D-Aminoacylase is an attractive candidate for commercial production of D-amino acids through its catalysis in the zinc-assistant hydrolysis of N-acyl-D-amino acids. We report here the cloning, expression, and structural-based mutation of the D-aminoacylase from Alcaligenes faecalis DA1. A 1,007-bp PCR product amplified with degenerate primers, was used to isolate a 4-kb genomic fragment, encoding a 484-residue D-aminoacylase. The enzyme amino-terminal segment shared significant homology within a variety of enzymes including urease. The structural fold was predicted by 3D-PSSM to be similar to urease and dihydroorotase, which have grouped into a novel ␣/-barrel amidohydrolase superfamily with a virtually indistinguishable binuclear metal centers containing six ligands, four histidines, one aspartate, and one carboxylated lysine. Three histidines, His-67, His-69, and His-250, putative metal ligands in D-aminoacylase, have been mutated previously, the remaining histidine (His-220) and aspartate (Asp-366) Asp-65, and four cysteines were then characterized. Substitution of Asp-65, Cys-96, His-220, and Asp-366 with alanine abolished the enzyme activity. The H220A mutant bound approximately half the normal complement of zinc ion as did H250N. However, the C96A mutant showed little zinc-binding ability, revealing that Cys-96 may replace the carboxylated lysine to serve as a bridging ligand. According to the urease structure, the conserved amino-terminal segment including Asp-65 may be responsible for structural stabilization. Therefore, production of D-amino acids by D-aminoacylase has commercial importance.To search for new D-aminoacylases suitable for D-amino acid production, microorganisms in various soils were screened. Two D-aminoacylases from Alcaligenes denitrificans DA181 (Tsai et al. 1988;Yang et al. 1992) and A. faecalis DA1 (Yang et al. 1991;Tsai et al. 1992) were isolated and showed higher specific activity and better stereospecificity than those from Pseudomonas and Streptomyces (Sugie and Suzuki 1978;Kubo et al. 1980). Two other D-aminoacylase-producing strains, A. denitrificans MI-4 (Sakai et al. 1991), and A. xylosoxydans A-6 (Moriguchi et al. 1993), were subsequently screened. Three genes encoding for the A-6 D-aminoacylases have been cloned and expressed in Escherichia coli (Wakayama et al. 1995a,b,c). These A-6 D-aminoacylases share 45%-50% sequence iden-