Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation

Retaining glycoside hydrolases use acid/base catalysis with an enzymatic acid/base protonating the glycosidic bond oxygen to facilitate leaving-group departure alongside attack by a catalytic nucleophile to form a covalent intermediate. Generally, this acid/base protonates the oxygen laterally with...

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Autores: Pengthaisong, Salila, Piniello, Beatriz, Davies, Gideon J., Rovira i Virgili, Carme, Ketudat Cairns, James R.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2023
País:España
Institución:Universidad de Barcelona
Repositorio:Dipòsit Digital de la UB
OAI Identifier:oai:diposit.ub.edu:2445/217718
Acceso en línea:https://hdl.handle.net/2445/217718
Access Level:acceso abierto
Palabra clave:Hidrolases
Dinàmica molecular
Metabolisme dels glúcids
Hydrolases
Molecular dynamics
Carbohydrate metabolism
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spelling Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular ProtonationPengthaisong, SalilaPiniello, BeatrizDavies, Gideon J.Rovira i Virgili, CarmeKetudat Cairns, James R.HidrolasesDinàmica molecularMetabolisme dels glúcidsHydrolasesMolecular dynamicsCarbohydrate metabolismRetaining glycoside hydrolases use acid/base catalysis with an enzymatic acid/base protonating the glycosidic bond oxygen to facilitate leaving-group departure alongside attack by a catalytic nucleophile to form a covalent intermediate. Generally, this acid/base protonates the oxygen laterally with respect to the sugar ring, which places the catalytic acid/base and nucleophile carboxylates within about 4.5–6.5 Å of each other. However, in glycoside hydrolase (GH) family 116, including disease-related human acid β-glucosidase 2 (GBA2), the distance between the catalytic acid/base and the nucleophile is around 8 Å (PDB: 5BVU) and the catalytic acid/base appears to be above the plane of the pyranose ring, rather than being lateral to that plane, which could have catalytic consequences. However, no structure of an enzyme–substrate complex is available for this GH family. Here, we report the structures of Thermoanaerobacterium xylanolyticum β-glucosidase (TxGH116) D593N acid/base mutant in complexes with cellobiose and laminaribiose and its catalytic mechanism. We confirm that the amide hydrogen bonding to the glycosidic oxygen is in a perpendicular rather than lateral orientation. Quantum mechanics/molecular mechanics (QM/MM) simulations of the glycosylation half-reaction in wild-type TxGH116 indicate that the substrate binds with the nonreducing glucose residue in an unusual relaxed 4C1 chair at the –1 subsite. Nevertheless, the reaction can still proceed through a 4H3 half-chair transition state, as in classical retaining β-glucosidases, as the catalytic acid D593 protonates the perpendicular electron pair. The glucose C6OH is locked in a gauche, trans orientation with respect to the C5–O5 and C4–C5 bonds to facilitate perpendicular protonation. These data imply a unique protonation trajectory in Clan-O glycoside hydrolases, which has strong implications for the design of inhibitors specific to either lateral protonators, such as human GBA1, or perpendicular protonators, such as human GBA2.American Chemical Society2023info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfhttps://hdl.handle.net/2445/217718Articles publicats en revistes (Química Inorgànica i Orgànica)reponame:Dipòsit Digital de la UBinstname:Universidad de BarcelonaInglésReproducció del document publicat a: https://doi.org/10.1021/acscatal.3c00620ACS Catalysis, 2023, vol. 13, num.9, p. 5850-5863https://doi.org/10.1021/acscatal.3c00620cc-by (c) Pengthaisong, Salila, et al., 2023http://creativecommons.org/licenses/by/3.0/es/info:eu-repo/semantics/openAccessoai:diposit.ub.edu:2445/2177182026-05-27T06:46:51Z
dc.title.none.fl_str_mv Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation
title Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation
spellingShingle Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation
Pengthaisong, Salila
Hidrolases
Dinàmica molecular
Metabolisme dels glúcids
Hydrolases
Molecular dynamics
Carbohydrate metabolism
