Although D-amino acids do not generally occur in proteins, they do serve some special functions in the structure of bacterial cell walls and peptide antibiotics.

Bacterial peptidoglycans contain both D-alanine and D-glutamate. D-Amino acids arise directly from the L isomers by the action of amino acid racemases, which have pyridoxal phosphate as cofactor. Amino acid racemization is uniquely important to bacterial metabolism, and enzymes such as alanine racemase are prime targets for pharmaceutical agents.

One such agent, L-fluoroalanine, is being tested as an antibacterial drug. Another, cycloserine, is used to treat tuberculosis.

Because these inhibitors also affect some PLP-requiring human enzymes, however, they have potentially undesirable side effects.