Structural basis of substrate recognition and conformational gating in the bacteriophage M15 metalloendopeptidase LysPH

The rapid emergence of antimicrobial resistance has led to a surge in multidrug-resistant strains, jeopardising the efficacy of frontline and last-resort antibiotics and thereby aggravating the antimicrobial resistance crisis. Bacteriophage-derived endolysins represent a promising class of next-generation antimicrobials. Here, we report the isolation of a novel bacteriophage, PA_Ganga_001, targeting multidrug-resistant Pseudomonas aeruginosa. Genomic sequencing of this phage identified a previously uncharacterised endolysin LysPH, a zinc-dependent globular endolysin that exhibits antibacterial activity against multiple multidrug-resistant Gram-negative pathogens, including Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae. Site-directed mutagenesis of the endolysin LysPH suggests that His77, Asp84, His159, Arg41, and Asp156 are essential for catalysis and substrate accommodation. To understand the structural basis of substrate binding and catalysis, we determined the crystal structures of the apo-enzyme (1.8 [A]) and the catalytically attenuated D156A mutant in complex with a synthetic pentapeptide stem (PGX) of peptidoglycan (2.0 [A]). The pentapeptide-bound complex revealed a defined substrate-binding groove, and a pronounced displacement of the Thr42-Ser75 loop was observed. This led to an approximately six-fold volumetric expansion of the catalytic cleft, indicative of a substrate-induced transition to an open, catalytically competent conformation. Notably, a distinctive C-terminal helical element, which diverges sequentially from characterised M15 homologues, is predicted to interact with the NAG-NAM scaffold and may contribute to the positioning of the stem pentapeptide for Zn2+ dependent catalysis. These distinct structural features establish the molecular basis for L-Ala-D-Glu hydrolysis by M15 bacteriophage endolysins and provide a foundational framework for the rational design and engineering of the next generation of antimicrobial enzymes.