title_short Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation
title_full Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation
title_fullStr Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation
title_full_unstemmed Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation
title_sort Reaction Mechanism of Glycoside Hydrolase Family 116 Utilizes Perpendicular Protonation
dc.creator.none.fl_str_mv Pengthaisong, Salila
Piniello, Beatriz
Davies, Gideon J.
Rovira i Virgili, Carme
Ketudat Cairns, James R.
author Pengthaisong, Salila
author_facet Pengthaisong, Salila
Piniello, Beatriz
Davies, Gideon J.
Rovira i Virgili, Carme
Ketudat Cairns, James R.
author_role author
author2 Piniello, Beatriz
Davies, Gideon J.
Rovira i Virgili, Carme
Ketudat Cairns, James R.
author2_role author
author
author
author
dc.subject.none.fl_str_mv Hidrolases
Dinàmica molecular
Metabolisme dels glúcids
Hydrolases
Molecular dynamics
Carbohydrate metabolism
topic Hidrolases
Dinàmica molecular
Metabolisme dels glúcids
Hydrolases
Molecular dynamics
Carbohydrate metabolism
description Retaining glycoside hydrolases use acid/base catalysis with an enzymatic acid/base protonating the glycosidic bond oxygen to facilitate leaving-group departure alongside attack by a catalytic nucleophile to form a covalent intermediate. Generally, this acid/base protonates the oxygen laterally with respect to the sugar ring, which places the catalytic acid/base and nucleophile carboxylates within about 4.5–6.5 Å of each other. However, in glycoside hydrolase (GH) family 116, including disease-related human acid β-glucosidase 2 (GBA2), the distance between the catalytic acid/base and the nucleophile is around 8 Å (PDB: 5BVU) and the catalytic acid/base appears to be above the plane of the pyranose ring, rather than being lateral to that plane, which could have catalytic consequences. However, no structure of an enzyme–substrate complex is available for this GH family. Here, we report the structures of Thermoanaerobacterium xylanolyticum β-glucosidase (TxGH116) D593N acid/base mutant in complexes with cellobiose and laminaribiose and its catalytic mechanism. We confirm that the amide hydrogen bonding to the glycosidic oxygen is in a perpendicular rather than lateral orientation. Quantum mechanics/molecular mechanics (QM/MM) simulations of the glycosylation half-reaction in wild-type TxGH116 indicate that the substrate binds with the nonreducing glucose residue in an unusual relaxed 4C1 chair at the –1 subsite. Nevertheless, the reaction can still proceed through a 4H3 half-chair transition state, as in classical retaining β-glucosidases, as the catalytic acid D593 protonates the perpendicular electron pair. The glucose C6OH is locked in a gauche, trans orientation with respect to the C5–O5 and C4–C5 bonds to facilitate perpendicular protonation. These data imply a unique protonation trajectory in Clan-O glycoside hydrolases, which has strong implications for the design of inhibitors specific to either lateral protonators, such as human GBA1, or perpendicular protonators, such as human GBA2.
publishDate 2023
dc.date.none.fl_str_mv 2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/217718
url https://hdl.handle.net/2445/217718
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a: https://doi.org/10.1021/acscatal.3c00620
ACS Catalysis, 2023, vol. 13, num.9, p. 5850-5863
https://doi.org/10.1021/acscatal.3c00620
dc.rights.none.fl_str_mv cc-by (c) Pengthaisong, Salila, et al., 2023
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv cc-by (c) Pengthaisong, Salila, et al., 2023
http://creativecommons.org/licenses/by/3.0/es/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv American Chemical Society
publisher.none.fl_str_mv American Chemical Society
dc.source.none.fl_str_mv Articles publicats en revistes (Química Inorgànica i Orgànica)
reponame:Dipòsit Digital de la UB
instname:Universidad de Barcelona
instname_str Universidad de Barcelona
reponame_str Dipòsit Digital de la UB
collection Dipòsit Digital de la UB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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score 15,811543

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