Structure analysis of the flavoredoxin from Desulfovibrio vulgaris Miyazaki F reveals key residues that discriminate the functions and properties of the flavin reductase family
Structure analysis of the flavoredoxin from Desulfovibrio vulgaris Miyazaki F reveals key residues that discriminate the functions and properties of the flavin reductase family
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DOI：
10.1111/j.1742-4658.2009.07184.x
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发表时间：
2009-09
期刊：
影响因子：
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通讯作者：
N. Shibata;Y. Ueda;Daisuke Takeuchi;Yoshihiro Haruyama;S. Kojima;Junichi Sato;Y. Niimura;M. Kitamura;Y. Higuchi
中科院分区：
文献类型：
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作者：
N. Shibata;Y. Ueda;Daisuke Takeuchi;Yoshihiro Haruyama;S. Kojima;Junichi Sato;Y. Niimura;M. Kitamura;Y. Higuchi
以 1.05 Å 分辨率测定了来自普通脱硫弧菌 Miyazaki F 的风味毒素的晶体结构，并检查了其三价铁还原酶活性。目的是基于与古生球菌三价铁还原酶的序列相似性，阐明风味蛋白是否与三价铁还原酶具有结构相似性以及三价铁还原酶活性。正如预期的那样，风味氧还蛋白与 A. fulgidus 铁还原酶具有共同的整体结构，并且表现出较弱的铁还原酶和黄素还原酶活性；然而，风味蛋白的每个二聚体含有两个 FMN 分子，这与每个二聚体仅含有一个 FMN 分子的 A. fulgidus 铁还原酶不同。与 A. fulgidus 铁还原酶相比，flavoredoxin 形成三个额外的氢键，并且具有明显较小的溶剂可及表面积。这些观察结果解释了风味蛋白对 FMN 的更高亲和力。出乎意料的是，电子密度图表明在 FMN 的异咯嗪环的末端存在 Mes 分子，并且两个锌离子与 FMN 相邻的两个半胱氨酸残基 Cys39 和 Cys40 结合。这两个半胱氨酸残基靠近三价铁还原酶的推定三价铁离子结合位点之一。基于它们结构的相似性，我们得出结论，三价铁还原酶的相应位点是三价铁离子结合的最可能的位点。将结构与相关黄素蛋白进行比较，揭示了有关功能区分（铁离子或黄素还原）和独特的电子传输系统的关键结构特征。
The crystal structure of flavoredoxin from Desulfovibrio vulgaris Miyazaki F was determined at 1.05 Å resolution and its ferric reductase activity was examined. The aim was to elucidate whether flavoredoxin has structural similarity to ferric reductase and ferric reductase activity, based on the sequence similarity to ferric reductase from Archaeoglobus fulgidus. As expected, flavoredoxin shared a common overall structure with A. fulgidus ferric reductase and displayed weak ferric reductase and flavin reductase activities; however, flavoredoxin contains two FMN molecules per dimer, unlike A. fulgidus ferric reductase, which has only one FMN molecule per dimer. Compared with A. fulgidus ferric reductase, flavoredoxin forms three additional hydrogen bonds and has a significantly smaller solvent‐accessible surface area. These observations explain the higher affinity of flavoredoxin for FMN. Unexpectedly, an electron‐density map indicated the presence of a Mes molecule on the re‐side of the isoalloxazine ring of FMN, and that two zinc ions are bound to the two cysteine residues, Cys39 and Cys40, adjacent to FMN. These two cysteine residues are close to one of the putative ferric ion binding sites of ferric reductase. Based on their structural similarities, we conclude that the corresponding site of ferric reductase is the most plausible site for ferric ion binding. Comparing the structures with related flavin proteins revealed key structural features regarding the discrimination of function (ferric ion or flavin reduction) and a unique electron transport system.