Isofunctional Clustering and Conformational Analysis of the Arsenate Reductase Superfamily Reveals Nine Distinct Clusters
Isofunctional Clustering and Conformational Analysis of the Arsenate Reductase Superfamily Reveals Nine Distinct Clusters
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DOI：
10.1021/acs.biochem.0c00651
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发表时间：
2020-11-10
期刊：
影响因子：
2.9
通讯作者：
Fetrow，Jacquelyn S.
中科院分区：
文献类型：
--
作者：
Rosen，Mikaela R.;Leuthaeuser，Janelle B.;Fetrow，Jacquelyn S.
砷酸盐还原酶（ArsC）是还原砷酸盐的酶超家族。由于活性位点的相似性，一些ArsC可以作为低分子量蛋白酪氨酸磷酸酶（LMW-PTP）发挥作用。广泛的超家族分类与氧化还原伴侣（Trx或Grx连接）一致。为了了解这个超家族的机制多样性，ArsC超家族的活性位点的功能的基础上，利用工具TuLIP（两级迭代聚类过程）和autoMISST（自动多级迭代序列搜索技术）进行分类。这种方法确定了9个功能相关的（也许是同功能的）蛋白质组。五组表现出不同的ArsC机制。三个是Grx连锁的：4AA组（经典ArsC），3AAA组（YffB样）和5 BAA组。两个是Trx连锁的：6AAAAA和7AAAAAAAA。一个是Spx样转录调控组，组5AAA。三个是潜在的LMW-PTP组：组7 BAAAA和7AAAABAA，这是以前没有确定的，以及充分研究的LMW-PTP家族组8AAA。分子动力学模拟被用来探索功能网站的细节。在几个家庭中，我们确认并添加详细的文献为基础的机械信息。机制的作用被假设为保守的活性位点残基在几个家庭。在三个家庭中，模拟的unliganded结构样本特定的构象合奏，这是建议代表一个更配体结合能力的构象或一个途径向一个更结合能力的状态，这些活性位点可能会被设计为穿越高能量的障碍，更容易结合配体所需的较低能量的构象。这种更详细的了解ArsC和ArsC类PTP机制的生物化学打开了进一步了解砷酸盐生物修复和LMW-PTP机制的可能性。
Arsenate reductase (ArsC) is a superfamily of enzymes that reduce arsenate. Due to active site similarities, some ArsC can function as low-molecular weight protein tyrosine phosphatases (LMW-PTPs). Broad superfamily classifications align with redox partners (Trx- or Grx-linked). To understand this superfamily’s mechanistic diversity, the ArsC superfamily is classified on the basis of active site features utilizing the tools TuLIP (two-level iterative clustering process) and autoMISST (automated multilevel iterative sequence searching technique). This approach identified nine functionally relevant (perhaps isofunctional) protein groups. Five groups exhibit distinct ArsC mechanisms. Three are Grx-linked: group 4AA (classical ArsC), group 3AAA (YffB-like), and group 5BAA. Two are Trx-linked: groups 6AAAAA and 7AAAAAAAA. One is an Spx-like transcriptional regulatory group, group 5AAA. Three are potential LMW-PTP groups: groups 7BAAAA, and 7AAAABAA, which have not been previously identified, and the well-studied LMW-PTP family group 8AAA. Molecular dynamics simulations were utilized to explore functional site details. In several families, we confirm and add detail to literature-based mechanistic information. Mechanistic roles are hypothesized for conserved active site residues in several families. In three families, simulations of the unliganded structure sample specific conformational ensembles, which are proposed to represent either a more ligand-binding-competent conformation or a pathway toward a more binding-competent state; these active sites may be designed to traverse high-energy barriers to the lower-energy conformations necessary to more readily bind ligands. This more detailed biochemical understanding of ArsC and ArsC-like PTP mechanisms opens possibilities for further understanding of arsenate bioremediation and the LMW-PTP mechanism.