Structural and kinetic studies on ligand binding in wild-type and active-site mutants of penicillin acylase

Wynand B L Alkema, Charles M H Hensgens, Harm J Snijder, Evelien Keizer, Bauke W Dijkstra, Dick B Janssen

Research output: Contribution to journalArticleAcademicpeer-review


Penicillin acylase catalyses the condensation of Calpha-substituted phenylacetic acids with beta-lactam nucleophiles, producing semi-synthetic beta-lactam antibiotics. For efficient synthesis a low affinity for phenylacetic acid and a high affinity for Calpha-substituted phenylacetic acid derivatives is desirable. We made three active site mutants, alphaF146Y, betaF24A and alphaF146Y/betaF24A, which all had a 2- to 10-fold higher affinity for Calpha-substituted compounds than wild-type enzyme. In addition, betaF24A had a 20-fold reduced affinity for phenylacetic acid. The molecular basis of the improved properties was investigated by X-ray crystallography. These studies showed that the higher affinity of alphaF146Y for (R)-alpha-methylphenylacetic acid can be explained by van der Waals interactions between alphaY146:OH and the Calpha-substituent. The betaF24A mutation causes an opening of the phenylacetic acid binding site. Only (R)-alpha-methylphenylacetic acid, but not phenylacetic acid, induces a conformation with the ligand tightly bound, explaining the weak binding of phenylacetic acid. A comparison of the betaF24A structure with other open conformations of penicillin acylase showed that betaF24 has a fixed position, whereas alphaF146 acts as a flexible lid on the binding site and reorients its position to achieve optimal substrate binding.

Original languageEnglish
Pages (from-to)473-480
JournalProtein Engineering, Design & Selection
Issue number5
Publication statusPublished - 14 Jul 2004
Externally publishedYes


  • catalytic domain/genetics
  • crystallization
  • escherichia coli/enzymology
  • kinetics
  • ligands
  • mutations
  • penicillin amidase/chemistry
  • phenylacetates/metabolism
  • protein binding
  • protein conformation


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