Large-Scale Determination of Sequence, Structure, and Function Relationships in Cytosolic Glutathione Transferases across the Biosphere
Large-Scale Determination of Sequence, Structure, and Function Relationships in Cytosolic Glutathione Transferases across the Biosphere
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DOI：
10.1371/journal.pbio.1001843
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发表时间：
2014-04-01
期刊：
影响因子：
9.8
通讯作者：
Babbitt, Patricia C.
中科院分区：
文献类型：
--
作者：
Mashiyama, Susan T.;Malabanan, M. Merced;Babbitt, Patricia C.
胞浆谷胱甘肽转移酶（cytGST）超家族包括在整个生物圈中发现的13，000多个非冗余序列。它们在新陈代谢和防御氧化损伤中的关键作用导致了数十年来数千项研究。尽管这种关注，很少有人知道他们催化的生理反应和大多数用于检测cytGST的底物是合成化合物。更深入地了解整个超家族的关系可以为它们的功能提供新的线索。为了建立cytGST扩展分类的基础，我们为整个超家族生成了基于相似性的亚组。使用由此产生的序列相似性网络，我们选择了广泛覆盖未知功能的靶标，并在这里报告了实验结果，证实了其中82个靶标的GST样活性，沿着了27个靶标的37个新的3D结构。这些新的数据，沿着与实验已知的GST反应和结构的文献中报道，被绘制到网络上，以生成其序列-结构-功能关系的全局视图。结果显示了已知和未知功能的蛋白质如何在整个超家族中相互关联，并揭示了绝大多数cytGST尚未通过实验表征或注释规范类。一个映射的分类类的超家族表明，许多分类群中的每个子组和突出的挑战，分类的超家族序列到功能相关的类。在许多不同的亚组中，二硫键还原酶活性的实验测定说明了许多反应类型的共同主题。最后，一种酶，催化还原脱氯反应的生物修复的努力与它的一些最接近的同源物之间的序列比较显示，它们之间的差异可能与这种不寻常的反应的演变。网络的交互式版本，与功能和其他类型的信息相关联，可以从结构-功能链接数据库（SFLD; http://sfld.rbvi.ucsf.edu）下载。作者摘要细胞溶质谷胱甘肽转移酶（cytGST）是一个大的和多样化的酶超家族，在代谢和防御氧化损伤中起重要作用。它们已经被研究了几十年，但由于用于测试这些蛋白质以确定它们是否具有cytGST活性的化学物质的合成性质，对cytGST的生理反应和作用知之甚少。在这项大型的合作研究中，我们构建了网络，其中超过13，000个cytGST序列按序列相似性进行分组，然后使用这些网络优先考虑在相对未探索的超家族区域进行实验表征的新目标。我们在这里报告的实验结果证实GST样活性的82个，沿着与37个新的三维分子结构确定的27个目标。这些新的数据，沿着与以前在文献中报道的实验数据，被绘制到网络上，以生成它们的序列-结构-功能关系的全局视图。结果显示了已知和未知功能的蛋白质如何在整个超家族中相互关联，并阐明了它们在序列和结构上的变化影响我们预测未知功能特性的能力的复杂方式。
The cytosolic glutathione transferase (cytGST) superfamily comprises more than 13,000 nonredundant sequences found throughout the biosphere. Their key roles in metabolism and defense against oxidative damage have led to thousands of studies over several decades. Despite this attention, little is known about the physiological reactions they catalyze and most of the substrates used to assay cytGSTs are synthetic compounds. A deeper understanding of relationships across the superfamily could provide new clues about their functions. To establish a foundation for expanded classification of cytGSTs, we generated similarity-based subgroupings for the entire superfamily. Using the resulting sequence similarity networks, we chose targets that broadly covered unknown functions and report here experimental results confirming GST-like activity for 82 of them, along with 37 new 3D structures determined for 27 targets. These new data, along with experimentally known GST reactions and structures reported in the literature, were painted onto the networks to generate a global view of their sequence-structure-function relationships. The results show how proteins of both known and unknown function relate to each other across the entire superfamily and reveal that the great majority of cytGSTs have not been experimentally characterized or annotated by canonical class. A mapping of taxonomic classes across the superfamily indicates that many taxa are represented in each subgroup and highlights challenges for classification of superfamily sequences into functionally relevant classes. Experimental determination of disulfide bond reductase activity in many diverse subgroups illustrate a theme common for many reaction types. Finally, sequence comparison between an enzyme that catalyzes a reductive dechlorination reaction relevant to bioremediation efforts with some of its closest homologs reveals differences among them likely to be associated with evolution of this unusual reaction. Interactive versions of the networks, associated with functional and other types of information, can be downloaded from the Structure-Function Linkage Database (SFLD; http://sfld.rbvi.ucsf.edu).Author Summary Cytosolic glutathione transferases (cytGSTs) are a large and diverse superfamily of enzymes that have important roles in metabolism and defense against oxidative damage. They have been studied for several decades but because of the synthetic nature of the chemicals used to test these proteins to determine if they have cytGST activity, little is known about the physiological reactions and roles of cytGSTs. In this large, collaborative study, we constructed networks where more than 13,000 cytGST sequences were grouped by sequence similarity and then used these networks to prioritize new targets for experimental characterization in relatively unexplored regions of the superfamily. We report here experimental results confirming GST-like activity for 82 of them, along with 37 new three-dimensional molecular structures determined for 27 targets. These new data, along with experimental data previously reported in the literature, were painted onto the networks to generate a global view of their sequence-structure-function relationships. The results show how proteins of both known and unknown function relate to each other across the entire superfamily and illuminate the complex ways in which their variations in sequence and structure affect our ability to predict unknown functional properties.