A theoretical study on the catalytic mechanism of Mus musculus adenosine deaminase

J Comput Chem. 2010 Sep;31(12):2238-47. doi: 10.1002/jcc.21513.

Abstract

The catalytic mechanism of Mus musculus adenosine deaminase (ADA) has been studied by quantum mechanics and two-layered ONIOM calculations. Our calculations show that the previously proposed mechanism, involving His238 as the general base to activate the Zn-bound water, has a high activation barrier of about 28 kcal/mol at the proposed rate-determining nucleophilic addition step, and the corresponding calculated kinetic isotope effects are significantly different from the recent experimental observations. We propose a revised mechanism based on calculations, in which Glu217 serves as the general base to abstract the proton of the Zn-bound water, and the protonated Glu217 then activates the substrate for the subsequent nucleophilic addition. The rate-determining step is the proton transfer from Zn-OH to 6-NH(2) of the tetrahedral intermediate, in which His238 serves as a proton shuttle for the proton transfer. The calculated kinetic isotope effects agree well with the experimental data, and calculated activation energy is also consistent with the experimental reaction rate.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Deaminase / chemistry*
  • Animals
  • Catalysis
  • Energy Transfer
  • Glutamic Acid / chemistry
  • Histidine / chemistry
  • Hydroxyl Radical / chemistry
  • Kinetics
  • Mice
  • Models, Chemical
  • Models, Molecular
  • Protein Conformation
  • Quantum Theory
  • Zinc / chemistry

Substances

  • Hydroxyl Radical
  • Glutamic Acid
  • Histidine
  • Adenosine Deaminase
  • Zinc