9HMB

Crystal structure of GH139 glycoside hydrolase from Verrucomicrobium sp. in the hexagonal space group P6522

9HMB の概要

• エントリーDOI: 10.2210/pdb9hmb/pdb
• 分子名称: DUF5703 domain-containing protein, GLYCEROL (3 entities in total)
• 機能のキーワード: alpha-l-fucosidase glycosyl hydrolase gh139, hydrolase
• 由来する生物種: Verrucomicrobium sp.
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 88830.86

構造登録者

Moraleda-Montoya, A.,Garcia-Alija, M.,Trastoy, B.,Guerin, M. (登録日: 2024-12-08, 公開日: 2025-07-02, 最終更新日: 2025-07-30)

主引用文献

McIver, Z.,Moraleda-Montoya, A.,Chen, Z.,Epa, R.,Starns, D.,Davy, M.,Garcia-Alija, M.,Basle, A.,Schubert, M.,Ndeh, D.,Trastoy, B.,Williams, S.J.,Guerin, M.E.,Cartmell, A.
Understanding the substrate recognition and catalytic mechanism of 2-O-methyl fucosidases from glycoside hydrolase family 139.
J.Biol.Chem., 301:110407-110407, 2025

PubMed Abstract: Rhamnogalacturonan II is one of the most complex plant cell wall carbohydrates and is composed of 13 different sugars and 21 different glycosidic linkages. It is abundant in fruit and indulgence foods, such as chocolate and wine, making it common in the human diet. The human colonic commensal Bacteroides thetaiotaomicron expresses a consortium of 22 enzymes to metabolize rhamnogalacturonan II, some of which exclusively target sugars unique to rhamnogalacturonan II. Several of these enzyme families remain poorly described, and, consequently, our knowledge of rhamnogalacturonan II metabolism is limited. Chief among the poorly understood activities is glycoside hydrolase (GH) family 139, which targets α1,2-2O-methyl L-fucoside linkages, a sugar residue not found in any other plant cell wall complex glycans. Although the founding enzyme BT0984 was placed in the RG-II degradative pathway, no GH139 structure or catalytic blueprint had been available. We report the crystal structures of BT0984 and a second homolog revealing that the family operates with inverting stereochemistry. Using these data, we undertook a mutagenic strategy, backed by molecular dynamics, to identify the important substrate binding and catalytic residues, mapping these residues throughout the GH139 family revealing the importance of the O2 methyl interaction of the substrate. We propose a catalytic mechanism that uses a non-canonical Asn as a catalytic base and shares similarity with L-fucosidases/L-galactosidases of family GH95.

PubMed: 40544995
DOI: 10.1016/j.jbc.2025.110407

実験手法

X-RAY DIFFRACTION (2.05 Å)