Catalytic Roles of the Metal Ion in the Substrate-Binding Site of Coenzyme B12-Dependent Diol Dehydratase
Catalytic Roles of the Metal Ion in the Substrate-Binding Site of Coenzyme B12-Dependent Diol Dehydratase
复制标题
DOI：
10.1021/ic102352b
复制
发表时间：
2011-04-04
影响因子：
4.6
通讯作者：
Yoshizawa, Kazunari
中科院分区：
文献类型：
--
作者：
Kamachi, Takashi;Doitomi, Kazuki;Yoshizawa, Kazunari
用量子力学/分子力学（QM/MM）方法研究了金属离子在二醇脱氢酶底物结合位点的作用。金属离子直接与底物配位，对结构保持和底物结合至关重要。金属离子最初被指定为K+离子;然而，QM/MM计算表明，Ca 2+离子作为金属离子更合理，因为计算的Ca-O距离比计算的K-O距离更适合X射线晶体结构中的配位距离。OH基团迁移的活化能对金属离子的身份敏感，OH基团迁移在二醇转化为相应的醛中是必不可少的。例如，在含Ca的QM/MM模型中，底物的旁观者OH基团被处于过渡态的Glu 170完全去质子化，因此在含Ca 2+离子的模型中势垒高度显著降低。另一方面，旁观者OH基团的去质子化不能被K+有效地触发。此外，在氢复合中，最需要能量的步骤在含Ca的模型中更有利。Ca 2+离子应该参与底物结合位点的提议与观察到的大氘动力学同位素效应10一致，这表明C-H键活化参与了速率决定步骤。Asp 335被发现有一个强大的反催化作用的OH基团迁移，尽管它在底物结合的重要作用。需要通过Ca 2+离子的O-C键断裂和Glu 170的旁观者OH基团的去质子化的协同相互作用来克服Asp 335的抗催化作用。
Functions of the metal ion in the substrate-binding site of diol dehydratase are studied on the basis of quantum mechanical/molecular mechanical (QM/MM) calculations. The metal ion directly coordinates to substrate and is essential for structural retention and substrate binding. The metal ion has been originally assigned to the K+ ion; however, QM/MM computations indicate that Ca2+ ion is more reasonable as the metal ion because calculated Ca-O distances better fit to the coordination distances in X-ray crystal structures rather than calculated K-O distances. The activation energy for the OH group migration, which is essential in the conversion of diols to corresponding aldehydes, is sensitive to the identity of the Metal ion. For example, the spectator OH group of substrate is fully deprotonated by Glu170 in the transition state for the OH group migration in the Ca-contained QM/MM model, and therefore the barrier height is significantly decreased in the model having Ca2+ ion. On the other hand, the deprotonation of the spectator OH group cannot effectively be triggered by the K+ Moreover, in the hydrogen recombination, the most energy-demanding step is more favorable in the Ca-contained model. The proposal that the Ca2+ ion should be involved in the substrate-binding site is consistent with an observed large deuterium kinetic isotope effect of, 10, which indicates that C-H bond activation is involved in the rate-determining step. Asp335 is found to have a strong anticatalytic effect on the OH group migration despite its important role in substrate binding. The synergistic interplay of the O-C bond cleavage by Ca2+ ion and the deprotonation of the spectator OH group by Glu170 is required to overcome the anticatalytic effect of Asp335.