7OJ5

Cryo-EM structure of Medicago truncatula HISN5 protein

7OJ5 の概要

• エントリーDOI: 10.2210/pdb7oj5/pdb
• EMDBエントリー: 12938
• 分子名称: Imidazoleglycerol-phosphate dehydratase, MANGANESE (II) ION (3 entities in total)
• 機能のキーワード: histidine biosynthesis, herbicide design, high-resolution cryo-em, lyase
• 由来する生物種: Medicago truncatula (Barrel medic, Medicago tribuloides)
• タンパク質・核酸の鎖数: 24
• 化学式量合計: 547255.90

構造登録者

Ruszkowski, M.,Witek, W. (登録日: 2021-05-13, 公開日: 2021-06-02, 最終更新日: 2024-10-30)

主引用文献

Witek, W.,Sliwiak, J.,Rawski, M.,Ruszkowski, M.
Targeting imidazole-glycerol phosphate dehydratase in plants: novel approach for structural and functional studies, and inhibitor blueprinting.
Front Plant Sci, 15:1343980-1343980, 2024

PubMed Abstract: The histidine biosynthetic pathway (HBP) is targeted for herbicide design with preliminary success only regarding imidazole-glycerol phosphate dehydratase (IGPD, EC 4.2.1.19), or HISN5, as referred to in plants. HISN5 catalyzes the sixth step of the HBP, in which imidazole-glycerol phosphate (IGP) is dehydrated to imidazole-acetol phosphate. In this work, we present high-resolution cryoEM and crystal structures of HISN5 (HISN5) in complexes with an inactive IGP diastereoisomer and with various other ligands. HISN5 can serve as a new model for plant HISN5 structural studies, as it enables resolving protein-ligand interactions at high (2.2 Å) resolution using cryoEM. We identified ligand-binding hotspots and characterized the features of plant HISN5 enzymes in the context of the HISN5-targeted inhibitor design. Virtual screening performed against millions of small molecules not only revealed candidate molecules but also identified linkers for fragments that were experimentally confirmed to bind. Based on experimental and computational approaches, this study provides guidelines for designing symmetric HISN5 inhibitors that can reach two neighboring active sites. Finally, we conducted analyses of sequence similarity networks revealing that plant HISN5 enzymes derive from cyanobacteria. We also adopted a new approach to measure HISN5 enzymatic activity using isothermal titration calorimetry and enzymatically synthesized IGP.

PubMed: 38559763
DOI: 10.3389/fpls.2024.1343980

実験手法

ELECTRON MICROSCOPY (2.4 Å)