Journal of Synchrotron Radiation

Volume 15, Part 3 (May 2008)

diffraction structural biology

J. Synchrotron Rad. (2008). 15, 250-253 [ doi:10.1107/S0909049507064655 ]

Deduced catalytic mechanism of D-amino acid amidase from Ochrobactrum anthropi SV3

S. Okazaki, A. Suzuki, H. Komeda, Y. Asano and T. Yamane

Abstract: D-Amino acid amidase (DAA) from Ochrobactrum anthropi SV3 catalyzes D-stereospecific hydrolysis of amino acid amides. DAA has attracted attention as a catalyst for the stereospecific production of D-amino acids, although the mechanism that drives the reaction has not been clear. Previously, the structure of DAA was classified into two types, a substrate-bound state with an ordered [Omega] loop, and a ground state with a disordered [Omega] loop. Because the binding of the substrate facilitates ordering, this transition was regarded to be induced fit motion. The angles and distances of hydrogen bonds at Tyr149 O [eta] , Ser60 O [gamma] and Lys63 N [zeta] revealed that Tyr149 O [eta] donates an H atom to a water molecule in the substrate-bound state, and that Tyr149 O [eta] donates an H atom to Ser60 O [gamma] or Lys63 N [zeta] in the ground state. Taking into consideration the locations of the H atoms of Tyr149 O [eta] , Ser60 O [gamma] and Lys63 N [zeta] , a catalytic mechanism of DAA activity is presented, wherein a shift of an H atom at Tyr149 O [eta] in the substrate-bound versus the ground state plays a significant role in the reaction. This mechanism explains well why acylation proceeds and deacylation does not proceed in the substrate-bound state.

Keywords: catalytic mechanisms; stereospecific hydrolysis; D-amino acid amidase.