title: Probing the Catalytic Mechanism Involved in the Isocitrate Lyase Superfamily: Hybrid Quantum Mechanical/Molecular Mechanical Calculations on 2,3-Dimethylmalate Lyase.
abstract: The isocitrate lyase (ICL) superfamily catalyzes the cleavage of the C(2)-C(3) bond of various α-hydroxy acid substrates. Members of the family are found in bacteria, fungi, and plants and include ICL itself, oxaloacetate hydrolase (OAH), 2-methylisocitrate lyase (MICL), and (2R,3S)-dimethylmalate lyase (DMML) among others. ICL and related targets have been the focus of recent studies to treat bacterial and fungal infections, including tuberculosis. The catalytic process by which this family achieves C(2)-C(3) bond breaking is still not clear. Extensive structural studies have been performed on this family, leading to a number of plausible proposals for the catalytic mechanism. In this paper, we have applied quantum mechanical/molecular mechanical (QM/MM) methods to the most recently reported family member, DMML, to assess whether any of the mechanistic proposals offers a clear energetic advantage over the others. Our results suggest that Arg161 is the general base in the reaction and Cys124 is the general acid, giving rise to a rate-determining barrier of approximately 10 kcal/mol.
authors.affiliation: Department of Social and Applied Science, College of Industrial Technology, King Mongkut's University of Technology, North Bangkok , Bangkok 10800, Thailand.
authors.forename: Nathjanan
authors.initials: N
authors.lastname: Jongkon
authors.affiliation: Department of Chemistry, Faculty of Science, Kasetsart University , Chatuchak, Bangkok 10903, Thailand.
authors.forename: Warot
authors.initials: W
authors.lastname: Chotpatiwetchkul
authors.affiliation: Department of Chemistry, Faculty of Science, Kasetsart University , Chatuchak, Bangkok 10903, Thailand.
authors.forename: M Paul
authors.initials: MP
authors.lastname: Gleeson
mesh_terms: D002244:Carbon / Q000737:chemistry; D002384:Catalysis; D007522:Isocitrate Lyase / Q000737:chemistry*; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D011422:Propionates / Q000737:chemistry; D011773:Pyruvates / Q000737:chemistry; D011789:Quantum Theory
chemical_list: D011422:Propionates; D011773:Pyruvates; D002244:Carbon; D007522:Isocitrate Lyase