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Penicillin binds at the active site of the transpeptidase enzyme that cross-links the peptidoglycan strands. It does this by mimicking the D-alanyl-D-alanine residues that would normally bind to this site.6 The similarity between the structures of the residues and the penicillin molecule can be seen below:
Using the Chime Plug-in, you can rotate the D-alanyl-D-alanine residues on the left and the penicillin molecule on the right to show the similarities between the two structures. The correlation between the structures is perhaps most obvious when the oxygen atoms [in red] are aligned, as shown in this manipulation of the molecules:
The labile β-lactam ring in penicillin reacts with a serine residue in the transpeptidase as shown below. This reaction is irreversible and so the growth of the bacterial cell wall is inhibited. The resulting complex is stable to water and remains attached to the polypeptide chain.4
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