D-amino acid aminotransferase (D-aAT, EC 2.6.1.21) is a pyridoxal-phosphate (PLP) dependent enzyme that specifically transaminates D-amino acids. D-aAT provides one of the routes for the biosynthesis of D-alanine and/or D-glutamate, which are essential constituents of the bacterial cell wall peptidoglycan, thereby making this enzyme a potential antimicrobial target. One agent that inhibits this enzyme is D-cycloserine, believed to react with the cofactor and subsequently form a covalent link to the protein. We have recently reported the high-resolution crystal structure of D-aAT from a thermophilic Bacillus species (Sugio et al. Biochemistry 1995, 34, 9961-9969). We now report the crystal structure (PDB accession code 2DAA) of this enzyme inactivated by D-cycloserine. Contrary to expectations, cycloserine is not covalently attached to the protein but rather forms a stable aromatic species attached to the cofactor and held in place by many noncovalent interactions. The chemical nature of the complex between D-aAT and cycloserine was confirmed by infrared and nuclear magnetic resonance spectroscopy. This observation sheds light not only on the mechanism of inhibition of PLP-dependent aminotransferases by cycloserine in general but also on the nature of substrate recognition by D-aAT.