FIGURE 8.

Proposed reaction mechanism of V. alginolyticus PepD. (1) Binding of the substrate to the substrate C-terminal anchoring residues; (2) protein conformational change from the open to closed form upon substrate binding, displacing the zinc-bound water by the substrate and activating the bridging water molecule by Glu¹⁴⁹; (3) nucleophilic attack of the carbonyl carbon of the substrate by the activated water molecule and formation of the tetrahedral intermediate; (4) cleavage of the carbon-nitrogen bond and formation of product; (5) opening of the active site and release of the product; (6) addition of a new bridging water molecule.