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6FWQ

Structure of an E333Q variant of the GH99 endo-alpha-mannanase from Bacteroides xylanisolvens in complex with alpha-1,3-mannobiose and alpha-1,2-mannobiose

6FWQ の概要
エントリーDOI10.2210/pdb6fwq/pdb
関連するPDBエントリー6FWG 6FWI 6FWJ 6FWL 6FWM 6FWO 6FWP
関連するBIRD辞書のPRD_IDPRD_900111 PRD_900112
分子名称Glycosyl hydrolase family 71, alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose, alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose, ... (5 entities in total)
機能のキーワードhydrolase
由来する生物種Bacteroides xylanisolvens XB1A
タンパク質・核酸の鎖数1
化学式量合計44640.19
構造登録者
主引用文献Sobala, L.F.,Speciale, G.,Zhu, S.,Raich, L.,Sannikova, N.,Thompson, A.J.,Hakki, Z.,Lu, D.,Shamsi Kazem Abadi, S.,Lewis, A.R.,Rojas-Cervellera, V.,Bernardo-Seisdedos, G.,Zhang, Y.,Millet, O.,Jimenez-Barbero, J.,Bennet, A.J.,Sollogoub, M.,Rovira, C.,Davies, G.J.,Williams, S.J.
An Epoxide Intermediate in Glycosidase Catalysis.
Acs Cent.Sci., 6:760-770, 2020
Cited by
PubMed Abstract: Retaining glycoside hydrolases cleave their substrates through stereochemical retention at the anomeric position. Typically, this involves two-step mechanisms using either an enzymatic nucleophile via a covalent glycosyl enzyme intermediate or neighboring-group participation by a substrate-borne 2-acetamido neighboring group via an oxazoline intermediate; no enzymatic mechanism with participation of the sugar 2-hydroxyl has been reported. Here, we detail structural, computational, and kinetic evidence for neighboring-group participation by a mannose 2-hydroxyl in glycoside hydrolase family 99 -α-1,2-mannanases. We present a series of crystallographic snapshots of key species along the reaction coordinate: a Michaelis complex with a tetrasaccharide substrate; complexes with intermediate mimics, a sugar-shaped cyclitol β-1,2-aziridine and β-1,2-epoxide; and a product complex. The 1,2-epoxide intermediate mimic displayed hydrolytic and transfer reactivity analogous to that expected for the 1,2-anhydro sugar intermediate supporting its catalytic equivalence. Quantum mechanics/molecular mechanics modeling of the reaction coordinate predicted a reaction pathway through a 1,2-anhydro sugar via a transition state in an unusual flattened, envelope ( ) conformation. Kinetic isotope effects ( / ) for anomeric-H and anomeric-C support an oxocarbenium ion-like transition state, and that for C2-O (1.052 ± 0.006) directly implicates nucleophilic participation by the C2-hydroxyl. Collectively, these data substantiate this unprecedented and long-imagined enzymatic mechanism.
PubMed: 32490192
DOI: 10.1021/acscentsci.0c00111
主引用文献が同じPDBエントリー
実験手法
X-RAY DIFFRACTION (1.65 Å)
構造検証レポート
Validation report summary of 6fwq
検証レポート(詳細版)ダウンロードをダウンロード

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件を2025-06-18に公開中

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