Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Sector H-12, 44000 Islamabad, Pakistan; Department of Biotechnology, University of Sialkot, 51310 Sialkot, Pakistan.
Research Center for Modeling and Simulation (RCMS), National University of Sciences and Technology (NUST), Sector H-12, 44000 Islamabad, Pakistan.
Biophys Chem. 2018 Sep;240:98-106. doi: 10.1016/j.bpc.2018.06.002. Epub 2018 Jun 12.
Hydrolysis reaction marks the basis of life yet the mechanism of this crucial biochemical reaction is not completely understood. We recently reported the mechanisms of hydrolysis of nucleoside triphosphate and phosphate monoester. These two reactions hydrolyze P-O-P and P-O-C linkages, respectively. Here, we present the mechanism of hydrolysis of δ-6-phosphogluconolactone, which is an important precursor in the second step of the pentose phosphate pathway. Its hydrolysis requires the cleavage of C-O-C linkage and its mechanism is hitherto unknown. We report three mechanisms of hydrolysis of δ-6-phosphogluconolactone based on density functional computations. In the energetically most favorable mechanism, two water molecules participate in the hydrolysis reaction and the mechanism is sequential, i.e., activation of the attacking water molecule (OH bond breaking) precedes that of the cleavage of the CO bond of the C-O-C linkage. The rate-limiting energy barrier of this mechanism is comparable to the reported experimental free energy barrier. This mechanism has similarities with the mechanism of triphosphate hydrolysis and that of hydrolytic cleavage of DNA in EcoRV enzyme. This two-water sequential hydrolysis mechanism could be the unified mechanism required for the hydrolysis of other hydrolysable species in living cells.
水解反应是生命的基础，但这种关键生化反应的机制尚未完全理解。我们最近报道了核苷三磷酸和磷酸单酯水解的机制。这两种反应分别水解 P-O-P 和 P-O-C 键。在这里，我们提出了δ-6-磷酸葡萄糖酸内酯水解的机制，它是戊糖磷酸途径第二步的重要前体。它的水解需要 C-O-C 键的断裂，其机制尚不清楚。我们基于密度泛函计算报告了δ-6-磷酸葡萄糖酸内酯水解的三种机制。在最有利的能量机制中，两个水分子参与水解反应，且机制是连续的，即攻击水分子（OH 键断裂）的活化先于 C-O-C 键 CO 键的断裂。该机制的速率限制能垒与报道的实验自由能垒相当。该机制与三磷酸水解机制和 EcoRV 酶中 DNA 水解断裂机制相似。这种双水分子连续水解机制可能是活细胞中水解其他可水解物质所需的统一机制。
