6GWF

Alpha-galactosidase mutant D387A from Thermotoga maritima in complex with intact cyclohexene-based carbasugar mimic of galactose with 2,4-dinitro leaving group

6GWF の概要

• エントリーDOI: 10.2210/pdb6gwf/pdb
• 関連するPDBエントリー: 6GTA 6GVD
• 分子名称: Alpha-galactosidase, SULFATE ION, (1~{S},2~{S},5~{S},6~{R})-5-(2,4-dinitrophenoxy)-6-fluoranyl-3-(hydroxymethyl)cyclohex-3-ene-1,2-diol, ... (5 entities in total)
• 機能のキーワード: glycoside hydrolase, galactosidase, carbohydrate processing enzyme, inhibitor, hydrolase
• 由来する生物種: Thermotoga maritima MSB8
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 66714.77

構造登録者

Gloster, T.M.,Oehler, V. (登録日: 2018-06-24, 公開日: 2018-08-22, 最終更新日: 2024-01-17)

主引用文献

Ren, W.,Pengelly, R.,Farren-Dai, M.,Shamsi Kazem Abadi, S.,Oehler, V.,Akintola, O.,Draper, J.,Meanwell, M.,Chakladar, S.,Swiderek, K.,Moliner, V.,Britton, R.,Gloster, T.M.,Bennet, A.J.
Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level.
Nat Commun, 9:3243-3243, 2018

PubMed Abstract: Mechanism-based glycoside hydrolase inhibitors are carbohydrate analogs that mimic the natural substrate's structure. Their covalent bond formation with the glycoside hydrolase makes these compounds excellent tools for chemical biology and potential drug candidates. Here we report the synthesis of cyclohexene-based α-galactopyranoside mimics and the kinetic and structural characterization of their inhibitory activity toward an α-galactosidase from Thermotoga maritima (TmGalA). By solving the structures of several enzyme-bound species during mechanism-based covalent inhibition of TmGalA, we show that the Michaelis complexes for intact inhibitor and product have half-chair (H) conformations for the cyclohexene fragment, while the covalently linked intermediate adopts a flattened half-chair (H) conformation. Hybrid QM/MM calculations confirm the structural and electronic properties of the enzyme-bound species and provide insight into key interactions in the enzyme-active site. These insights should stimulate the design of mechanism-based glycoside hydrolase inhibitors with tailored chemical properties.

PubMed: 30104598
DOI: 10.1038/s41467-018-05702-7

実験手法

X-RAY DIFFRACTION (1.72 Å)