7WDK

The structure of PldA-PA3488 complex

Summary for 7WDK

• Entry DOI: 10.2210/pdb7wdk/pdb
• EMDB information: 32438
• Descriptor: Phospholipase D, Tli4_C domain-containing protein (2 entities in total)
• Functional Keywords: plda, pa3488, complex, immune system
• Biological source: Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1); More
• Total number of polymer chains: 2
• Total formula weight: 165566.70

Authors

Zhao, L.,Yang, X.Y.,Li, Z.Q. (deposition date: 2021-12-21, release date: 2022-10-26, Last modification date: 2025-06-25)

Primary citation

Yang, X.,Li, Z.,Zhao, L.,She, Z.,Gao, Z.,Sui, S.F.,Dong, Y.,Li, Y.
Structural insights into PA3488-mediated inactivation of Pseudomonas aeruginosa PldA
Nat Commun, 13:5979-5979, 2022

PubMed Abstract: 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.

PubMed: 36216841
DOI: 10.1038/s41467-022-33690-2

Experimental method

ELECTRON MICROSCOPY (3.05 Å)