2ZQ0

Crystal structure of SusB complexed with acarbose

2ZQ0 の概要

• エントリーDOI: 10.2210/pdb2zq0/pdb
• 関連するPDBエントリー: 2D73
• 関連するBIRD辞書のPRD_ID: PRD_900007
• 分子名称: Alpha-glucosidase (Alpha-glucosidase SusB), 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose, CALCIUM ION, ... (4 entities in total)
• 機能のキーワード: glycoside hydrolase family 97, tim barrel, hydrolase
• 由来する生物種: Bacteroides thetaiotaomicron
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 170208.49

構造登録者

Yao, M.,Tanaka, I.,Kitamura, M. (登録日: 2008-07-31, 公開日: 2008-10-28, 最終更新日: 2023-11-01)

主引用文献

Kitamura, M.,Okuyama, M.,Tanzawa, F.,Mori, H.,Kitago, Y.,Watanabe, N.,Kimura, A.,Tanaka, I.,Yao, M.
Structural and functional analysis of a glycoside hydrolase family 97 enzyme from Bacteroides thetaiotaomicron.
J.Biol.Chem., 283:36328-36337, 2008

PubMed Abstract: SusB, an 84-kDa alpha-glucoside hydrolase involved in the starch utilization system (sus) of Bacteroides thetaiotaomicron, belongs to glycoside hydrolase (GH) family 97. We have determined the enzymatic characteristics and the crystal structures in free and acarbose-bound form at 1.6A resolution. SusB hydrolyzes the alpha-glucosidic linkage, with inversion of anomeric configuration liberating the beta-anomer of glucose as the reaction product. The substrate specificity of SusB, hydrolyzing not only alpha-1,4-glucosidic linkages but also alpha-1,6-, alpha-1,3-, and alpha-1,2-glucosidic linkages, is clearly different from other well known glucoamylases belonging to GH15. The structure of SusB was solved by the single-wavelength anomalous diffraction method with sulfur atoms as anomalous scatterers using an in-house x-ray source. SusB includes three domains as follows: the N-terminal, catalytic, and C-terminal domains. The structure of the SusB-acarbose complex shows a constellation of carboxyl groups at the catalytic center; Glu532 is positioned to provide protonic assistance to leaving group departure, with Glu439 and Glu508 both positioned to provide base-catalyzed assistance for inverting nucleophilic attack by water. A structural comparison with other glycoside hydrolases revealed significant similarity between the catalytic domain of SusB and those of alpha-retaining glycoside hydrolases belonging to GH27, -36, and -31 despite the differences in catalytic mechanism. SusB and the other retaining enzymes appear to have diverged from a common ancestor and individually acquired the functional carboxyl groups during the process of evolution. Furthermore, sequence comparison of the active site based on the structure of SusB indicated that GH97 included both retaining and inverting enzymes.

PubMed: 18981178
DOI: 10.1074/jbc.M806115200

実験手法

X-RAY DIFFRACTION (1.6 Å)