Bacterial peptidoglycan deacetylase enzymes are potentially important targets for the design of new drug In pathogenic bacteria, they modify cell-wall peptidoglycan by removing the acetyl group, which makes the bacteria more resistant to the host's immune response and other forms of attack, such as degradation by lysozyrne. In this study, we have investigated the mechanism of reaction of acetyl removal from a model substrate, the N-acetylglucosamine/N-acetylituramic acid dimer, by peptidogylcan deacetylase from Hdicabactcr pylori. For this, we employed a range of computational approaches, including molecular docking, Poisson-Boltzmann.electtnstatic,pk(a) calculations, molecular dynamics simulations, and hybrid, quantum chemical/molecular mechanical potential calculations in conjunction with reaction-path-finding algorithms. The active site of this enzyme is in a region of highly negative-electrostatic potential and contains a zinc dication with a bound water molecule. In the docked enzyme-substrate:Complex, our pK(a) Calculations indicate that in the most stable protonation states of the active site the zinc-bound water molecule is in:its hydroxide form and that the adjacent histidine residue, His247, is doubly protonated. In addition, there are one or two excess protons, with the neighboring aspartate residues, Asp12 and/or Asp199, being protonated. Overall, we find five clases of feasible-reaction mechanisms, with the favored mechanism depending heavily on the protonation state,of the active site:In the major one-excess-proton form, the mechanism with the lowest barrier (84 kJ mol(-1)) involves an initial protonation of the substrate nitrogen, followed by nucleophilic attack of the zinc-bound hydroxide and rupture of the substrate's carbon-nitrogen bond. However, in the minor two-excess-proton form, four mechanisms are almost equienergetic (83-86 kJ mol-1), comprising both those that start with nitrogen protonation and those in which nucleophilic attack by hydroxide occurs first.