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

Autor(es)

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]

Afiliação do(s) autor(es)

^[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

• Tipo de documento: Artigo Científico
• Fonte: NATURE COMMUNICATIONS; v. 12, n. 1 JAN 14 2021.
• Citações Web of Science: 0

Resumo

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)

• Processo FAPESP: 18/22138-8 - Desvendando o papel do cálcio na catálise de beta-xilosidases / alfa-L-arabinofuranosidases da família GH43 através de métodos de dinâmica molecular "QM / MM"
• Beneficiário: Mariana Abrahão Bueno de Morais
• Modalidade de apoio: Bolsas no Exterior - Estágio de Pesquisa - Pós-Doutorado
• Processo FAPESP: 16/19995-0 - Análise da diversidade estrutural e funcional das enzimas pertencentes à família GH43 em Xanthomonas axonopodis pv. citri: implicações biológicas e possíveis aplicações biotecnológicas
• Beneficiário: Mariana Abrahão Bueno de Morais
• Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado
• Processo FAPESP: 15/26982-0 - Explorando novas estratégias para a despolimerização de polissacarídeos da parede celular vegetal: da estrutura, função e desenho racional de hidrolases glicosídicas às implicações biológicas e potenciais aplicações biotecnológicas
• Beneficiário: Mário Tyago Murakami
• Modalidade de apoio: Auxílio à Pesquisa - Temático