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.

本课题的主要目的是通过X射线结构分析的方法，从一株硫酸盐还原菌中解析出镍铁氢酶的三维结构，并阐明其结构与功能的关系。氢酶的结构在3.0分辨率下得到解析，并在1.8分辨率下进行了精制，R值为22.9%。其结构揭示了Ni-Fe活性中心有一种不寻常的配体。非正常弥散技术可以确定铁原子位于Ni-Fe中心，它含有四个非蛋白质配体。它们被指定为三个双原子分子和一个类似硫的原子。从精制结构的立体化学几何构型和原子参数来看，四个配体最有可能的候选者是S=O，C=N，C=O和一个硫。红外光谱和裂解质谱学数据支持这一指认。在距离Ni-Fe活性中心约13的大亚基的羧基末端还发现了一个额外的镁中心。

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: "“High resolution Crystal Structures of Two Polymorphs of Cvtochromec' from Purple Phototrophic Bacterium,Rhodobacter capsulatus"" J.Mol.Biol. 259. 467‐479 (1996)

Yoshiki Higuchi 等人：“来自紫色光养细菌、荚膜红细菌的两种 Cvtochromec 多晶型物的高分辨率晶体结构”，J.Mol.Biol. 259. 467-479 (1996)

Yoshiki Higuchi et al: "“Single crystal EPR study of the Ni center of NiFe hydrogenase"" Chemical Physics Letters. 256. 518‐524 (1996)

Yoshiki Higuchi 等人：“NiFe 氢化酶 Ni 中心的单晶 EPR 研究””《化学物理快报》256. 518-524 (1996)。

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》。