Pseudomonos aeruginosa LD-carboxypeptidase, a serine peptidase with a Ser-His-Glu Triad and a nucleophilic elbow

Abstract

LD-Carboxypeptidases (EC 3.4.17.13) are named for their ability to cleave amide bonds between L- and D-amino acids, which occur naturally in bacterial peptidoglycan. They are specific for the link between meso-diaminopimelic acid and D-alanine and therefore degrade GlcNAc-MurNAc tetrapeptides to the corresponding tripeptides. As only the tripeptides can be reused as peptidoglycan building blocks, LD-carboxypeptidases are thought to play a role in peptidoglycan recycling. Despite the pharmaceutical interest in peptidoglycan biosynthesis, the fold and catalytic type of LD-carboxypeptidases are unknown. Here, we show that a previously uncharacterized open reading frame in Pseudomonas aeruginosa has LD-carboxypeptidase activity and present the crystal structure of this enzyme. The structure shows that the enzyme consists of an N-terminal β-sheet and a C-terminal β-barrel domain. At the interface of the two domains, Ser115 adopts a highly strained conformation in the context of a strand-turn-helix motif that is similar to the "nucleophilic elbow" in αβ-hydrolases. Ser115 is hydrogen-bonded to a histidine residue, which is oriented by a glutamate residue. All three residues, which occur in the order Ser-Glu-His in the amino acid sequence, are strictly conserved in naturally occurring LD-carboxypeptidases and cannot be mutated to alanines without loss of activity. We conclude that LD-carboxypeptidases are serine peptidases with Ser-His-Glu catalytic triads. © 2005 by The American Society for Biochemistry and Molecular Biology, Inc.