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

Author(s)

Morais, Mariana A. B. ^{[1, 2, 3]} ; Coines, Joan ^{[2, 3]} ; Domingues, Mariane N. ^[1] ; Pirolla, Renan A. S. ^[1] ; Tonoli, Celisa C. C. ^[4] ; Santos, Camila R. ^[1] ; Correa, Jessica B. L. ^[1] ; Gozzo, Fabio C. ^[5] ; Rovira, Carme ^{[2, 3, 6]} ; Murakami, Mario T. ^[1]

Affiliation

^[1] Brazilian Ctr Res Energy & Mat CNPEM, Brazilian Biorenewables Natl Lab LNBR, BR-13083100 Campinas - Brazil

^[2] Univ Barcelona, Dept Quim Inorgan & Organ, Barcelona 08028 - Spain

^[3] Univ Barcelona, Inst Quim Teor & Computac IQTCUB, Barcelona 08028 - Spain

^[4] Brazilian Ctr Res Energy & Mat CNPEM, Brazilian Biosci Natl Lab LNBio, BR-13083100 Campinas - Brazil

^[5] Univ Estadual Campinas, Inst Chem, Dalton Mass Spectrometry Lab, BR-13083970 Campinas - Brazil

^[6] Inst Catalana Recerca & Estudis Avancats ICREA, Barcelona 08010 - Spain

• Document type: Journal article
• Source: NATURE COMMUNICATIONS; v. 12, n. 1 JAN 14 2021.
• Web of Science Citations: 0

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. 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. (AU)

• FAPESP's process: 18/22138-8 - Unveiling the calcium role on GH43 beta-xylosidases / alpha-L-arabinofuranosidases catalysis by QM/MM molecular dynamics methods
• Grantee: Mariana Abrahão Bueno de Morais
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor
• FAPESP's process: 16/19995-0 - Analysis of structural and functional diversity of GH43 enzymes from Xanthomonas axonopodis pv. citri: biological implications and potential biotechnological applications
• Grantee: Mariana Abrahão Bueno de Morais
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 15/26982-0 - Exploring novel strategies for depolymerization of plant cell-wall polysaccharides: from structure, function and rational design of glycosyl hydrolases to biological implications and potential biotechnological applications
• Grantee: Mário Tyago Murakami
• Support Opportunities: Research Projects - Thematic Grants