Structural insights into PA3488-mediated inactivation of Pseudomonas aeruginosa PldA

• Published in: Nature communications 2022-10, Vol.13 (1), p.5979-5979, Article 5979
• Main Authors: Yang, Xiaoyun, Li, Zongqiang, Zhao, Liang, She, Zhun, Gao, Zengqiang, Sui, Sen-Fang, Dong, Yuhui, Li, Yanhua
• Format: Article
• Language: English
• Subjects: 101/28; 101/58; 147/28; 631/45/173; 631/535/1266; 631/57/2271; Cell membranes; Crystal structure; Domains; Drug development; Electron microscopy; Enzymatic activity; Humanities and Social Sciences; Hydrolysis; Inactivation; Intermediates; Molecular modelling; multidisciplinary; Neutralization; Opportunist infection; Pathogens; Phosphodiester bonds; Phospholipase; Phospholipase D; Pseudomonas aeruginosa; Residues; Science; Science (multidisciplinary); Structural analysis; Substrates; Toxicity
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-022-33690-2

PldA, a phospholipase D (PLD) effector, catalyzes hydrolysis of the phosphodiester bonds of glycerophospholipids—the main component of cell membranes—and assists the invasion of the opportunistic pathogen Pseudomonas aeruginosa . As a cognate immunity protein, PA3488 can inhibit the activity of PldA to avoid self-toxicity. However, the precise inhibitory mechanism remains elusive. We determine the crystal structures of full-length and truncated PldA and the cryogenic electron microscopy structure of the PldA–PA3488 complex. Structural analysis reveals that there are different intermediates of PldA between the “open” and “closed” states of the catalytic pocket, accompanied by significant conformational changes in the “lid” region and the peripheral helical domain. Through structure-based mutational analysis, we identify the key residues responsible for the enzymatic activity of PldA. Together, these data provide an insight into the molecular mechanisms of PldA invasion and its neutralization by PA3488, aiding future design of PLD-targeted inhibitors and drugs. PldA, a phospholipase D (PLD) effector, catalyzes hydrolysis of the phosphodiester bonds of glycerophospholipids—the main component of cell membranes—and assists the invasion of the opportunistic pathogen Pseudomonas aeruginosa . In this work, the authors report three intermediate structures of PldA by employing an integrated approach combining structural biology and biochemistry. Structural analysis reveals that the significant conformational changes in the “lid” region and the peripheral helical domain trigger the switch of the active pocket of PldA to regulate the enzymatic activity. The structure-based mutational experiments identified a series of key residues responsible for substrate hydrolysis activity and the interactions between PldA and PA3488. In summary, this work provides the structural basis for understanding the PldA-mediated invasion of P. aeruginosa and can aid the future drug development targeting PldA.