title: Inactivation mechanism of glycerol dehydration by diol dehydratase from combined quantum mechanical/molecular mechanical calculations.
abstract: Inactivation of diol dehydratase during the glycerol dehydration reaction is studied on the basis of quantum mechanical/molecular mechanical calculations. Glycerol is not a chiral compound but contains a prochiral carbon atom. Once it is bound to the active site, the enzyme adopts two binding conformations. One is predominantly responsible for the product-forming reaction (G(R) conformation), and the other primarily contributes to inactivation (G(S) conformation). Reactant radical is converted into a product and byproduct in the product-forming reaction and inactivation, respectively. The OH group migrates from C2 to C1 in the product-forming reaction, whereas the transfer of a hydrogen from the 3-OH group of glycerol to C1 takes place during the inactivation. The activation barrier of the hydrogen transfer does not depend on the substrate-binding conformation. On the other hand, the activation barrier of OH group migration is sensitive to conformation and is 4.5 kcal/mol lower in the G(R) conformation than in the G(S) conformation. In the OH group migration, Glu170 plays a critical role in stabilizing the reactant radical in the G(S) conformation. Moreover, the hydrogen bonding interaction between Ser301 and the 3-OH group of glycerol lowers the activation barrier in G(R)-TS2. As a result, the difference in energy between the hydrogen transfer and the OH group migration is reduced in the G(S) conformation, which shows that the inactivation is favored in the G(S) conformation.
authors.affiliation: Institute for Materials Chemistry and Engineering and International Research Center for Molecular Systems, Kyushu University, Fukuoka 819-0395, Japan.
authors.forename: Kazuki
authors.initials: K
authors.lastname: Doitomi
authors.forename: Takashi
authors.initials: T
authors.lastname: Kamachi
authors.forename: Tetsuo
authors.initials: T
authors.lastname: Toraya
authors.forename: Kazunari
authors.initials: K
authors.lastname: Yoshizawa
mesh_terms: D005990:Glycerol / Q000378:metabolism*; D006859:Hydrogen / Q000737:chemistry*; D008958:Models, Molecular; D011408:Propanediol Dehydratase / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000378:metabolism*; D011487:Protein Conformation; D011789:Quantum Theory
chemical_list: D006859:Hydrogen; D011408:Propanediol Dehydratase; D005990:Glycerol