The Catalytic Mechanism of Pdx2 Glutaminase Driven by a Cys‐His‐Glu Triad: A Computational Study
| العنوان: | The Catalytic Mechanism of Pdx2 Glutaminase Driven by a Cys‐His‐Glu Triad: A Computational Study |
|---|---|
| المؤلفون: | Nuno M. F. S. A. Cerqueira, Sérgio F. Sousa, André Pina |
| المصدر: | ChemBioChem. 23 |
| بيانات النشر: | Wiley, 2021. |
| سنة النشر: | 2021 |
| مصطلحات موضوعية: | ONIOM, biology, Chemistry, Stereochemistry, Glutamine, Organic Chemistry, Deamination, Glutamic Acid, Active site, Reaction intermediate, Biochemistry, Catalysis, Malaria, Amidase, Glutaminase, Pyridoxal Phosphate, Catalytic triad, biology.protein, Humans, Molecular Medicine, Molecular Biology |
| الوصف: | The catalytic mechanism of Pdx2 was herein studied with atomic detail employing the computational ONIOM hybrid QM/MM methodology. Pdx2 employs a Cys-His-Glu catalytic triad to deaminate glutamine to glutamate and ammonia-the source of the nitrogen of pyridoxal 5'-phosphate(PLP). This enzyme is, therefore, a rate-limiting step in the PLP biosynthetic pathway of Malaria and Tuberculosis pathogens. For this reason,Pdx2 is considered a novel and promising drug target to treat these diseases. The results herein obtained show that the catalytic mechanism of Pdx2 occurs in six steps that can be divided into four stages: (i) activation of Cys87, (ii) deamination of glutamine with the formation of the glutamyl-thioester intermediate, (iii) hydrolysis of the formed intermediate, and (iv) enzymatic turnover. The kinetic data available in the literature(19.1-19.5 kcal mol-1) agrees very well with the calculated free energy barrier of the hydrolytic step(18.2 kcal.mol-1), which is the rate-limiting step of the catalytic process when substrate is readily available in the active site. This catalytic mechanism differs from other known amidases in three main points: i)it requires the activation of the nucleophile Cys87 to a thiolate; ii)the hydrolysis occurs in a single step and therefore does not require the formation of a second tetrahedral reaction intermediate, as it is proposed, and iii)Glu198 does not have a direct role in the catalytic process. |
| تدمد: | 1439-7633 1439-4227 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::72efb5d3802ec4a214f980ca98417fe5 https://doi.org/10.1002/cbic.202100555 |
| حقوق: | CLOSED |
| رقم الأكسشن: | edsair.doi.dedup.....72efb5d3802ec4a214f980ca98417fe5 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 14397633 14394227 |
|---|