Two distinct catalytic pathways for GH43 xylanolytic enzymes unveiled by X-ray and QM/MM simulations

• Published in: Nature communications 2021-01, Vol.12 (1), p.367-367, Article 367
• Main Authors: Morais, Mariana A. B., Coines, Joan, Domingues, Mariane N., Pirolla, Renan A. S., Tonoli, Celisa C. C., Santos, Camila R., Correa, Jessica B. L., Gozzo, Fabio C., Rovira, Carme, Murakami, Mario T.
• Format: Article
• Language: English
• Subjects: 119/118; 631/114/2411; 631/45/173; 631/45/221; 631/535/1266; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Binding Sites; Breakdown; Calcium; Carbohydrates; Catalysis; Catalytic Domain; Computer applications; Crystal structure; Crystallography, X-Ray; Ductile-brittle transition; Enzymes; Glycosidases; Glycoside hydrolase; Glycoside Hydrolases - chemistry; Glycoside Hydrolases - genetics; Glycoside Hydrolases - metabolism; Glycosides; Hemicellulose; Humanities and Social Sciences; Hydrolase; Hydrolysis; Kinetics; Models, Molecular; multidisciplinary; Oligosaccharides - chemistry; Oligosaccharides - metabolism; Open architectures; Science; Science (multidisciplinary); Structural analysis; Structure-function relationships; Substrate inhibition; Substrates; Xanthomonas - chemistry; Xanthomonas - enzymology; Xanthomonas - genetics; Xylose - chemistry; Xylose - metabolism
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-20620-3

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. Family 43 glycoside hydrolases (GH43) are involved in the breakdown of hemicellulose. Functional, structural and computational characterization of a GH43 enzyme, including a snapshot of an active Michaelis complex, reveal the hydrolysis mechanism and suggest two possible reaction pathways.