Higuchi Y, Yagi T, Yasuoka N
Division of Chemistry, Graduate School of Science, Kyoto University, Japan.
Structure. 1997 Dec 15;5(12):1671-80. doi: 10.1016/s0969-2126(97)00313-4.
The hydrogenase of Desulfovibrio sp. catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3. The Ni-Fe active center of Desulfovibrio hydrogenase has an unusual ligand structure with non-protein ligands. An atomic model at high resolution is required to make concrete assignment of the ligands which coordinate the Ni-Fe center. These in turn will provide insight into the mechanism of electron transfer, during the reaction catalysed by hydrogenase.
The X-ray structure of the hydrogenase from Desulfovibrio vulgaris Miyazaki has been solved at 1.8 A resolution and refined to a crystallographic R factor of 0.229. The overall folding pattern and the spatial arrangement of the metal centers are very similar to those found in Desulfovibrio gigas hydrogenase. This high resolution crystal structure enabled us to assign the non-protein ligands to the Fe atom in the Ni-Fe site and revealed the presence of a Mg center, located approximately 13 A from the Ni-Fe active center.
From the nature of the electron-density map, stereochemical geometry and atomic parameters of the refined structure, the most probable candidates for the four ligands, coordinating the Ni-Fe center, have been proposed to be diatomic S=O, C triple bond O and C triple bond N molecules and one sulfur atom. The assignment was supported by pyrolysis mass spectrometry measurements. These ligands may have a role as an electron sink during the electron transfer reaction between the hydrogenase and its biological counterparts, and they could stabilize the redox state of Fe(II), which may not change during the catalytic cycle and is independent of the redox transition of the Ni. The hydrogen-bonding system between the Ni-Fe and the Mg centers suggests the possible.
脱硫弧菌属的氢化酶与特定电子受体细胞色素c3协同催化分子氢的可逆氧化还原反应。脱硫弧菌氢化酶的镍铁活性中心具有带有非蛋白质配体的不寻常配体结构。需要高分辨率的原子模型来具体确定配位镍铁中心的配体。这反过来将有助于深入了解氢化酶催化反应过程中的电子转移机制。
已解析出宫崎脱硫弧菌氢化酶的X射线结构，分辨率为1.8埃，并精修至晶体学R因子为0.229。其整体折叠模式和金属中心的空间排列与巨大脱硫弧菌氢化酶中的非常相似。这种高分辨率晶体结构使我们能够确定镍铁位点中铁原子的非蛋白质配体，并揭示了一个镁中心的存在，该中心距离镍铁活性中心约13埃。
根据电子密度图的性质、精修结构的立体化学几何形状和原子参数，已提出配位镍铁中心的四个配体最可能的候选物是双原子S=O、C≡O和C≡N分子以及一个硫原子。该归属得到了热解质谱测量的支持。这些配体可能在氢化酶与其生物对应物之间的电子转移反应中充当电子汇，并且它们可以稳定Fe(II)的氧化还原状态，Fe(II)在催化循环中可能不会改变且独立于镍的氧化还原转变。镍铁中心和镁中心之间的氢键系统表明了可能性。
