9N3D

Crystal structure of Arabidopsis metacaspase 9 C147G at pH 4.2

9N3D の概要

• エントリーDOI: 10.2210/pdb9n3d/pdb
• 分子名称: Metacaspase-9 (2 entities in total)
• 機能のキーワード: plant immunity, metacaspase, ph-dependent activation, cysteine protease, plant protein
• 由来する生物種: Arabidopsis thaliana (thale cress)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 35503.34

構造登録者

Liu, H.,Liu, Q. (登録日: 2025-01-30, 公開日: 2025-06-11)

主引用文献

Liu, H.,Henderson, M.,Pang, Z.,Zhang, Q.,Lam, E.,Liu, Q.
Structural determinants for pH-dependent activation of a plant metacaspase.
Nat Commun, 16:4973-4973, 2025

PubMed Abstract: Arabidopsis thaliana metacaspase 9 (AtMC9) plays roles in clearing dead cells, forming xylem vessels, and regulating immunity and programmed cell death in plants. The protease's activation is controlled by pH levels, but the exact structural mechanism behind this has not been elucidated. In this work, we report high-resolution crystal structures for AtMC9 under both active (pH 5.5 and pH 4.2) and inactive (pH 7.5) conditions. The three structures are similar except for local conformations where their hydrogen bonding interactions with solvents are mediated through the protonation of specific titratable amino acid residues' side chains. By combining structural analysis, molecular dynamics simulations under constant pHs, and biochemical assays coupled with site-directed mutagenesis, we show that the regulation of AtMC9 activation involves multiple titratable glutamate and histidine residues across the three domains of p20, linker, and p10. Specifically, deprotonated Glu112, His193, and His208 can suppress AtMC9 proteolytic activity, while protonation of Glu255 and His307 at acidic pH may promote it. This study provides valuable insights into the pH-dependent activation of AtMC9 and could potentially lead to improving crops with enhanced immunity and controlled cell death, ultimately increasing agricultural productivity.

PubMed: 40442124
DOI: 10.1038/s41467-025-60253-y

実験手法

X-RAY DIFFRACTION (1.7 Å)