Inactivation mechanism of glycerol dehydration by diol dehydratase from combined quantum mechanical/molecular mechanical calculations

Kazuki Doitomi, Takashi Kamachi, Tetsuo Toraya, Kazunari Yoshizawa

Research output: Contribution to journalArticlepeer-review

13 Citations (Scopus)

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 (GR 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 GR conformation than in the GS conformation. In the OH group migration, Glu170 plays a critical role in stabilizing the reactant radical in the GS conformation. Moreover, the hydrogen bonding interaction between Ser301 and the 3-OH group of glycerol lowers the activation barrier in GR-TS2. As a result, the difference in energy between the hydrogen transfer and the OH group migration is reduced in the GS conformation, which shows that the inactivation is favored in the GS conformation.

Original languageEnglish
Pages (from-to)9202-9210
Number of pages9
JournalBiochemistry
Volume51
Issue number45
DOIs
Publication statusPublished - Nov 13 2012

All Science Journal Classification (ASJC) codes

  • Biochemistry

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