In rat dipeptidyl peptidase III, His568 is essential for catalysis, and Glu507 or Glu512 stabilizes the coordination bond between His455 or His450 and zinc ion

Dipeptidyl peptidase (DPP) III is a zinc-dependent exopeptidase that has a unique motif, “HELLGH,” as the zinc-binding site. In the present study, a three-dimensional (3D) model of rat DPP III was generated with the X-ray crystal structure of human DPP III (PDB: 3FVY [Dobrovetsky E. et al. (2009) SGC]) as a template. The replacement of the seven charged amino acid residues with a hydrophobic amino acid around the zinc ion did not cause any significant changes in Km values or in the substrate specificity. However, the kcat values of H568R and H568Y were remarkably reduced, by factors of 50 and 400, respectively. The His568 residue of rat DPP III is essential for enzyme catalysis. The kcat values of the mutants E507A and E512A were 2.38 and 3.88 s− 1 toward Arg-Arg-NA, and 0.097 and 0.59 s−1 toward Phe-Arg-NA, respectively. These values were markedly lower than those of the wild-type DPP III. Furthermore, the zinc contents of E507A and E512A were 0.29 and 0.08 atom per mol of protein, respectively, and those mutations caused remarkable increases in the dissociation constants of the zinc ions from DPP III by factors of 5 × 103 to 2 × 104. The 3D model of the catalytic domain of rat DPP III showed that the carboxyl oxygen atoms of Glu507 and Glu512 form the hydrogen bonds to the nitrogen atoms of His455 and His450. All of these results showed that Glu507 or Glu512 stabilizes the coordination bond between the zinc ion and His455 or His450.