Carp D-amino acid oxidase: Structural active site basis of its catalytic mechanisms

The three-dimensional structure of the flavoprotein D-amino acid oxidase (DAO, EC 1.4.3.3) from carp hepatopancreas (chDAO) and its active site cavity was modelled using ProModII. The structural features relevant for the overall conformation and for the catalytic activity are described. Secondary structure topology consists of 11 -helices and 17 -strands, which differs slightly from pig kidney, and Rhodotorula gracilis DAOs. chDAO showed a theoretical 'head-to-head' mode of dimerization. The presence of a short 'lid' in chDAO covering the active site, commonly found in mammalian DAO but absent in R. gracilis DAO, is interpreted as the origin of the differences in kinetic mechanism among these enzymes. This lid has been proposed to control the access of the substrate to the active site and to regulate dissociation of products. The conformational change in the large size active site loop determines the overall rate of turnover of DAOs. The shorter active site loop found in chDAO might be responsible for the higher turnover rate in chDAO compared to that of pkDAO.