Crystal structures of penicillin acylase enzyme-substrate complexes: structural insights into the catalytic mechanism

J Mol Biol. 2001 Oct 12;313(1):139-50. doi: 10.1006/jmbi.2001.5043.


The crystal structure of penicillin G acylase from Escherichia coli has been determined to a resolution of 1.3 A from a crystal form grown in the presence of ethylene glycol. To study aspects of the substrate specificity and catalytic mechanism of this key biotechnological enzyme, mutants were made to generate inactive protein useful for producing enzyme-substrate complexes. Owing to the intimate association of enzyme activity and precursor processing in this protein family (the Ntn hydrolases), most attempts to alter active-site residues lead to processing defects. Mutation of the invariant residue Arg B263 results in the accumulation of a protein precursor form. However, the mutation of Asn B241, a residue implicated in stabilisation of the tetrahedral intermediate during catalysis, inactivates the enzyme but does not prevent autocatalytic processing or the ability to bind substrates. The crystal structure of the Asn B241 Ala oxyanion hole mutant enzyme has been determined in its native form and in complex with penicillin G and penicillin G sulphoxide. We show that Asn B241 has an important role in maintaining the active site geometry and in productive substrate binding, hence the structure of the mutant protein is a poor model for the Michaelis complex. For this reason, we subsequently solved the structure of the wild-type protein in complex with the slowly processed substrate penicillin G sulphoxide. Analysis of this structure suggests that the reaction mechanism proceeds via direct nucleophilic attack of Ser B1 on the scissile amide and not as previously proposed via a tightly H-bonded water molecule acting as a "virtual" base.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Substitution / genetics
  • Binding Sites
  • Catalysis
  • Crystallization
  • Crystallography, X-Ray
  • Escherichia coli / enzymology*
  • Escherichia coli / genetics
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Ethylene Glycol
  • Kinetics
  • Models, Molecular
  • Mutation / genetics
  • Penicillin Amidase / chemistry*
  • Penicillin Amidase / genetics
  • Penicillin Amidase / metabolism*
  • Penicillin G / analogs & derivatives*
  • Penicillin G / metabolism
  • Protein Binding
  • Protein Conformation
  • Structure-Activity Relationship
  • Substrate Specificity


  • Escherichia coli Proteins
  • penicillin G sulfoxide
  • Penicillin Amidase
  • Ethylene Glycol
  • Penicillin G

Associated data

  • PDB/1GK9
  • PDB/1GKF
  • PDB/1GM7
  • PDB/1GM8
  • PDB/1GM9