Direct participation of potassium ion in the catalysis of coenzyme B(12)-dependent diol dehydratase.
The direct ion-dipolar interactions between potassium ion (K(+)) and the two hydroxyl groups of the substrate are the most striking feature of the crystal structure of coenzyme B(12)-dependent diol dehydratase. We carried out density-functional-theory computations to determine whether K(+) can assist the 1,2-shift of the hydroxyl group in the substrate-derived radical. Between a stepwise abstraction/recombination reaction proceeding via a direct hydroxide abstraction by K(+) and a concerted hydroxyl group migration assisted by K(+), only a transition state for the latter concerted mechanism was found from our computations. The barrier height for the transition state from the complexed radical decreases by only 2.3 kcal/mol upon coordination of the migrating hydroxyl group to K(+), which corresponds to a 42-fold rate acceleration at 37 degrees C. The net binding energy upon replacement of the K(+)-bound water for substrate was calculated to be 10.7 kcal/mol. It can be considered that such a large binding energy is at least partly used for the substrate-induced conformational changes in the enzyme that trigger the homolytic cleavage of the Co-C bond of the coenzyme and the subsequent catalysis by a radical mechanism. We propose here a new mechanism for diol dehydratase in which K(+) plays a direct role in the catalysis.
Toraya
T
T
Department of Bioscience and Biotechnology, Faculty of Engineering, Okayama University, Tsushima-naka, Okayama, 700-8530, Japan. toraya@biotech.okayama-u.ac.jp
Yoshizawa
K
K
Eda
M
M
Yamabe
T
T
D002384:Catalysis; D020134:Catalytic Domain; D003038:Cobamides / Q000378:metabolism*; D008956:Models, Chemical; D008958:Models, Molecular; D011188:Potassium / Q000378:metabolism*; D011408:Propanediol Dehydratase / Q000737:chemistry / Q000378:metabolism*; D011487:Protein Conformation; D013816:Thermodynamics
D003038:Cobamides; D011408:Propanediol Dehydratase; C000913:cobamamide; D011188:Potassium