Protein Name

Penicillin acylase


Escherichia coli (bacteria)

Biological Context

Penicillin was discovered in the culture of the fungus Penicillium notatum by A. Fleming in 1929. Subsequently, it has been extensively used as an antibiotic due to its excellent antibacterial effect. The effect is due to its ability to inhibit the synthesis of cell walls in bacteria, causing bacteriolysis and death of the bacterium. Because the natural penicillin is very sensitive to acids, it is difficult to administer orally. Furthermore penicillin-resistant bacteria have appeared. Recently semisynthetic penicillin in which a part of its basic skeleton differs from that of natural penicillin is used as a penicillin antibiotic. It is hardly decomposed with acids and partly effective for the resistant bacteria, furthermore has also a broader antibacterial spectrum than the natural one. Penicillin acylase is used in the industrial production of 6-aminopenicillanic acid, the starting material for the synthesis of the semisynthetic penicillin. This enzyme is widely distributed among microorganisms such as bacteria, yeast and filamentous fungi. The crystal structures of the complex of penicillin acylase derived from Escherichia coli with a substrate has been determined.

Structure Description


This enzyme is a heterodimer, with a 54-amino acid spacer between the two chains influencing the final protein fold. The catalytically active residue is the N-terminal serine of the B chain. The replacement of this residue with a cysteine inactivates the enzyme. In terms of the hydrolysis of an amide using a catalytic serine residue, this enzyme is similar to serine proteases. In contrast to the catalytic triad of serine proteases, however, there is no adjacent basic histidine in the vicinity of the catalytic serine of penicillin acylase. The base nearest to the hydroxyl group of this serine is its own alpha-amino group. From this structure analysis, the 'water-bridging' mechanism has been proposed; a water molecule mediates between the hydroxyl group and the alpha-amino group of the catalytic serine. A hydrogen-bond network is formed, in which the oxygen of a water molecule subtracts a hydrogen from the hydroxyl group of serine and a hydrogen is subtracted from a water molecule by the nitrogen of the alpha-amino group. As a result, the oxygen of the hydroxyl group becomes more active for a nucleophilic reaction. The phenyl moiety of a substrate tightly fits into the hydrophobic pocket, which is lined with many hydrophobic and aromatic side chains. This tight fit contributes to the specific recognition of the enzyme for the phenyl moiety of a substrate or inhibitor.

Protein Data Bank (PDB)



  • Duggleby, H.J. Tolley, S.P. Hill, C.P. Dodson, E.J. Dodson, G. Moody, P.C.; "Penicillin acylase has a single-amino-acid catalytic centre."; Nature; (1995) 373:264-268 PubMed:7816145.


author: Yuko Tsuchiya

Japanese version:PDB:1PNL