@article{f5bee985d87e49a0923a8e6ebce9cb73,
title = "Enzymatic Hydrolysis of Human Milk Oligosaccharides. The Molecular Mechanism of Bifidobacterium Bifidum Lacto- N-biosidase",
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]‡→ 4C1/4H5and 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 pKaof 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.",
keywords = "carbohydrates, glycosidases, human milk oligosaccharides, lacto- N-biosidase, metadynamics, quantum mechanics/molecular mechanics",
author = "Irene Cuxart and Joan Coines and Oriol Esquivias and Magda Faijes and Antoni Planas and Xevi Biarn{\'e}s and Carme Rovira",
note = "Funding Information: We thank the Spanish Ministry of Science, Innovation and Universities (MICINN/AEI/FEDER, UE, PID2020-118893GB-100 to C.R. and PID2019-104350RB-I00 to A.P.), the Spanish Structures of Excellence Mar{\'i}a de Maeztu (MDM-2017-0767 to C.R.), the Agency for Management of University and Research Grants of Generalitat de Catalunya (AGAUR, 2017SGR-1189 to C.R. and 2017SGR-727 to A.P.), the European Research Council (ERC-2020-SyG-95123 “CARBOCENTRE” to C.R.) and the Marie Sk{\l}odowska-Curie Innovative Training Networks (H2020-MSCA-ITN-2018–814102 “Sweet Crosstalk” to C. R.). The authors thank the technical support provided by the Barcelona Supercomputing Center (BSC) and Red Nacional de Supercomputaci{\'o}n (RES) for computer resources at MareNostrum IV and CTE-Power supercomputers. I.C. and O.E. acknowledge predoctoral fellowshisp from MICINN (ref PRE2019-089272 and PRE2018-083184 respectively). Funding Information: We thank the Spanish Ministry of Science, Innovation and Universities (MICINN/AEI/FEDER, UE, PID2020-118893GB-100 to C.R. and PID2019-104350RB-I00 to A.P.), the Spanish Structures of Excellence Mari?a de Maeztu (MDM-2017-0767 to C.R.), the Agency for Management of University and Research Grants of Generalitat de Catalunya (AGAUR 2017SGR-1189 to C.R. and 2017SGR-727 to A.P.), the European Research Council (ERC-2020-SyG-95123 {"}CARBOCENTRE{"} to C.R.) and the Marie Sk?odowska-Curie Innovative Training Networks (H2020-MSCA-ITN-2018?814102 {"}Sweet Crosstalk{"} to C. R.). The authors thank the technical support provided by the Barcelona Supercomputing Center (BSC) and Red Nacional de Supercomputacio?n (RES) for computer resources at MareNostrum IV and CTE-Power supercomputers. I.C. and O.E. acknowledge predoctoral fellowshisp from MICINN (ref PRE2019-089272 and PRE2018-083184 respectively). Publisher Copyright: {\textcopyright} 2022 American Chemical Society. All rights reserved.",
year = "2022",
month = apr,
day = "15",
doi = "10.1021/acscatal.2c00309",
language = "English",
volume = "12",
pages = "4737--4743",
journal = "ACS Catalysis",
issn = "2155-5435",
publisher = "American Chemical Society",
number = "8",
}