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

Protein Eng Des Sel. 2004 May;17(5):473-80. doi: 10.1093/protein/gzh057. Epub 2004 Jul 14.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Catalytic Domain / genetics*
  • Catalytic Domain / physiology
  • Crystallization
  • Escherichia coli / enzymology
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Kinetics
  • Ligands
  • Mutation
  • Penicillin Amidase / chemistry
  • Penicillin Amidase / genetics*
  • Penicillin Amidase / metabolism
  • Phenylacetates / metabolism
  • Protein Binding
  • Protein Conformation


  • Ligands
  • Phenylacetates
  • Penicillin Amidase
  • phenylacetic acid