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TitleMechanistic insights into single-stranded DNA degradation by lysosomal exonucleases PLD3 and PLD4 from structural snapshots.
Journal, issue, pagesNat Commun, Year 2025
Publish dateDec 11, 2025
AuthorsYoshinori Hirano / Wakiko Ezaki / Ryota Sato / Umeharu Ohto / Kensuke Miyake / Toshiyuki Shimizu /
PubMed AbstractLysosomal 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 ...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.
External linksNat Commun / PubMed:41381514
MethodsEM (single particle)
Resolution2.85 - 3.31 Å
Structure data

64921

9vbg

EMDB-64921, PDB-9vbg:
Cryo-EM structure of human PLD3 apo form
Method: EM (single particle) / Resolution: 2.9 Å

64922

9vbh

EMDB-64922, PDB-9vbh:
Cryo-EM structure of human PLD3 bound to ssDNA (poly(T))
Method: EM (single particle) / Resolution: 2.85 Å

64923

9vbi

EMDB-64923, PDB-9vbi:
Cryo-EM structure of PLD3 bound to ssDNA (poly(A))
Method: EM (single particle) / Resolution: 2.87 Å

64924

9vbj

EMDB-64924, PDB-9vbj:
Cryo-EM structure of human PLD4 apo form
Method: EM (single particle) / Resolution: 3.31 Å

64925

9vbk

EMDB-64925, PDB-9vbk:
Cryo-EM structure of human PLD4 bound to ssDNA (poly(T))
Method: EM (single particle) / Resolution: 3.06 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-T3P:
THYMIDINE-3'-PHOSPHATE

Source
  • homo sapiens (human)
  • synthetic construct (others)
KeywordsIMMUNE SYSTEM / Exonuclease

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