A Leukotriene A4 Hydrolase-Related Aminopeptidase from Yeast Undergoes Induced Fit upon Inhibitor Binding

Vertebrate leukotriene A4 hydrolases are bifunctional zinc metalloenzymes with an epoxide hydrolase and an aminopeptidase activity. In contrast, highly homologous enzymes from lower organisms only have the aminopeptidase activity. From sequence comparisons, it is not clear why this difference occurs. In order to obtain more information on the evolutionary relationship between these enzymes and their activities, the structure of a closely related leucine aminopeptidase from Saccharomyces cerevisiae that only shows a very low epoxide hydrolase activity was determined. To investigate the molecular architecture of the active site, the structures of both the native protein and the protein in complex with the aminopeptidase inhibitor bestatin were solved. These structures show a more spacious active site, and the protected cavity in which the labile substrate leukotriene A4 is bound in the human enzyme is partially obstructed and in other parts is more solvent accessible. Furthermore, the enzyme undergoes induced fit upon binding of the inhibitor bestatin, leading to a movement of the C-terminal domain. The main triggers for the domain movement are a conformational change of Tyr312 and a subtle change in backbone conformation of the PYGAMEN fingerprint region for peptide substrate recognition. This leads to a change in the hydrogen-bonding network pulling the C-terminal domain into a different position. Inasmuch as bestatin is a structural analogue of a leucyl dipeptide and may be regarded as a transition state mimic, our results imply that the enzyme undergoes induced fit during substrate binding and turnover.

Graphical abstractFigure optionsDownload full-size imageDownload high-quality image (56 K)Download as PowerPoint slideResearch Highlights► Several structures of a yeast Leucine Aminopeptidase was solved. ► This enzyme has a more open active site than the related human LTA4 hydrolase. ► The C-terminal domain rotates upon inhibitor binding and the active site closes. ► The binding pocket cannot provide efficient and specific LTA4 hydrolysis. ► We suggest an evolutionary mechanism to aquire the epoxide hydrolase activity.