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Computational Mechanistic Study of l-Aspartate Oxidase by ONIOM Method
[Image: see text] l-Aspartate oxidase (Laspo) is responsible for the oxidation of l-aspartate into iminoaspartate using flavin as a cofactor. During this process flavin is reduced, and it can be reoxidized by either molecular oxygen or fumarate. The overall fold and the catalytic residues of Laspo a...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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American Chemical Society
2023
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10249383/ https://www.ncbi.nlm.nih.gov/pubmed/37305300 http://dx.doi.org/10.1021/acsomega.3c01949 |
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author | Yildiz, Ibrahim |
author_facet | Yildiz, Ibrahim |
author_sort | Yildiz, Ibrahim |
collection | PubMed |
description | [Image: see text] l-Aspartate oxidase (Laspo) is responsible for the oxidation of l-aspartate into iminoaspartate using flavin as a cofactor. During this process flavin is reduced, and it can be reoxidized by either molecular oxygen or fumarate. The overall fold and the catalytic residues of Laspo are similar to succinate dehydrogenase and fumarate reductase. On the basis of deuterium kinetic isotope effects as well as other kinetic and structural data, it is proposed that the enzyme can catalyze the oxidation of l-aspartate through a mechanism similar to amino acid oxidases. It is suggested that a proton is removed from the α-amino group, while a hydride is transferred from C2 to flavin. It is also suggested that the hydride transfer is a rate-limiting step. However, there is still an ambiguity about the stepwise or concerted mechanism of hydride- and proton-transfer steps. In this study, we formulated some computational models to study the hydride-transfer mechanism using the crystal structure of Escherichia colil-aspartate oxidase in complexes with succinate. The calculations involved our own N-layered integrated molecular orbital and molecular mechanics method, and we evaluated the geometry and energetics of the hydride/proton-transfer processes while probing the roles of active site residues. Based on the calculations, it is concluded that proton- and hydride-transfer steps are decoupled, and a stepwise mechanism might be operative as opposed to the concerted one. |
format | Online Article Text |
id | pubmed-10249383 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-102493832023-06-09 Computational Mechanistic Study of l-Aspartate Oxidase by ONIOM Method Yildiz, Ibrahim ACS Omega [Image: see text] l-Aspartate oxidase (Laspo) is responsible for the oxidation of l-aspartate into iminoaspartate using flavin as a cofactor. During this process flavin is reduced, and it can be reoxidized by either molecular oxygen or fumarate. The overall fold and the catalytic residues of Laspo are similar to succinate dehydrogenase and fumarate reductase. On the basis of deuterium kinetic isotope effects as well as other kinetic and structural data, it is proposed that the enzyme can catalyze the oxidation of l-aspartate through a mechanism similar to amino acid oxidases. It is suggested that a proton is removed from the α-amino group, while a hydride is transferred from C2 to flavin. It is also suggested that the hydride transfer is a rate-limiting step. However, there is still an ambiguity about the stepwise or concerted mechanism of hydride- and proton-transfer steps. In this study, we formulated some computational models to study the hydride-transfer mechanism using the crystal structure of Escherichia colil-aspartate oxidase in complexes with succinate. The calculations involved our own N-layered integrated molecular orbital and molecular mechanics method, and we evaluated the geometry and energetics of the hydride/proton-transfer processes while probing the roles of active site residues. Based on the calculations, it is concluded that proton- and hydride-transfer steps are decoupled, and a stepwise mechanism might be operative as opposed to the concerted one. American Chemical Society 2023-05-25 /pmc/articles/PMC10249383/ /pubmed/37305300 http://dx.doi.org/10.1021/acsomega.3c01949 Text en © 2023 The Author. Published by American Chemical Society https://creativecommons.org/licenses/by-nc-nd/4.0/Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Yildiz, Ibrahim Computational Mechanistic Study of l-Aspartate Oxidase by ONIOM Method |
title | Computational Mechanistic
Study of l-Aspartate
Oxidase by ONIOM Method |
title_full | Computational Mechanistic
Study of l-Aspartate
Oxidase by ONIOM Method |
title_fullStr | Computational Mechanistic
Study of l-Aspartate
Oxidase by ONIOM Method |
title_full_unstemmed | Computational Mechanistic
Study of l-Aspartate
Oxidase by ONIOM Method |
title_short | Computational Mechanistic
Study of l-Aspartate
Oxidase by ONIOM Method |
title_sort | computational mechanistic
study of l-aspartate
oxidase by oniom method |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10249383/ https://www.ncbi.nlm.nih.gov/pubmed/37305300 http://dx.doi.org/10.1021/acsomega.3c01949 |
work_keys_str_mv | AT yildizibrahim computationalmechanisticstudyoflaspartateoxidasebyoniommethod |