title: Glycerol dehydratation by the B12-independent enzyme may not involve the migration of a hydroxyl group: a computational study.
abstract: A combination of continuum electrostatic and density functional calculations has been employed to study the mechanism of the B(12)-independent glycerol dehydratase, a novel glycyl-radical enzyme involved in the microbial conversion of glycerol to 3-hydroxylpropionaldehyde. The calculations indicate that the dehydratation of glycerol by the B(12)-independent enzyme does not need to involve a mechanistically complicated migration of the middle hydroxyl group to one of the two terminal positions of a molecule, as previously suggested. Instead, the reaction can proceed in three elementary steps. First, a radical transfer from the catalytically active Cys433 to the ligand generates a substrate-related intermediate. Second, a hydroxyl group splits off at the middle position of the ligand and is protonated by the neighboring His164 to form a water molecule. The other active site residue Glu435 accepts a proton from one of the terminal hydroxyl groups of the ligand and a C═O double bond is created. Third, the reaction is completed by a radical back transfer from the product-related intermediate to Cys433. On the basis of our calculations, the catalytic functions of the active site residues have been suggested. Cys433 is a radical relay site; His164 and Glu435 make up a proton accepting/donating system; Asn156, His281, and Asp447 form a network of hydrogen bonds responsible for the electrostatic stabilization of the transition state. A synergistic participation of these residues in the reaction seems to be crucial for the catalysis.
authors.affiliation: Computational Biochemistry Group, University of Bayreuth, Universitätsstr. 30, BGI, 95447 Bayreuth, Germany.
authors.forename: Mikolaj
authors.initials: M
authors.lastname: Feliks
authors.forename: G Matthias
authors.initials: GM
authors.lastname: Ullmann
mesh_terms: D055162:Biocatalysis; D020134:Catalytic Domain; D006836:Hydro-Lyases / Q000737:chemistry / Q000378:metabolism*; D006860:Hydrogen Bonding; D006878:Hydroxides / Q000737:chemistry; D008958:Models, Molecular; D011522:Protons; D011789:Quantum Theory; D055672:Static Electricity; D014805:Vitamin B 12 / Q000737:chemistry / Q000378:metabolism*
chemical_list: D006878:Hydroxides; D011522:Protons; C031356:hydroxide ion; D006836:Hydro-Lyases; C020671:glycerol dehydratase; D014805:Vitamin B 12