Oxazoline Or Oxazolinium Ion? The Protonation State and Conformation of the Reaction Intermediate of Chitinase Enzymes Revisited

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Oxazoline Or Oxazolinium Ion? The Protonation State and Conformation of the Reaction Intermediate of Chitinase Enzymes Revisited

Joan Coines 1 , Mercedes Alfonso-Prieto 1 , Xevi Biarnés 2 , Antoni Planas 2 , Carme Rovira 1,3

1 Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB) , Barcelona, Spain, 2 Laboratory of Biochemistry, Institut Químic de Sarrià. Universitat Ramon Llull, Barcelona, Spain, 3 Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain

Chitinases are glycosidases responsible for cleaving the glycosidic bond of chitin, one of the most abundant carbohydrates in nature. These enzymes have gained interest because of their medical and industrial applications.[1] Family GH18 chitinases, unlike most retaining glycosidases,[2] follow a substrate-assisted mechanism in which the 2-acetamido group of the N-acetylglucosamine located at the -1 subsite reacts with the sugar anomeric carbon, forming an intermediate which is commonly described as an oxazolinium ion.[3,4] By means of QM/MM metadynamics simulations on chitinase B from Serratia marcescens, we analyzed the entire reaction mechanism, showing that the reaction intermediate features a neutral oxazoline, with an oxazolinium ion being formed only on the pathway toward the reaction products. The role of a well-defined hydrogen bond network that orchestrates catalysis by protonation events, is discussed.[5]

Reaction intermediate of GH18 chitinase B from Serratia marcescens obtained from QM/MM simulations.

Adrangi, S.; Faramarzi, M. A. From Bacteria to Human: A Journey into the World of Chitinases. Biotechnol. Adv. 2013, 31 (8), 1786–1785.

Ardèvol, A.; Rovira, C. Reaction Mechanisms in Carbohydrate-Active Enzymes: Glycoside Hydrolases and Glycosyltransferases. Insights from First Principles QM/MM Molecular Dynamics Simulations. J. Am. Chem. Soc. 2015, 137, 7528–7547.

van Aalten, D. M.; Komander, D.; Synstad, B.; Gåseidnes, S.; Peter, M. G.; Eijsink, V. G. Structural Insights into the Catalytic Mechanism of a Family 18 Exo-Chitinase. Proc. Natl. Acad. Sci. U. S. A. 2001, 98 (16), 8979–8984.

Jitonnom, J.; Lee, V. S.; Nimmanpipug, P.; Rowlands, H. a.; Mulholland, A. J. Quantum Mechanics/Molecular Mechanics Modeling of Substrate-Assisted Catalysis in Family 18 Chitinases: Conformational Changes and the Role of Asp142 in Catalysis in ChiB. Biochemistry 2011, 50 (21), 4697–4711.

Coines, J.; Alfonso-Prieto, M.; Biarnés, X.; Planas, A.; Rovira, C. Oxazoline or Oxazolinium Ion? The Protonation State and Conformation of the Reaction Intermediate of Chitinase Enzymes Revisited. Chem. – A Eur. J. 2018, 24, 19258–19265.

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