Department of Chemistry and Biochemistry, University of Windsor, Windsor, Ontario, Canada.
J Phys Chem B. 2012 May 3;116(17):5205-12. doi: 10.1021/jp302556e. Epub 2012 Apr 18.
The structure and nature of the fully bound active site of Threonyl-tRNA Synthetase (ThrRS) for the second half-reaction has been investigated using molecular dynamics simulations. More specifically, we examined the ThrRS active site with both the substrate Threonyl-AMP and the cosubstrate cognate Threonyl-tRNA bound. Furthermore, we also considered the cases in which an active-site histidyl residue (His309) is either neutral or protonated. Moreover, we considered the role a water molecule may play in formation of a viable Michaelis complex. From the results it is found that the most likely role of His309 is in binding and properly orientating the ribose of the Ado76 nucleotidyl residue of the threonyl-tRNA via formation of a direct His309···Ado76 hydrogen bond, i.e., without involvement of a water. In addition, the imidazole of the His309 residue is likely neutral. It was found that upon protonation the positioning of the Ado76-3'-OH was perturbed, leading to a reduced chance for nucleophilic attack of the threonyl's C1 center.
使用分子动力学模拟研究了苏氨酰-tRNA 合成酶（ThrRS）完全结合的活性部位的结构和性质，用于第二半反应。更具体地，我们研究了与底物苏氨酰-AMP 和共底物对应苏氨酰-tRNA 结合的 ThrRS 活性部位。此外，我们还考虑了活性部位组氨酸残基（His309）为中性或质子化的情况。此外，我们还考虑了水分子在形成可行的米氏复合物中可能发挥的作用。结果表明，His309 的最可能作用是通过形成直接的 His309···Ado76 氢键，即不涉及水，来结合并正确定向苏氨酰-tRNA 的 Ado76 核苷酸残基的核糖。此外，His309 残基的咪唑可能为中性。研究发现，质子化后，Ado76-3'-OH 的定位受到干扰，导致苏氨酸 C1 中心亲核攻击的机会减少。
