期刊名称：Computational and Structural Biotechnology Journal
印刷版ISSN：2001-0370
出版年度：2019
卷号：17
页码：770-784
DOI：10.1016/j.csbj.2019.06.016
出版社：Computational and Structural Biotechnology Journal
摘要：ATPS Sulfurylase (ATPS) is the first of three enzymes in the sulfate reduction pathway - one of the oldest metabolic pathways on Earth, utilized by Sulfate Reducing Bacteria (SRB). Due to the low redox potential of the sulfate ion, its reduction requires activation via formation of adenosine 5′-phosphosulfate (APS), which is catalyzed by ATPS. Dispersion-corrected hybrid density functional theory (DFT/B3LYP-D3) was used to test three reaction mechanisms proposed for conversion of ATP to APS: two-step SN-1 reaction running through AMP anhydride intermediate, two-step reaction involving cyclic AMP intermediate and direct SN-2 conversion of ATP to APS molecule. The study employed five different cluster models of the ATPS active site: one containing magnesium cation and four without it, constructed based on the crystal structure (PDB code: 1G8H ) solved for ATPS from Saccharomyces cerevisiae in complex with APS and pyrophosphate (PPi), where Mg 2 was not detected. The model with magnesium ion was constructed based on the representative structure obtained from trajectory analysis of the molecular dynamics simulations (MD) performed for the hexameric ATPS-APS-Mg 2 -PPi complex. The results obtained for all considered models suggest that ATPS-AMP anhydride intermediate is a highly energetic and unstable complex, while formation of cyclic AMP molecule requires formation of unfavorable hypervalent geometry at the transition state. Among all tested mechanism, the energetically most feasible mechanism of the ATPS reaction is SN-2 one-step conversion of ATP to APS occurring via a pentavalent transition state. Interestingly, such a reaction is inhibited by the presence of Mg 2 in the ATPS active site. Magnesium cation forces unfavorable geometry of reactants for SN-2 mechanism and formation of pentavalent transition state. Such a reaction requires rearrangement of Mg 2 ligands, which raises the barrier from 11-14 kcal/mol for the models without Mg 2 to 48 kcal/mol for model with magnesium ion included.
关键词：Sulfate Reducing Bacteria ; ATP ; Sulfurylase ; Density functional calculations ; Sulfate reduction ; Adenosine 5′-phosphosulfate ; APS
