Theoretical Studies on Mechanism of Inactivation of Kanamycin A by 4′-O-Nucleotidyltransferase
This work is focused on mechanistic studies of the transfer of an adenylyl group (Adenoside-5′-monophosfate) from adenosine 5′-triphosphate (ATP) to a OH-4′ hydroxyl group of an antibiotic. Using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques, we study the substrate and base-assiste...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-01-01
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| Series: | Frontiers in Chemistry |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fchem.2018.00660/full |
| _version_ | 1819157174331375616 |
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| author | Sergio Martí Agatha Bastida Katarzyna Świderek |
| author_facet | Sergio Martí Agatha Bastida Katarzyna Świderek |
| author_sort | Sergio Martí |
| collection | DOAJ |
| description | This work is focused on mechanistic studies of the transfer of an adenylyl group (Adenoside-5′-monophosfate) from adenosine 5′-triphosphate (ATP) to a OH-4′ hydroxyl group of an antibiotic. Using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques, we study the substrate and base-assisted mechanisms of the inactivation process of kanamycin A (KAN) catalyzed by 4′-O-Nucleotidyltransferase [ANT(4′)], an active enzyme against almost all aminoglycoside antibiotics. Free energy surfaces, obtained with Free Energy Perturbation methods at the M06-2X/MM level of theory, show that the most favorable reaction path presents a barrier of 12.2 kcal·mol−1 that corresponds to the concerted activation of O4′ from KAN by Glu145. In addition, the primary and secondary 18O kinetic isotope effects (KIEs) have been computed for bridge O3α, and non-bridge O1α, O2α, and O5′ atoms of ATP. The observed normal 1°-KIE of 1.2% and 2°-KIE of 0.07% for the Glu145-assisted mechanism are in very good agreement with experimentally measured data. Additionally, based on the obtained results, the role of electrostatic and compression effects in enzymatic catalysis is discussed. |
| first_indexed | 2024-12-22T16:04:34Z |
| format | Article |
| id | doaj.art-22c0140b8bc6440fade62ede61df8e64 |
| institution | Directory Open Access Journal |
| issn | 2296-2646 |
| language | English |
| last_indexed | 2024-12-22T16:04:34Z |
| publishDate | 2019-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Chemistry |
| spelling | doaj.art-22c0140b8bc6440fade62ede61df8e642022-12-21T18:20:37ZengFrontiers Media S.A.Frontiers in Chemistry2296-26462019-01-01610.3389/fchem.2018.00660438560Theoretical Studies on Mechanism of Inactivation of Kanamycin A by 4′-O-NucleotidyltransferaseSergio Martí0Agatha Bastida1Katarzyna Świderek2Departament de Química Física i Analítica, Universitat Jaume I, Castelló de La Plana, SpainDepartamento de Química Bio-orgánica, Instituto de Química Orgánica General (CSIC), Madrid, SpainDepartament de Química Física i Analítica, Universitat Jaume I, Castelló de La Plana, SpainThis work is focused on mechanistic studies of the transfer of an adenylyl group (Adenoside-5′-monophosfate) from adenosine 5′-triphosphate (ATP) to a OH-4′ hydroxyl group of an antibiotic. Using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques, we study the substrate and base-assisted mechanisms of the inactivation process of kanamycin A (KAN) catalyzed by 4′-O-Nucleotidyltransferase [ANT(4′)], an active enzyme against almost all aminoglycoside antibiotics. Free energy surfaces, obtained with Free Energy Perturbation methods at the M06-2X/MM level of theory, show that the most favorable reaction path presents a barrier of 12.2 kcal·mol−1 that corresponds to the concerted activation of O4′ from KAN by Glu145. In addition, the primary and secondary 18O kinetic isotope effects (KIEs) have been computed for bridge O3α, and non-bridge O1α, O2α, and O5′ atoms of ATP. The observed normal 1°-KIE of 1.2% and 2°-KIE of 0.07% for the Glu145-assisted mechanism are in very good agreement with experimentally measured data. Additionally, based on the obtained results, the role of electrostatic and compression effects in enzymatic catalysis is discussed.https://www.frontiersin.org/article/10.3389/fchem.2018.00660/fullkanamycinantibioticQM/MMaminoglycosideskinetic isotope effectsO-Nucleotidyltransferase |
| spellingShingle | Sergio Martí Agatha Bastida Katarzyna Świderek Theoretical Studies on Mechanism of Inactivation of Kanamycin A by 4′-O-Nucleotidyltransferase Frontiers in Chemistry kanamycin antibiotic QM/MM aminoglycosides kinetic isotope effects O-Nucleotidyltransferase |
| title | Theoretical Studies on Mechanism of Inactivation of Kanamycin A by 4′-O-Nucleotidyltransferase |
| title_full | Theoretical Studies on Mechanism of Inactivation of Kanamycin A by 4′-O-Nucleotidyltransferase |
| title_fullStr | Theoretical Studies on Mechanism of Inactivation of Kanamycin A by 4′-O-Nucleotidyltransferase |
| title_full_unstemmed | Theoretical Studies on Mechanism of Inactivation of Kanamycin A by 4′-O-Nucleotidyltransferase |
| title_short | Theoretical Studies on Mechanism of Inactivation of Kanamycin A by 4′-O-Nucleotidyltransferase |
| title_sort | theoretical studies on mechanism of inactivation of kanamycin a by 4 o nucleotidyltransferase |
| topic | kanamycin antibiotic QM/MM aminoglycosides kinetic isotope effects O-Nucleotidyltransferase |
| url | https://www.frontiersin.org/article/10.3389/fchem.2018.00660/full |
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