Wang Jimin, Konigsberg William H
Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States.
Front Mol Biosci. 2022 Mar 1;9:824794. doi: 10.3389/fmolb.2022.824794. eCollection 2022.
Almost all DNA polymerases (pols) exhibit bell-shaped activity curves as a function of both pH and Mg concentration. The pol activity is reduced when the pH deviates from the optimal value. When the pH is too low the concentration of a deprotonated general base (namely, the attacking 3'-hydroxyl of the 3' terminal residue of the primer strand) is reduced exponentially. When the pH is too high the concentration of a protonated general acid (i.e., the leaving pyrophosphate group) is reduced. Similarly, the pol activity also decreases when the concentration of the divalent metal ions deviates from its optimal value: when it is too low, the binding of the two catalytic divalent metal ions required for the full activity is incomplete, and when it is too high a third divalent metal ion binds to pyrophosphate, keeping it in the replication complex longer and serving as a substrate for pyrophosphorylysis within the complex. Currently, there is a controversy about the role of the third metal ion which we will address in this review.
几乎所有的DNA聚合酶（pols）的活性曲线都呈钟形，是pH值和镁离子浓度的函数。当pH值偏离最佳值时，聚合酶活性会降低。当pH值过低时，去质子化的通用碱（即引物链3'末端残基的进攻性3'-羟基）的浓度会呈指数级降低。当pH值过高时，质子化的通用酸（即离去的焦磷酸基团）的浓度会降低。同样，当二价金属离子的浓度偏离其最佳值时，聚合酶活性也会下降：当浓度过低时，充分发挥活性所需的两个催化二价金属离子的结合不完整；当浓度过高时，第三个二价金属离子会与焦磷酸结合，使其在复制复合物中保留更长时间，并作为复合物内焦磷酸水解的底物。目前，关于第三个金属离子的作用存在争议，我们将在本综述中予以探讨。
