9VBK

Cryo-EM structure of human PLD4 bound to ssDNA (poly(T))

9VBK の概要

• エントリーDOI: 10.2210/pdb9vbk/pdb
• EMDBエントリー: 64925
• 分子名称: 5'-3' exonuclease PLD4, DNA (5'-D(*TP*TP*T)-3'), 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (5 entities in total)
• 機能のキーワード: exonuclease, immune system
• 由来する生物種: Homo sapiens (human); 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 221905.61

構造登録者

Hirano, Y.,Ezaki, W.,Ohto, U.,Shimizu, T. (登録日: 2025-06-04, 公開日: 2025-12-24, 最終更新日: 2026-01-14)

主引用文献

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, 16:11431-11431, 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

実験手法

ELECTRON MICROSCOPY (3.06 Å)