinate dehydratase

Type II dehydroquinate dehydratase (DHQD), catalyzing the dehydration of dehydroquinate to dehydroshikimate, is considered as an attractive target for developing non-toxic antimicrobials, anti-fungals, and herbicides. The enzymes from different sources show distinguishable kinetic isotope effects, suggesting that they probably employ different reaction mechanisms. In the present study, the catalytic mechanism of type II DHQD from Mycobacterium tuberculosis has been reported by performing molecular dynamics simulations and quantum chemical calculations. The results revealed that this enzyme undergoes a two-step E1cB trans-elimination reaction mechanism and the calculated overall energy barrier of ∼17.7 kcal/mol is in excellent agreement with the experimental value. The developed enolate intermediate does not convert to enol intermediate by abstracting a solvent-derived proton and is therefore stabilized by Asn12 residue through strong hydrogen bonding interaction, reasonably explaining the observed kinetic isotope effect. Without the catalytic role of Asn12 residue, the overall energy barrier raises ∼4.5 kcal/mol.