Pseudomonas aeruginosa LD-carboxypeptidase, a serine peptidase with a Ser-His-Glu triad and a nucleophilic elbow

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 beta-sheet and a C-terminal beta-barrel domain. At the interface of the two domains, Ser(115) adopts a highly strained conformation in the context of a strand-turn-helix motif that is similar to the nucleophilic elbow in alpha beta-hydrolases. Ser(115) 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.