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Conformational Itinerary of Sucrose During Hydrolysis by Retaining Amylosucrase
By means of QM(DFT)/MM metadynamics we have unraveled the hydrolytic reaction mechanism of Neisseria polysaccharea amylosucrase (NpAS), a member of GH13 family. Our results provide an atomistic picture of the active site reorganization along the catalytic double-displacement reaction, clarifying whe...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6502901/ https://www.ncbi.nlm.nih.gov/pubmed/31114783 http://dx.doi.org/10.3389/fchem.2019.00269 |
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author | Alonso-Gil, Santiago Coines, Joan André, Isabelle Rovira, Carme |
author_facet | Alonso-Gil, Santiago Coines, Joan André, Isabelle Rovira, Carme |
author_sort | Alonso-Gil, Santiago |
collection | PubMed |
description | By means of QM(DFT)/MM metadynamics we have unraveled the hydrolytic reaction mechanism of Neisseria polysaccharea amylosucrase (NpAS), a member of GH13 family. Our results provide an atomistic picture of the active site reorganization along the catalytic double-displacement reaction, clarifying whether the glycosyl-enzyme reaction intermediate features an α-glucosyl unit in an undistorted (4)C(1) conformation, as inferred from structural studies, or a distorted (1)S(3)-like conformation, as expected from mechanistic analysis of glycoside hydrolases (GHs). We show that, even though the first step of the reaction (glycosylation) results in a (4)C(1) conformation, the α-glucosyl unit undergoes an easy conformational change toward a distorted conformation as the active site preorganizes for the forthcoming reaction step (deglycosylation), in which an acceptor molecule, i.e., a water molecule for the hydrolytic reaction, performs a nucleophilic attack on the anomeric carbon. The two conformations ((4)C(1) ad E(3)) can be viewed as two different states of the glycosyl-enzyme intermediate (GEI), but only the E(3) state is preactivated for catalysis. These results are consistent with the general conformational itinerary observed for α-glucosidases. |
format | Online Article Text |
id | pubmed-6502901 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-65029012019-05-21 Conformational Itinerary of Sucrose During Hydrolysis by Retaining Amylosucrase Alonso-Gil, Santiago Coines, Joan André, Isabelle Rovira, Carme Front Chem Chemistry By means of QM(DFT)/MM metadynamics we have unraveled the hydrolytic reaction mechanism of Neisseria polysaccharea amylosucrase (NpAS), a member of GH13 family. Our results provide an atomistic picture of the active site reorganization along the catalytic double-displacement reaction, clarifying whether the glycosyl-enzyme reaction intermediate features an α-glucosyl unit in an undistorted (4)C(1) conformation, as inferred from structural studies, or a distorted (1)S(3)-like conformation, as expected from mechanistic analysis of glycoside hydrolases (GHs). We show that, even though the first step of the reaction (glycosylation) results in a (4)C(1) conformation, the α-glucosyl unit undergoes an easy conformational change toward a distorted conformation as the active site preorganizes for the forthcoming reaction step (deglycosylation), in which an acceptor molecule, i.e., a water molecule for the hydrolytic reaction, performs a nucleophilic attack on the anomeric carbon. The two conformations ((4)C(1) ad E(3)) can be viewed as two different states of the glycosyl-enzyme intermediate (GEI), but only the E(3) state is preactivated for catalysis. These results are consistent with the general conformational itinerary observed for α-glucosidases. Frontiers Media S.A. 2019-04-30 /pmc/articles/PMC6502901/ /pubmed/31114783 http://dx.doi.org/10.3389/fchem.2019.00269 Text en Copyright © 2019 Alonso-Gil, Coines, André and Rovira. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Chemistry Alonso-Gil, Santiago Coines, Joan André, Isabelle Rovira, Carme Conformational Itinerary of Sucrose During Hydrolysis by Retaining Amylosucrase |
title | Conformational Itinerary of Sucrose During Hydrolysis by Retaining Amylosucrase |
title_full | Conformational Itinerary of Sucrose During Hydrolysis by Retaining Amylosucrase |
title_fullStr | Conformational Itinerary of Sucrose During Hydrolysis by Retaining Amylosucrase |
title_full_unstemmed | Conformational Itinerary of Sucrose During Hydrolysis by Retaining Amylosucrase |
title_short | Conformational Itinerary of Sucrose During Hydrolysis by Retaining Amylosucrase |
title_sort | conformational itinerary of sucrose during hydrolysis by retaining amylosucrase |
topic | Chemistry |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6502901/ https://www.ncbi.nlm.nih.gov/pubmed/31114783 http://dx.doi.org/10.3389/fchem.2019.00269 |
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