9RCP

1,2-propanediol dehydratase with 0.1 % 1,3-propanediol additive

9RCP の概要

• エントリーDOI: 10.2210/pdb9rcp/pdb
• 分子名称: Glycyl radical protein, 1,2-ETHANEDIOL (3 entities in total)
• 機能のキーワード: glycyl radical enzyme, 1, 2-propanediol, lyase
• 由来する生物種: Raoultella planticola; 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 366590.03

構造登録者

Kalnins, G.,Estere, M. (登録日: 2025-05-29, 公開日: 2025-06-11, 最終更新日: 2025-12-17)

主引用文献

Mitjkova, E.,Tars, K.,Kalnins, G.
Chymotrypsin digestion analysis of glycyl radical and B12-dependent radical enzymes indicates common substrate-induced structural shifts.
Sci Rep, 2025

PubMed Abstract: Radical enzymes, including glycyl radical enzymes (GREs) and B12-dependent enzymes, catalyze a wide range of biochemical transformations through radical-based mechanisms. An unusual property-conditional resistance to chymotrypsin digestion-has previously been reported for two GREs. However, whether this feature is broadly conserved among related radical enzymes and what factors trigger it has remained unclear. In this study, we investigated five radical enzymes: four GREs and one B12-dependent diol dehydratase. Proteolytic assays demonstrated that substrate binding significantly enhances resistance to chymotrypsin degradation, suggesting a conserved conformational shift from an open, protease-sensitive state to a closed, protease-resistant form. X-ray crystallographic analysis of a GRE-type 1,2-propanediol dehydratase from Raoultella planticola confirmed that active site occupancy correlates with increased protease resistance. Importantly, non-substrate analogs such as 1,3-propanediol and β-methylcholine failed to induce protection, underscoring the specificity of ligand-induced stabilization. These findings reveal a broadly conserved mechanism of substrate-induced conformational stabilization in GREs and B12-dependent radical enzymes and offer a scalable strategy for ligand identification with potential applications in enzyme engineering.

PubMed: 41360885
DOI: 10.1038/s41598-025-28641-y

実験手法

X-RAY DIFFRACTION (1.9 Å)