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A more recent version of this article appeared on December 9, 2005
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Papers In Press, published online ahead of print September 14, 2005
J. Biol. Chem, 10.1074/jbc.M506328200
Submitted on June 10, 2005
Revised on September 9, 2005
Accepted on September 13, 2005

P. aeruginosa LD-carboxypeptidase: A serine peptidase with a Ser-His-Glu triad and a nucleophilic elbow

Henryk J. Korza and Matthias Bochtler

MPG-PAN Joint Junior Research Group, MPI-CBG, Warsaw 02109

Corresponding Author: MBochtler{at}iimcb.gov.pl

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 NAG-NAM 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 sheet and a C-terminal barrel domain. At the interface of the two domains, serine 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. Serine 115 is hydrogen-bonded to a histidine residue, which is oriented by a glutamate residue. All three residues, which occur in the order serine, glutamate, histidine 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 serine, histidine, glutamate catalytic triads.


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