Structure of proline iminopeptidase from Xanthomonas campestris pv. citri: a prototype for the prolyl oligopeptidase family

The proline iminopeptidase from Xanthomonas campestris pv. citri is a serine peptidase that catalyses the removal of N‐terminal proline residues from peptides with high specificity. We have solved its three‐dimensional structure by multiple isomorphous replacement and refined it to a crystallographic R ‐factor of 19.2% using X‐ray data to 2.7 A resolution. The protein is folded into two contiguous domains. The larger domain shows the general topology of the α/β hydrolase fold, with a central eight‐stranded β‐sheet flanked by two helices and the 11 N‐terminal residues on one side, and by four helices on the other side. The smaller domain is placed on top of the larger domain and essentially consists of six helices. The active site, located at the end of a deep pocket at the interface between both domains, includes a catalytic triad of Ser110, Asp266 and His294. Cys269, located at the bottom of the active site very close to the catalytic triad, presumably accounts for the inhibition by thiol‐specific reagents. The overall topology of this iminopeptidase is very similar to that of yeast serine carboxypeptidase. The striking secondary structure similarity to human lymphocytic prolyl oligopeptidase and dipeptidyl peptidase IV makes this proline iminopeptidase structure a suitable model for the three‐dimensional structure of other peptidases of this family.