Crystal structure of rubredoxin from Desulfovibrio gigas to ultra-high 0.68Å resolution
Crystal structure of rubredoxin from Desulfovibrio gigas to ultra-high 0.68Å resolution
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DOI：
10.1016/j.bbrc.2006.07.205
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发表时间：
2006-10-13
影响因子：
3.1
通讯作者：
Liu, Ming-Yih
中科院分区：
文献类型：
--
作者：
Chen, Chun-Jung;Lin, Yi-Hung;Liu, Ming-Yih
Rubredoxin (D.g. Rd) 是一种小型非血红素铁硫蛋白，显示出作为硫酸盐还原菌 Desulfovibrio gigas 的氧化还原偶联蛋白的功能。该蛋白质通常从厌氧细菌中纯化，据认为在厌氧细菌中参与电子转移或交换过程。 Rd 将电子转移到氧气形成水，作为独特电子转移链的一部分，该电子转移链由 D.g. 中的 NADH：红氧还蛋白氧化还原酶 (NRO)、红氧还蛋白和红氧还蛋白：氧氧化还原酶 (ROO) 组成。 D.g.的晶体结构Rd 通过 Fe 单波长反常色散 (SAD) 信号和直接法测定，并使用来自同步加速器的 X 射线精炼至超高 0.68 埃分辨率。 Rd 含有一个铁原子，与四个半胱氨酰残基的硫原子以四面体配位键合。疏水性和 pi-pi 相互作用维持内部 Rd 折叠。观察到铁硫簇和氨基酸残基的多种构象，表明其独特的电子转移机制。电子密度图中清楚地显示了几个氢键，包括铁硫的 N-H(...)SG。大量的水与残基 Val8、Cys9、Gly10、Ala38 和 Gly43 的 C-O 肽结合，可能参与电子转移。这种超高分辨率的结构使我们能够详细研究红氧还蛋白的结构和功能之间的关系，例如盐桥、氢键、水结构、半胱氨酸配体、铁硫。簇以及活性位点之间的电子密度分布。这一信息将首次明确该蛋白质在严格厌氧细菌中的作用。 (c) 2006 Elsevier Inc. 保留所有权利。
Rubredoxin (D.g. Rd) is a small non-heme iron-sulfur protein shown to function as a redox coupling protein from the sulfate reducing bacteria Desulfovibrio gigas. The protein is generally purified from anaerobic bacteria in which it is thought to be involved in electron transfer or exchange processes. Rd transfers an electron to oxygen to form water as part of a unique electron transfer chain, composed by NADH:rubredoxin oxidoreductase (NRO), rubredoxin and rubredoxin: oxygen oxidoreductase (ROO) in D.g. The crystal structure of D.g. Rd has been determined by means of both a Fe single-wavelength anomalous dispersion (SAD) signal and the direct method, and refined to an ultra-high 0.68 angstrom resolution, using X-ray from a synchrotron. Rd contains one iron atom bound in a tetrahedral coordination by the sulfur atoms of four cysteinyl residues. Hydrophobic and it pi-pi interactions maintain the internal Rd folding. Multiple conformations of the iron-sulfur cluster and amino acid residues are observed and indicate its unique mechanism of electron transfer. Several hydrogen bonds, including N-H(...)SG of the iron-sulfur, are revealed clearly in maps of electron density. Abundant waters bound to C-O peptides of residues Val8, Cys9, Gly10, Ala38, and Gly43, which may be involved in electron transfer. This ultra-high-resolution structure allows us to study in great detail the relationship between structure and function of rubredoxin, such as salt bridges, hydrogen bonds, water structures, cysteine ligands, iron-sulfur. cluster, and distributions of electron density among activity sites. For the first time, this information will provide a clear role for this protein in a strict anaerobic bacterium. (c) 2006 Elsevier Inc. All rights reserved.