The crystal structure and oligomeric form of Escherichia coli l , d -carboxypeptidase A

Abstract

Bacterial peptidoglycan is constructed by cross-linking sugar chains carrying pentapeptide building blocks with two d-alanine residues at the C-terminus. Incorporation into the polymer and subsequent breakdown of peptidoglycan releases a tetrapeptide with a single d-alanine residue. Removal of this residue is necessary for the tripeptide to receive a new D-Ala-D-Ala dipeptide in the synthetic pathway, but proteases are generally unable to work with substrates having residues of unusual chirality close to the scissile bond. Processing of the tetrapeptide is carried out by a dedicated ld-carboxypeptidase, which is of interest as a novel drug target. We describe the high resolution crystal structure of the enzyme from E. coli, and demonstrate the dimeric structure is highly conserved.

A Francisella tularensis L,D‐carboxypeptidase plays important roles in cell morphology, envelope integrity, and virulence

“…As noted above and highlighted in Figure 1, P. aeruginosa LdcA contains a Ser‐Glu‐His catalytic triad which is essential for function and is characteristic of Ldc in the Peptidase_S66 family (Korza and Bochtler, 2005). The same catalytic triad also has been confirmed in Ldc from E. coli (Meyer et al., 2018), Novosphingobium aromaticivorans (Das et al., 2013), and N. gonorrhoeae (Lenz et al., 2017). Given the relatively conserved spacing of Ser134‐Glu239‐His308 residues in FTL1678 (Figure 1) and our findings that both double (S134A/E239A, S134A/H308A, and E239A/H308A) and triple (S134A/E239A/H308A) mutants did not exhibit LdcA activity (Table ), we tested if individual amino acid residues of the catalytic triad were required for F. tularensis virulence (similar to Figure 5a virulence assessments for Δ FTL1678 and the FTL1678 complemented strain).…”

Cell-Wall Recycling of the Gram-Negative Bacteria and the Nexus to Antibiotic Resistance

“…75–83 LdcA is a serine-dependent l , d -carboxypeptidase that recognizes the tetrapeptide stem structure (but not the pentapeptide stem), and catalyzes the hydrolysis of the meso -diaminopimelate- d -Ala amide bond with release of d -Ala, to give the tripeptide. 84–86 LdcA acts on the tetrapeptide stems of MurNAc mono-saccharides, the tetrapeptide stems of the GlcNAc-MurNAc disaccharide ( 1 , Scheme 3), and the free tetrapeptide ( 3b ). In Neisseria gonorrheae LdcA contributes to muropeptide release from the bacterium as a periplasmic enzyme, in contrast to cytoplasmic localization of the enzyme in E. coli and P. aeruginosa , for the ultimate purpose of inducing an inflammatory response in the host inflammation.…”

A Francisella tularensis L,D-carboxypeptidase plays important roles in cell morphology, envelope integrity, and virulence

“…As noted above and highlighted in Figure 1, P. aeruginosa LdcA contains a Ser-Glu-His catalytic triad which is essential for function and is characteristic of Ldc in the Peptidase_S66 family (Korza, 2005). The same catalytic triad also has been confirmed in Ldc from E. coli (Meyer, 2018), Novosphingobium aromaticivorans (Das, 2013), and N. gonorrhoeae (Lenz, 2017). Given the relatively conserved spacing of Ser134-Glu239-His308 residues in FTL1678 (Figure 1) and our findings that both double (S134A/E239A, S134A/H308A, E239A/H308A) and triple (S134A/E239A/H308A) mutants did not exhibit LdcA activity (Table S3), we tested if individual amino acid residues of the catalytic triad were required for F. tularensis virulence (similar to Figure 5A virulence assessments for Δ FTL1678 and the FTL1678 complemented strain).…”

“…1, P. aeruginosa LdcA contains a Ser-His-Glu catalytic triad which is essential for function and is characteristic of Ldc in the Peptidase_S66 family (30). The Ser-His-Glu catalytic triad also has been confirmed in Ldc from E. coli (47), Novosphingobium aromaticivorans (48), and N. gonorrhoeae (31). Given the relatively conserved spacing of Ser-His-Glu residues in FTL1678 (Fig.…”