Structural insights into the catalytic and substrate recognition mechanisms of bacterial L‐arabinose 1‐dehydrogenase
Structural insights into the catalytic and substrate recognition mechanisms of bacterial L‐arabinose 1‐dehydrogenase
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细菌 L-阿拉伯糖 1-脱氢酶催化和底物识别机制的结构见解
DOI：
10.1002/1873-3468.13424
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发表时间：
2019
期刊：
影响因子：
3.5
通讯作者：
Watanabe Seiya
中科院分区：
文献类型：
--
作者：
Watanabe Yasunori;Iga Chinatsu;Watanabe Yasuo;Watanabe Seiya
在巴西固氮菌（一种革兰氏阴性固氮菌）中，l-阿拉伯糖通过非磷酸化代谢途径转化为α-酮戊二酸。在该途径的第一步中，L-阿拉伯糖被属于葡萄糖-果糖氧化还原酶/肌醇脱氢酶/根碱催化蛋白（Gfo/Idh/莫卡）家族的NAD（P）依赖性L-阿拉伯糖1-脱氢酶（AraDH）氧化为tol-阿拉伯糖-γ-内酯。在这里，我们分别以1.5和2.2 μ m的分辨率确定了apo和NADP结合的AraDH的晶体结构。l-阿拉伯糖和NADP结合的AraDH的对接模型和基于结构的突变分析表明，Lys 91或Asp 169作为催化碱基，Glu 147，His 153和Asn 173负责底物识别。特别是，Asn 173可能在l-阿拉伯糖和d-木糖（l-阿拉伯糖的C4差向异构体）之间的区分中发挥作用。
InAzospirillum brasilense, a gram‐negative nitrogen‐fixing bacterium,l‐arabinose is converted to α‐ketoglutarate through a nonphosphorylative metabolic pathway. In the first step in the pathway,l‐arabinose is oxidized tol‐arabino‐γ‐lactone by NAD(P)‐dependentl‐arabinose 1‐dehydrogenase (AraDH) belonging to the glucose‐fructose oxidoreductase/inositol dehydrogenase/rhizopine catabolism protein (Gfo/Idh/MocA) family. Here, we determined the crystal structures of apo‐ and NADP‐bound AraDH at 1.5 and 2.2 Å resolutions, respectively. A docking model ofl‐arabinose and NADP‐bound AraDH and structure‐based mutational analyses suggest that Lys91 or Asp169 serves as a catalytic base and that Glu147, His153, and Asn173 are responsible for substrate recognition. In particular, Asn173 may play a role in the discrimination betweenl‐arabinose andd‐xylose, the C4 epimer ofl‐arabinose.