1K9D

The 1.7 A crystal structure of alpha-D-glucuronidase, a family-67 glycoside hydrolase from Bacillus stearothermophilus T-1

1K9D の概要

• エントリーDOI: 10.2210/pdb1k9d/pdb
• 関連するPDBエントリー: 1K9E 1K9F
• 分子名称: alpha-D-glucuronidase, GLYCEROL (3 entities in total)
• 機能のキーワード: hydrolase
• 由来する生物種: Geobacillus stearothermophilus
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 79776.46

構造登録者

Golan, G.,Shallom, D.,Teplitsky, A.,Zaide, G.,Shulami, S.,Baasov, T.,Stojanoff, V.,Thompson, A.,Shoham, Y.,Shoham, G. (登録日: 2001-10-29, 公開日: 2002-10-29, 最終更新日: 2024-04-03)

主引用文献

Golan, G.,Shallom, D.,Teplitsky, A.,Zaide, G.,Shulami, S.,Baasov, T.,Stojanoff, V.,Thompson, A.,Shoham, Y.,Shoham, G.
Crystal Structures of Geobacillus stearothermophilus {alpha}-Glucuronidase Complexed with Its Substrate and Products: MECHANISTIC IMPLICATIONS.
J.Biol.Chem., 279:3014-3024, 2004

PubMed Abstract: Alpha-glucuronidases cleave the alpha-1,2-glycosidic bond between 4-O-methyl-d-glucuronic acid and short xylooligomers as part of the hemicellulose degradation system. To date, all of the alpha-glucuronidases are classified as family 67 glycosidases, which catalyze the hydrolysis via the investing mechanism. Here we describe several high resolution crystal structures of the alpha-glucuronidase (AguA) from Geobacillus stearothermophilus, in complex with its substrate and products. In the complex of AguA with the intact substrate, the 4-O-methyl-d-glucuronic acid sugar ring is distorted into a half-chair conformation, which is closer to the planar conformation required for the oxocarbenium ion-like transition state structure. In the active site, a water molecule is coordinated between two carboxylic acids, in an appropriate position to act as a nucleophile. From the structural data it is likely that two carboxylic acids, Asp(364) and Glu(392), activate together the nucleophilic water molecule. The loop carrying the catalytic general acid Glu(285) cannot be resolved in some of the structures but could be visualized in its "open" and "closed" (catalytic) conformations in other structures. The protonated state of Glu(285) is presumably stabilized by its proximity to the negative charge of the substrate, representing a new variation of substrate-assisted catalysis mechanism.

PubMed: 14573597
DOI: 10.1074/jbc.M310098200

実験手法

X-RAY DIFFRACTION (1.7 Å)