9VBI

Cryo-EM structure of PLD3 bound to ssDNA (poly(A))

Summary for 9VBI

• Entry DOI: 10.2210/pdb9vbi/pdb
• EMDB information: 64923
• Descriptor: DNA (5'-D(*AP*AP*AP*AP*A)-3'), 5'-3' exonuclease PLD3, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (5 entities in total)
• Functional Keywords: exonuclease, immune system
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 4
• Total formula weight: 132231.74

Authors

Hirano, Y.,Ezaki, W.,Ohto, U.,Shimizu, T. (deposition date: 2025-06-04, release date: 2025-12-24)

Primary citation

Hirano, Y.,Ezaki, W.,Sato, R.,Ohto, U.,Miyake, K.,Shimizu, T.
Mechanistic insights into single-stranded DNA degradation by lysosomal exonucleases PLD3 and PLD4 from structural snapshots.
Nat Commun, 2025

PubMed Abstract: Lysosomal exonuclease phospholipase D (PLD) family PLD3 and PLD4 degrade single-stranded RNA or DNA and regulate TLR7 or TLR9 responses. Polymorphisms of these enzymes are associated with human diseases: PLD4 is associated with inflammatory diseases, and PLD3 is associated with neurodegenerative diseases. Here, we determine the structures of substrate-bound PLD3 and PLD4 by cryo-electron microscopy. Our structures reveal that PLD3 rebuilds a substrate-binding pocket, depending on the substrate, mainly via motion of the Phe335-containing loop. Furthermore, we captured the structure in a metastable state that appears during substrate rearrangement following product release. Together, our findings identify the residues that underlie the distinct activities of PLD3 and PLD4. This study provides a mechanistic basis for the exonuclease activity of PLD3 and PLD4 in single-stranded DNA degradation.

PubMed: 41381514
DOI: 10.1038/s41467-025-66261-2

Experimental method

ELECTRON MICROSCOPY (2.87 Å)