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An Epoxide Intermediate in Glycosidase Catalysis

submitted on 02.09.2019, 01:35 and posted on 04.09.2019, 17:13 by Lukasz F. Sobala, Gaetano Speciale, Sha Zhu, Lluís Raich, Natalia Sannikova, Andrew J. Thompson, ZALIHE HAKKI, Dan Lu, Saeideh Shamsi Kazem Abadi, Andrew R. Lewis, Victor Rojas-Cervellera, Ganeko Bernardo-Seisdedos, Yongmin Zhang, Oscar Millet, Jesús Jiménez-Barbero, Andrew J. Bennett, Matthieu Sollogoub, Carme Rovira, Gideon J. Davies, Spencer Williams
Retaining glycoside hydrolases cleave their substrates through stereochemical retention at the anomeric position. Typically, this involves two-step mechanisms using either an enzymatic nucleophile via a covalent glycosyl enzyme intermediate, or neighboring group participation by a substrate-borne 2-acetamido neighboring group via an oxazoline intermediate; no enzymatic mechanism with participation of the sugar 2-hydroxyl has been reported. Here, we detail structural, computational and kinetic evidence for neighboring group participation by a mannose 2-hydroxyl in glycoside hydrolase family 99 endo-α-1,2-mannanases. We present a series of crystallographic snapshots of key species along the reaction coordinate: a Michaelis complex with a tetrasaccharide substrate; complexes with intermediate mimics, β-1,2-aziridine and β-1,2-epoxide; and a product complex. The 1,2-epoxide intermediate mimic displayed hydrolytic and transfer reactivity analogous to that expected for the 1,2-anhydro sugar intermediate supporting its catalytic equivalence. Quantum mechanics/molecular mechanics modelling of the reaction coordinate predicted a reaction pathway through a 1,2-anhydro sugar via a transition state in an unprecedented flattened, envelope (E3) conformation. Kinetic isotope effects for anomeric-2H and anomeric-13C support an oxocarbenium ion-like transition state and that for C2-18O (1.052 ± 0.006) directly implicates nucleophilic participation by the C2-hydroxyl. Collectively, these data substantiate this unprecedented and long-imagined enzymatic mechanism.


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Diamond Light Source

Agency for Management of University and Research Grants of Generalitat de Catalunya

Natural Sciences and Engineering Research Council of Canada


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University of Melbourne



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Declaration of Conflict of Interest

No conflict of interest

Version Notes

Version 1.1