title: Catalytic Mechanism of Peptidoglycan Deacetylase: A Computational Study.
abstract: Bacterial peptidoglycan deacetylase enzymes are potentially important targets for the design of new drugs. 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 lysozyme. In this study, we have investigated the mechanism of reaction of acetyl removal from a model substrate, the N-acetylglucosamine/N-acetylmuramic acid dimer, by peptidogylcan deacetylase from Helicobacter pylori. For this, we employed a range of computational approaches, including molecular docking, Poisson-Boltzmann electrostatic pKacalculations, 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 pKacalculations 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 classes 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.
authors.affiliation: Dynamo Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale , 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France.
authors.forename: Nicholus
authors.initials: N
authors.lastname: Bhattacharjee
authors.affiliation: Dynamo Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale , 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France.
authors.forename: Mikolaj
authors.initials: M
authors.lastname: Feliks
authors.affiliation: Division of Molecular Medicine, Boston Children's Hospital , Boston, Massachusetts 02115, United States.|Department of Pediatrics, Harvard Medical School , 3 Blackfan Street, Boston, Massachusetts 02115, United States.
authors.forename: Md Munan
authors.initials: MM
authors.lastname: Shaik
authors.affiliation: Dynamo Team/DYNAMOP Group, UMR5075, Université Grenoble I, CEA, CNRS, Institut de Biologie Structurale , 71 Avenue des Martyrs, CS 10090, 38044 Grenoble Cedex 9, France.
authors.forename: Martin J
authors.identifier: 0000-0001-8674-7997
authors.initials: MJ
authors.lastname: Field
mesh_terms: D000465:Algorithms; D055162:Biocatalysis; D010450:Endopeptidases / Q000737:chemistry / Q000378:metabolism*; D016480:Helicobacter pylori / Q000201:enzymology*; D006801:Humans; D011789:Quantum Theory
chemical_list: C051467:peptidoglycan endopeptidase; D010450:Endopeptidases