Increase of the P1 Lys/Leu substrate preference of carboxypeptidase Y by rational design based on known primary and tertiary structures of serine carboxypeptidases.

The P1 substrate preference of serine carboxypeptidases, as expressed by the Lys/Leu ratio, differs by up to 10(5)-fold. Predictions of the major determinants of this preference are made by correlating primary and tertiary structures to substrate preferences. In carboxypeptidase Y from yeast it is predicted that Trp312 constitutes such a determinant, reducing the P1 Lys/Leu substrate preference of this enzyme. The predictions are tested by the construction and kinetic characterization of ten mutant enzymes of carboxypeptidase Y. All of these enzymes exhibit changes in their P1 substrate preference. Generally, small decreases in activity (kcat/Km) are observed with substrates containing uncharged P1 side chains. With substrates containing acidic P1 side chains, i.e., FA-Glu-Ala-OH, the activity generally increases slightly, 7-fold in the case of W312K. The most dramatic effects of the Trp312 substitutions are observed with substrates containing basic P1 side chains, i.e., kcat/Km for the hydrolysis of Fa-Lys-Ala-OH with W312E has increased 1150-fold, exclusively as a result of increased kcat values. Similar results have previously been obtained by mutational substitution at position 178 of carboxypeptidase Y. The construction and kinetic characterization of position 178 + 312 double mutants demonstrate that the kinetic effects of substitutions at these two positions are not additive. The P1 Lys/Leu substrate preference of one double mutant, L178D + W312D, has changed 380,000-fold as compared to the wild type enzyme, and the overall P1 substrate preference of this enzyme closely resembles that of carboxypeptidase WII from wheat.