6XN2

Crystal structure of the GH43_1 enzyme from Xanthomonas citri complexed with xylotriose

6XN2 の概要

• エントリーDOI: 10.2210/pdb6xn2/pdb
• 関連するBIRD辞書のPRD_ID: PRD_900117
• 分子名称: Xylosidase, beta-D-xylopyranose-(1-4)-beta-D-xylopyranose-(1-4)-beta-D-xylopyranose, CALCIUM ION, ... (7 entities in total)
• 機能のキーワード: glycoside hydrolase, gh43, hydrolase
• 由来する生物種: Xanthomonas axonopodis pv. citri (strain 306)
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 82235.07

構造登録者

Morais, M.A.B.,Tonoli, C.C.C.,Santos, C.R.,Murakami, M.T. (登録日: 2020-07-02, 公開日: 2020-12-02, 最終更新日: 2023-10-18)

主引用文献

Morais, M.A.B.,Coines, J.,Domingues, M.N.,Pirolla, R.A.S.,Tonoli, C.C.C.,Santos, C.R.,Correa, J.B.L.,Gozzo, F.C.,Rovira, C.,Murakami, M.T.
Two distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X-ray and QM/MM simulations.
Nat Commun, 12:367-367, 2021

PubMed Abstract: Xylanolytic enzymes from glycoside hydrolase family 43 (GH43) are involved in the breakdown of hemicellulose, the second most abundant carbohydrate in plants. Here, we kinetically and mechanistically describe the non-reducing-end xylose-releasing exo-oligoxylanase activity and report the crystal structure of a native GH43 Michaelis complex with its substrate prior to hydrolysis. Two distinct calcium-stabilized conformations of the active site xylosyl unit are found, suggesting two alternative catalytic routes. These results are confirmed by QM/MM simulations that unveil the complete hydrolysis mechanism and identify two possible reaction pathways, involving different transition state conformations for the cleavage of xylooligosaccharides. Such catalytic conformational promiscuity in glycosidases is related to the open architecture of the active site and thus might be extended to other exo-acting enzymes. These findings expand the current general model of catalytic mechanism of glycosidases, a main reaction in nature, and impact on our understanding about their interaction with substrates and inhibitors.

PubMed: 33446650
DOI: 10.1038/s41467-020-20620-3

実験手法

X-RAY DIFFRACTION (1.652 Å)