Enzymatic Hydrolysis of Human Milk Oligosaccharides. The Molecular Mechanism of Bifidobacterium Bifidum Lacto-N-biosidase
Author
Cuxart, Irene
Coines, Joan
Esquivias, Oriol
Faijes, Magda
Planas, Antoni (Planas Sauter)
Biarnés Fontal, Xevi
Rovira, Carme
Other authors
Universitat Ramon Llull. IQS
Publication date
2022ISSN
2155-5435
Abstract
Bifidobacterium bifidum lacto-N-biosidase (LnbB) is a critical enzyme for the degradation of human milk oligosaccharides in the gut microbiota of breast-fed infants. Guided by recent crystal structures, we unveil its molecular mechanism of catalysis using QM/MM metadynamics. We show that the oligosaccharide substrate follows 1S3/1,4B → [4E]‡ → 4C1/4H5 and 4C1/4H5 → [4E/4H5]‡ → 1,4B conformational itineraries for the two successive reaction steps, with reaction free energy barriers in agreement with experiments. The simulations also identify a critical histidine (His263) that switches between two orientations to modulate the pKa of the acid/base residue, facilitating catalysis. The reaction intermediate of LnbB is best depicted as an oxazolinium ion, with a minor population of neutral oxazoline. The present study sheds light on the processing of oligosaccharides of the early life microbiota and will be useful for the engineering of LnbB and similar glycosidases for biocatalysis.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
547 - Organic chemistry
Keywords
Human milk oligosaccharides
Lacto-N-biosidase
Carbohydrates
Glycosidase
Quantum mechanics
Molecular mechanics
Metadynamics
Glicosidases
Hidrats de carboni
Llet materna
Pages
p.7
Publisher
American Chemical Society
Is part of
ACS Catalysis 2022, 12(8), 4737–4743
Grant agreement number
info:eu-repo/grantAgreement/MCIU/PN I+D/PID2019-104350RB-I00
info:eu-repo/grantAgreement/MCI/PN I+D/PID2020-118893GB-100
info:eu-repo/grantAgreement/MEIC/Unidades de excelencia María de Maeztu/MDM-2017-0767
info:eu-repo/grantAgreement/SUR del DEC/SGR/2017SGR-1189
info:eu-repo/grantAgreement/SUR del DEC/SGR/2017SGR-727
info:eu-repo/grantAgreement/EU/H2020/Grant agreement ID:814102
info:eu-repo/grantAgreement/EU/SyG/Grant agreement ID:95123
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Rights
© L'autor/a
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/4.0/