5M03

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

5M03 の概要

• エントリーDOI: 10.2210/pdb5m03/pdb
• 関連するPDBエントリー: 4AD1 4AD2 4AD3 4AD4 4AD5 4UTF 4V27 4V28 5LYR
• 関連するBIRD辞書のPRD_ID: PRD_900111
• 分子名称: Glycosyl hydrolase family 71, alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose, ACETATE ION, ... (6 entities in total)
• 機能のキーワード: endomannanase endomannosidase gh99 noeuromycin hydrolase n-glycosylation glycosylation inhibitor inhibition shape charge mannobiose, 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: 44678.26

構造登録者

Petricevic, M.,Sobala, L.F.,Fernandes, P.Z.,Raich, L.,Thompson, A.J.,Bernardo-Seisdedos, G.,Millet, O.,Zhu, S.,Sollogoub, M.,Rovira, C.,Jimenez-Barbero, J.,Davies, G.J.,Williams, S.J. (登録日: 2016-10-03, 公開日: 2017-01-11, 最終更新日: 2024-01-17)

主引用文献

Petricevic, M.,Sobala, L.F.,Fernandes, P.Z.,Raich, L.,Thompson, A.J.,Bernardo-Seisdedos, G.,Millet, O.,Zhu, S.,Sollogoub, M.,Jimenez-Barbero, J.,Rovira, C.,Davies, G.J.,Williams, S.J.
Contribution of Shape and Charge to the Inhibition of a Family GH99 endo-alpha-1,2-Mannanase.
J. Am. Chem. Soc., 139:1089-1097, 2017

PubMed Abstract: Inhibitor design incorporating features of the reaction coordinate and transition-state structure has emerged as a powerful approach for the development of enzyme inhibitors. Such inhibitors find use as mechanistic probes, chemical biology tools, and therapeutics. Endo-α-1,2-mannosidases and endo-α-1,2-mannanases, members of glycoside hydrolase family 99 (GH99), are interesting targets for inhibitor development as they play key roles in N-glycan maturation and microbiotal yeast mannan degradation, respectively. These enzymes are proposed to act via a 1,2-anhydrosugar "epoxide" mechanism that proceeds through an unusual conformational itinerary. Here, we explore how shape and charge contribute to binding of diverse inhibitors of these enzymes. We report the synthesis of neutral dideoxy, glucal and cyclohexenyl disaccharide inhibitors, their binding to GH99 endo-α-1,2-mannanases, and their structural analysis by X-ray crystallography. Quantum mechanical calculations of the free energy landscapes reveal how the neutral inhibitors provide shape but not charge mimicry of the proposed intermediate and transition state structures. Building upon the knowledge of shape and charge contributions to inhibition of family GH99 enzymes, we design and synthesize α-Man-1,3-noeuromycin, which is revealed to be the most potent inhibitor (K 13 nM for Bacteroides xylanisolvens GH99 enzyme) of these enzymes yet reported. This work reveals how shape and charge mimicry of transition state features can enable the rational design of potent inhibitors.

PubMed: 27992199
DOI: 10.1021/jacs.6b10075

実験手法

X-RAY DIFFRACTION (1.05 Å)