Comparative functional and structural analysis of Pseudomonas aeruginosad‐alanine–d‐alanine ligase isoforms as prospective antibiotic targets

Abstract

Pseudomonas aeruginosa is a major human pathogen in the healthcare setting. The emergence of multi‐drug‐resistant and extensive drug‐resistant P. aeruginosa is of great concern, and clearly indicates that new alternatives to current first‐line antibiotics are required in the future. Inhibition of d‐alanine–d‐alanine production presents as a promising avenue as it is a key component in the essential process of cell wall biosynthesis. In P. aeruginosa, d‐alanine–d‐alanine production is facilitated by two isoforms, d‐alanine–d‐alanine ligase A (PaDdlA) and d‐alanine–d‐alanine ligase B (PaDdlA), but neither enzyme has been individually characterised to date. Here, we present the functional and structural characterisation of PaDdlA and PaDdlB, and assess their potential as antibiotic targets. This was achieved using a combination of in vitro enzyme‐activity assays and X‐ray crystallography. The former revealed that both isoforms effectively catalyse d‐alanine–d‐alanine production with near identical efficiency, and that this is effectively disrupted by the model d‐alanine–d‐alanine ligase inhibitor, d‐cycloserine. Next, each isoform was co‐crystallised with ATP and either d‐alanine–d‐alanine or d‐cycloserine, allowing direct comparison of the key structural features. Both isoforms possess the same structural architecture and share a high level of conservation within the active site. Although residues forming the d‐alanine pocket are completely conserved, the ATP‐binding pocket possesses several amino acid substitutions resulting in a differing chemical environment around the ATP adenine base. Together, these findings support that the discovery of dual PaDdlA/PaDdlB competitive inhibitors is a viable approach for developing new antibiotics against P. aeruginosa.