2EAE

Crystal structure of 1,2-a-L-fucosidase from Bifidobacterium bifidum in complexes with products

2EAE の概要

• エントリーDOI: 10.2210/pdb2eae/pdb
• 関連するPDBエントリー: 2EAB 2EAC 2EAD 2EAF
• 関連するBIRD辞書のPRD_ID: PRD_900008
• 分子名称: Alpha-fucosidase, beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose, alpha-L-fucopyranose, ... (6 entities in total)
• 機能のキーワード: fucosidase, glycoside hydrolase, hydrolase
• 由来する生物種: Bifidobacterium bifidum
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 97546.76

構造登録者

Nagae, M.,Tsuchiya, A.,Katayama, T.,Yamamoto, K.,Wakatsuki, S.,Kato, R. (登録日: 2007-01-31, 公開日: 2007-04-24, 最終更新日: 2024-05-29)

主引用文献

Nagae, M.,Tsuchiya, A.,Katayama, T.,Yamamoto, K.,Wakatsuki, S.,Kato, R.
Structural basis on the catalytic reaction mechanism of novel 1,2-alpha-L-fucosidase (AFCA) from Bifidobacterium bifidum
J.Biol.Chem., 282:18497-18509, 2007

PubMed Abstract: 1,2-alpha-L-fucosidase (AfcA), which hydrolyzes the glycosidic linkage of Fucalpha1-2Gal via an inverting mechanism, was recently isolated from Bifidobacterium bifidum and classified as the first member of the novel glycoside hydrolase family 95. To better understand the molecular mechanism of this enzyme, we determined the x-ray crystal structures of the AfcA catalytic (Fuc) domain in unliganded and complexed forms with deoxyfuconojirimycin (inhibitor), 2'-fucosyllactose (substrate), and L-fucose and lactose (products) at 1.12-2.10 A resolution. The AfcA Fuc domain is composed of four regions, an N-terminal beta region, a helical linker, an (alpha/alpha)6 helical barrel domain, and a C-terminal beta region, and this arrangement is similar to bacterial phosphorylases. In the complex structures, the ligands were buried in the central cavity of the helical barrel domain. Structural analyses in combination with mutational experiments revealed that the highly conserved Glu566 probably acts as a general acid catalyst. However, no carboxylic acid residue is found at the appropriate position for a general base catalyst. Instead, a water molecule stabilized by Asn423 in the substrate-bound complex is suitably located to perform a nucleophilic attack on the C1 atom of L-fucose moiety in 2'-fucosyllactose, and its location is nearly identical near the O1 atom of beta-L-fucose in the products-bound complex. Based on these data, we propose and discuss a novel catalytic reaction mechanism of AfcA.

PubMed: 17459873
DOI: 10.1074/jbc.M702246200

実験手法

X-RAY DIFFRACTION (1.8 Å)