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![[Figure 2]](ys5010fig2mag.jpg)
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Figure 2
Proposed catalytic mechanism of DAA. The numerals in parentheses show the steps in the reaction. Proposed hydrogen bonds are represented as broken lines. The substrate D-phenylalanine is shown in red. In this model, enzyme catalysis proceeds according to the following steps. (1) By approaching the substrate D-Phe-NH2 at the active site of DAA, Tyr149 Oη makes a transition to the location found in the substrate-bound state by induced fit motion. (2) Lys63 Nζ enhances the nucleophilic attack of Ser60 Oγ on D-Phe-NH2 as general base, and a tetrahedral intermediate forms (light-green arrow). Finally, acyl enzyme is formed (cyan arrow). (3) NH3 is released via a channel; Tyr149 Oη makes a transition to the location found in the ground state; and a nucleophilic water molecule enters. (4) Finally, deacylation occurs via formation of a tetrahedral intermediate (light-green arrow) and regeneration of the free enzyme (cyan arrow). (a) Arrangement of the active site residues in the free enzyme. (b) A noncovalent substrate complex is transferred to a tetrahedral intermediate in the substrate-bound state. (c) Acyl enzyme right after acylation. Black arrows indicate proton transfer facilitated by the location of Tyr149 in substrate-bound state, and circled numbers indicate the order of transition. (d) Acyl enzyme observed in the D-phenylalanine complex (Okazaki et al., 2007  ), in which NH3 is replaced by H2O. (e) and (f) Acyl enzyme is transferred to a tetrahedral intermediate in the ground state. Either Tyr149 Oη (e) or Lys63 Nζ (f) may act as the general acid for deacylation. |
![[Figure 2]](ys5010fig2.jpg)
 | JOURNAL OF SYNCHROTRON RADIATION |
ISSN: 1600-5775
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