King W A, Gready J E, Andrews T J
Computational Molecular Biology and Drug Design Group, John Curtin School of Medical Research, Australian National University, Canberra.
Biochemistry. 1998 Nov 3;37(44):15414-22. doi: 10.1021/bi981598e.
A study, using ab initio quantum chemical methods, of the first step in the reaction mechanism of Rubisco, the enolization of the substrate, ribulose bisphosphate, is reported. This is the first such study that takes into account the likely roles of critical features within the active site. On the basis of molecular dynamics relaxation of the complex between activated enzyme and substrate using X-ray crystallographic structures as starting coordinates, a 29-atom fragment that mimicked the active site was constructed. States along a proposed reaction pathway were calculated using density functional theory and Moller-Plesset second-order perturbation theory. The results are consistent with the postulate that the base that abstracts the C3 proton of ribulose bisphosphate is the metal-stabilized carbamate of Lys-201 formed during the activation process. The calculations suggest that the active-site residue, Lys-175, is charged before enolization commences and they indicate a possible means by which the enzyme directs the incoming CO2 to attack the C2 carbon atom of the enediol, rather than the chemically very similar C3 atom.
报道了一项使用从头算量子化学方法对核酮糖-1,5-二磷酸羧化酶/加氧酶（Rubisco）反应机制第一步，即底物核酮糖二磷酸的烯醇化反应进行的研究。这是第一项考虑活性位点内关键特征可能作用的此类研究。基于以X射线晶体学结构为起始坐标对活化酶与底物之间复合物进行的分子动力学弛豫，构建了一个模拟活性位点的29原子片段。使用密度泛函理论和莫勒-普莱塞特二阶微扰理论计算了沿提议反应途径的各个状态。结果与以下假设一致：夺取核酮糖二磷酸C3质子的碱是活化过程中形成的赖氨酸-201的金属稳定氨基甲酸盐。计算表明，活性位点残基赖氨酸-175在烯醇化开始前带电荷，并且它们指出了一种可能的方式，通过这种方式酶引导进入的二氧化碳攻击烯二醇的C2碳原子，而不是化学性质非常相似的C3原子。
