School of Chemistry, UNSW Sydney, Sydney 2000, Australia.
Dalton Trans. 2019 Jan 28;48(4):1251-1262. doi: 10.1039/c8dt04531c. Epub 2019 Jan 4.
The active site of the enzyme nitrogenase (N→ NH) is a FeMoSC cluster that contains three doubly-bridging μ-S atoms around a central belt. A vanadium nitrogenase variant has a slightly different cluster, containing two μ-S atoms. Recent crystal structures have revealed substitution of one μ-S (S2B, bridging Fe2 and Fe6), by CO in Mo-nitrogenase and an uncertain light atom in V-nitrogenase. These systems retained catalytic activity, and were able to recover the lost μ-S atom. Electron density attributed to the dissociated S is displaced by 7 Å in the crystal structure of the non-standard V-protein. The hypothesis arising from these observations is that the chemical mechanism of nitrogenase involves reversible dissociation of S2B, leaving Fe2 and Fe6 seriously under-coordinated and reactive in trapping N and binding reaction intermediates. Accumulated experimental evidence points to the Fe2-S2B-Fe6 domain as the centre of catalytic hydrogenation of N. Using DFT simulations of a large model (>488 atoms) containing all relevant surrounding protein residues, I have investigated the chemical steps that could allow dissociation of S2B. The participation of H atoms is crucial, as is involvement of the nearby side chain of His195 that can function as proton donor to S2B and hydrogen-bonding supporter of displaced S2B. A significant result is that after ingress and binding of N at Fe2 the breaking of the Fe2-S2B bond can be strongly exergonic with negligible kinetic barrier. Subsequent extension of the Fe6-S2B bond and dissociation as HS (or SH) is endergonic by 20-25 kcal mol, partly because the separating HS is restricted by surrounding amino-acids. I present a number of reaction sequences and energy landscapes, and derive thirteen chemical principles relevant to the postulated S-dissociation mechanism. A key conclusion is that unhooking of S2BH or S2BH from Fe2 is favourable, likely, and propitious for subsequent H transfer to bound N or reaction intermediates. The space between Fe2 and Fe6 supports two bridging ligands, and another H atom on Fe6 can move without kinetic barrier to occupy the bridging position vacated by S2B.
酶氮还原酶(N→NH)的活性部位是一个 FeMoSC 簇,其中包含三个围绕中央带的双桥联 μ-S 原子。一种钒氮还原酶变体具有略有不同的簇,其中包含两个 μ-S 原子。最近的晶体结构揭示了 Mo-氮还原酶中一个 μ-S(S2B,桥接 Fe2 和 Fe6)被 CO 取代,而 V-氮还原酶中一个不确定的轻原子取代。这些系统保留了催化活性,并能够恢复失去的 μ-S 原子。在非标准 V-蛋白的晶体结构中,归因于解离 S 的电子密度被位移 7 Å。这些观察结果产生的假设是,氮还原酶的化学机制涉及 S2B 的可逆解离,使 Fe2 和 Fe6 严重配位不足且具有反应性,从而捕获 N 并结合反应中间体。积累的实验证据表明,Fe2-S2B-Fe6 结构域是 N 催化加氢的中心。使用包含所有相关周围蛋白质残基的大型 (>488 个原子) 模型的 DFT 模拟,我研究了允许 S2B 解离的化学步骤。H 原子的参与至关重要,附近 His195 的侧链的参与也至关重要,它可以作为 S2B 的质子供体,并作为被取代 S2B 的氢键支持。一个重要的结果是,在 Fe2 上 N 进入和结合后,Fe2-S2B 键的断裂可以是强烈的放能,几乎没有动力学障碍。随后,Fe6-S2B 键的延伸和作为 HS(或 SH)的解离是吸热的,增加 20-25 kcal mol,部分原因是分离的 HS 受到周围氨基酸的限制。我提出了一些反应序列和能量景观,并得出了与假设的 S 解离机制相关的十三个化学原理。一个关键的结论是,S2BH 或 S2BH 从 Fe2 的解钩是有利的、可能的,并且有利于随后向结合的 N 或反应中间体转移 H。Fe2 和 Fe6 之间的空间支持两个桥联配体,Fe6 上的另一个 H 原子可以无动力学障碍地移动,占据 S2B 空出的桥联位置。