8HJ8

Crystal structure of barley exohydrolase isoform ExoI E220A mutant in complex with 2-deoxy-2-fluoro-D-glucopyranosides

8HJ8 の概要

• エントリーDOI: 10.2210/pdb8hj8/pdb
• 関連するPDBエントリー: 1IEW 3WLI
• 分子名称: Glyco_hydro_3 domain-containing protein, 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-deoxy-2-fluoro-alpha-D-glucopyranose, ... (8 entities in total)
• 機能のキーワード: barley exohydrolasei, hydrolase, enzyme function
• 由来する生物種: Hordeum vulgare
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 68262.09

構造登録者

Luang, S.,Streltsov, V.A.,Hrmova, M. (登録日: 2022-11-22, 公開日: 2024-12-25, 最終更新日: 2025-05-21)

主引用文献

Luang, S.,Fernandez-Luengo, X.,Streltsov, V.A.,Marechal, J.D.,Masgrau, L.,Hrmova, M.
The structure and dynamics of water molecule networks underlie catalytic efficiency in a glycoside exo-hydrolase.
Commun Biol, 8:729-729, 2025

PubMed Abstract: Glycoside hydrolases break glycosidic bonds by transferring a water molecule onto the glycosidic oxygen of carbohydrates, but on the nanoscale, the dynamics of water molecules remains unclear. We investigate the role of the non-nucleophilic E220 glutamate, essential for maintaining the water molecule network in a family 3 β-D-glucan glucohydrolase, but not involved directly in catalysis. Kinetic data disclose that the E220A mutant retains substrate poly-specificity but has drastically reduced catalytic efficiency compared to the wild-type. High-resolution structures in-complex with a hydrolytic product and a mechanism-based inhibitor reveal that in wild-type, the concatenated water molecules near acid/base E491 and neighbouring N219 and E220 form a harmonised network. In contrast, in the E220A mutant, this network is uncoordinated. Computational models of covalent complexes show that water flux through the wild-type protein correlates with high catalytic efficiency dissimilar to E220A, where this correlation is lost. Ancestral sequence reconstructions of family 3 enzymes divulge the evolutionary conservation of residues participating in water molecule networks, which underlie substrate-product-assisted processivity. Our findings provide a blueprint for the dynamics of catalysis mediated by hydrolytic enzymes, which could inspire bioengineering to create a sustainable bio-economy.

PubMed: 40348901
DOI: 10.1038/s42003-025-08113-9

実験手法

X-RAY DIFFRACTION (1.95 Å)