Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, ul. Niezapominajek 8, 30-239 Kraków, Poland.
J Am Chem Soc. 2010 Sep 22;132(37):12887-98. doi: 10.1021/ja101877a.
The mechanism of the chlorination reaction of SyrB2, a representative α-ketoglutarate dependent halogenase, was studied with computational methods. First, a macromolecular model of the Michaelis complex was constructed using molecular docking procedures. Based on this structure, a smaller model comprising the first- and some of the second-shell residues of iron and a model substrate was constructed and used in DFT investigations on the reaction mechanism. Computed relative energies and Mössbauer isomer shifts as well as quadrupole splittings indicate that the two oxoferryl species observed experimentally are two stereoisomers resulting from an exchange of the coordination sites occupied by the oxo and chloro ligands. In principle both Fe(IV)═O species are reactive and decay to Fe(III)Cl (OH)/carbon radical intermediates via C-H bond cleavage. In the final rebound step, which is very fast and thus precluding equilibration between the two forms of the radical intermediate, the ligand (oxo or chloro) placed closest to the carbon radical (trans to His235) is transferred to the carbon. For the native substrate (L-Thr) the lowest barrier for C-H cleavage was found for an isomer of the oxoferryl species favoring chlorination in the rebound step. CASPT2 calculations for the spin state splittings in the oxoferryl species support the conclusion that once the Fe(IV)═O intermediate is formed, the reaction proceeds on the quintet potential energy surface.
采用计算方法研究了代表 α-酮戊二酸依赖卤化酶的 SyrB2 的氯化反应机制。首先，使用分子对接程序构建了迈克尔利斯复合物的大分子模型。基于该结构，构建了一个较小的模型，包括铁的第一和一些第二壳层残基以及一个模型底物，并在反应机制的 DFT 研究中使用了该模型。计算的相对能量和穆斯堡尔同晶位移以及四极分裂表明，实验中观察到的两种双氧铁物种是两种由氧和氯配体占据的配位位交换产生的立体异构体。原则上，两种 Fe(IV)=O 物种都是反应性的，并且通过 C-H 键断裂，衰减为 Fe(III)Cl(OH)/碳自由基中间体。在非常快的最终回弹步骤中，排除了两种自由基中间体之间的平衡，与碳自由基（反式 His235）最接近的配体（氧或氯）被转移到碳上。对于天然底物（L-Thr），在回弹步骤中有利于氯化的双氧铁物种的异构体的 C-H 断裂的最低势垒。对于双氧铁物种中自旋态分裂的 CASPT2 计算支持这样的结论，即一旦形成 Fe(IV)=O 中间体，反应就在 quintet 势能表面上进行。
