Åqvist Johan, Kamerlin Shina C L
Department of Cell & Molecular Biology, Uppsala University, Biomedical Center , Box 596, SE-751 24 Uppsala, Sweden.
Biochemistry. 2015 Jan 20;54(2):546-56. doi: 10.1021/bi501373g. Epub 2014 Dec 30.
The translational GTPases hydrolyze GTP on the ribosome at several stages of the protein synthesis cycle. Because of the strong conservation of their catalytic center, these enzymes are expected to operate through a universal hydrolysis mechanism, in which a critical histidine residue together with the sarcin-ricin loop of the large ribosomal subunit is necessary for GTPase activation. Here we examine different possible pathways for GTP hydrolysis by EF-Tu through extensive computer simulations. We show that a conformational change of the peptide plane preceding this histidine has a decisive effect on the energetics of the reaction. This transition was predicted earlier by us and has recently been confirmed experimentally. It is found to promote early proton transfer from water to the γ-phosphate group of GTP, followed by nucleophilic attack by hydroxide ion. The calculated reaction energetics is in good agreement with available kinetic data, for both wild-type and mutant versions of EF-Tu, and indicates that the latter may enforce a change in mechanism toward more concerted pathways.
翻译后鸟苷三磷酸酶在蛋白质合成周期的几个阶段水解核糖体上的鸟苷三磷酸。由于其催化中心具有高度保守性，这些酶预计通过一种通用的水解机制发挥作用，在该机制中，一个关键的组氨酸残基与大核糖体亚基的帚曲霉素-蓖麻毒素环对于鸟苷三磷酸酶激活是必需的。在此，我们通过广泛的计算机模拟研究了延伸因子-Tu（EF-Tu）水解鸟苷三磷酸的不同可能途径。我们表明，在这个组氨酸之前的肽平面的构象变化对反应的能量学有决定性影响。这种转变此前由我们预测，最近已得到实验证实。结果发现它促进质子从水向鸟苷三磷酸的γ-磷酸基团的早期转移，随后氢氧根离子进行亲核攻击。计算得到的反应能量学与野生型和突变型EF-Tu的现有动力学数据高度吻合，并表明后者可能促使机制向更协同的途径转变。
