Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations
Molecular Mechanism of the Reaction Specificity in Threonine Synthase: Importance of the Substrate Conformations
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苏氨酸合酶反应特异性的分子机制：底物构象的重要性
DOI：
10.1021/acs.jpcb.7b02932
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发表时间：
2017
期刊：
影响因子：
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通讯作者：
Ujiie Yuzuru，Tanaka Wataru，Hanaoka Kyohei，Harada Ryuhei，Kayanuma Megumi，Shoji Mitsuo，Murakawa Takeshi，Ishida Toyokazu，Shigeta Yasuteru，Hayashi Hideyuki
中科院分区：
文献类型：
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作者：
Ryuhei Harada;Yasuteru Shigeta;Kitajima T.S.;Ujiie Yuzuru，Tanaka Wataru，Hanaoka Kyohei，Harada Ryuhei，Kayanuma Megumi，Shoji Mitsuo，Murakawa Takeshi，Ishida Toyokazu，Shigeta Yasuteru，Hayashi Hideyuki
苏氨酸合成酶（ThrS）催化苏氨酸由其前体O-磷酸-L-高丝氨酸生物合成的最终化学反应。由于前半反应中产生的磷酸根离子有助于后半反应，ThrS被认为是产物辅助催化的最佳例子之一。在我们以前的QM/MM研究中，揭示了后半反应的化学反应，这是产物辅助催化的关键。然而，准确的自由能变化所造成的构象合奏和入口的水分子进入活性位点是未知的。在本研究中，通过进行长时间尺度的MD模拟，自由能的变化，由二价阴离子（磷酸根或硫酸根离子）和中间状态的构象状态进行了理论研究。我们发现，计算的自由能双差与实验结果符合得很好。我们还发现，磷酸根离子有助于形成适合于主要反应进程的氢键。这意味着活性位点氨基酸残基和底物的构象，以及因此可调的催化，由产物磷酸根离子控制，这清楚地表明了ThrS中产物辅助催化的分子机制。
Threonine synthase (ThrS) catalyzes the final chemical reaction ofl-threonine biosynthesis from its precursor,O-phospho-l-homoserine. As the phosphate ion generated in its former half reaction assists its latter reaction, ThrS is recognized as one of the best examples of product-assisted catalysis. In our previous QM/MM study, the chemical reactions for the latter half reactions, which are critical for the product-assisted catalysis, were revealed. However, accurate free energy changes caused by the conformational ensembles and entrance of water molecules into the active site are unknown. In the present study, by performing long-time scale MD simulations, the free energy changes by the divalent anions (phosphate or sulfate ions) and conformational states of the intermediate states were theoretically investigated. We found that the calculated free energy double differences are in good agreement with the experimental results. We also revealed that the phosphate ion contributes to forming hydrogen bonds that are suitable for the main reaction progress. This means that the conformation of the active site amino acid residues and the substrate, and hence, the tunable catalysis, are controlled by the product phosphate ion, and this clearly demonstrates a molecular mechanism of the product-assisted catalysis in ThrS.