Estimation of the lipase PS (Pseudomonas cepacia) active site dimensions based on molecular mechanics calculations

Estimation of the active site dimensions of lipase PS (Amano) has been carried out for the first time through molecular modelling studies. The proposed model has been based on secondary alcohols, which are efficiently enantiodifferentiated by the enzyme as substrates. Some molecules which are not good substrates for the enzyme have also been used to define more precisely the limits of the active site. The model comprises three well- defined pockets: a large hydrophobic pocket of 7 x 6.6 x 4.4 Å 3 to interact with large hydrophobic substituents; a more hydrophilic pocket of ca 1.8 x 1.8 x 1.5 Å 3 to bind the hydroxyl group and a tunnel-shaped hydrophobic pocket (2 Å wide and 1.9 Å high) able to accomodate long side chains. The latter pocket is unique among the active site models described so far for other enzymes, which are essentially cubic in space. The model is of predictive value and accounts for the enantioselectivity shown by the enzyme in transesterification reactions of secondary alcohols.