Structural Study of Hydrogenase

氢化酶的结构研究

• 批准号: 08458209
• 负责人: HIGUCHI Yoshiki
• 金额: $ 4.22万
• 依托单位: KYOTO UNIVERSITY
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (B)
• 财政年份: 1996
• 资助国家: 日本
• 起止时间: 1996 至 1997
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-08458209/
• 关键词: Hydrogenase; Ni-Fe active center; S=O ligand; MAD analysis; X-ray structure analysis; Iron-Sulfur cluster; non-protein ligand; High resolution analysis; Ni-Fe中心; 配位子; X線結晶解析; 硫酸還元菌

The main purpose of this project is to solve the three-dimensional structure of Ni-Fe hydrogenase from one of the sulfate-reducing bacterium by X-ray structure analysis method, and clarify the relationship between the structure and function of it. The structure of the hydrogenase was solved at 3.0 resolution, and has been refined at 1.8 resolution with R-value of 22.9%. The structure reveals an unusual ligands in the Ni-Fe active center. The Fe atom, which was able to be assined in the Ni-Fe center by anoumalous dispersion technique has four non-protein ligands. They have been assigned as three diatomic molecules, and one atom like sulfur. From the stereochemical geometry and atomic parameters of the refined structure, the most probable candidates for the four ligands are S=O,C=N,C=O and one sulfur. The assignment is supported by the data obtained by infrared spectroscopy and pyrolysis-mass spectroscopy. One additional Mg site has been found in the carboxy-terminal region of the large subunit, which is approximately 13 distant from the Ni-Fe active center.

该项目的主要目的是通过X射线结构分析方法从一种减少硫酸盐的细菌之一来解决Ni-Fe氢化酶的三维结构，并阐明其结构和功能之间的关系。以3.0分辨率求解氢化酶的结构，并以1.8的分辨率进行了改进，R值为22.9％。该结构在Ni-Fe活跃中心揭示了异常的配体。 Fe原子可以在Ni-Fe中心通过无质分散技术在Ni-Fe中心进行，具有四个非蛋白质配体。它们已被分配为三个双原子分子，一个原子像硫。从精制结构的立体化学几何形状和原子参数中，四个配体的最可能的候选物为s = o，c = n，c = o和一个硫。通过红外光谱和热解质量光谱获得的数据支持分配。在大亚基的羧基末端区域中发现了一个额外的MG位点，距Ni-Fe活性中心约13个。

项目成果

Higuchi, Y.et al.: ""Single crystal EPR study of the Ni center of NiFe hydrogenase"" Chemical Physics Letters. 256,5. 18-524 (1996)

Higuchi, Y.et al.:““NiFe 氢化酶 Ni 中心的单晶 EPR 研究””化学物理快报。

Yoshiki Higuchi et al: ""Concerted movement of side chains in the haem vicinity observed in ligand binding in cytochrome c' from Rhodobacter capsulatus"" Nature Structural Biology. vol 3 no5. 459-464 (1996)

Yoshiki Higuchi 等人：“在荚膜红杆菌细胞色素 c 的配体结合中观察到血红素附近侧链的协同运动”，《自然结构生物学》。

Yoshiki Higuchi et al: ""Single crystal EPR study of the NiFe hydrogenase"" Chemical PHYSICS Letters. 256. 518-524. (1996)

Yoshiki Higuchi 等人：“NiFe 氢化酶的单晶 EPR 研究”《化学物理快报》。

YOSHIKI Higuchi et al.: "Unusual ligand sturucture in Ni-Fe active center and an additional Mg site inhydorogenase revealed by high resolution X-ray structure analysis" Structure. 5. 1671-1680 (1997)

YOSHIKI Higuchi 等人：“通过高分辨率 X 射线结构分析揭示了 Ni-Fe 活性中心的不寻常配体结构和氢化酶中的额外 Mg 位点” 结构。

Yoshiki Higuchi et al.: ""The Heterogeneity in a Protein Crystal Revealed by Synchrotron Radiation"" J.Crystal Growth. 168. 99-105 (1996)

Yoshiki Higuchi 等人：“同步辐射揭示的蛋白质晶体的异质性”J.Crystal Growth。