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Structural insights into the NAD+-dependent formate dehydrogenase mechanism revealed from the NADH complex and the formate NAD+ ternary complex of the Chaetomium thermophilum enzyme
Journal of Structural Biology ( IF 3 ) Pub Date : 2020-10-24 , DOI: 10.1016/j.jsb.2020.107657
Berin Yilmazer 1 , Michail N Isupov 2 , Simone A De Rose 2 , Huri Bulut 3 , Jens C Benninghoff 2 , Barış Binay 4 , Jennifer A Littlechild 2
Affiliation  

The removal of carbon dioxide from the waste streams of industrial processes is a major challenge for creation of a sustainable circular economy. This makes the synthesis of formate from CO2 by NAD+ dependent formate dehydrogenases (FDHs) an attractive process for this purpose. The efficiency of this reaction is however low and to achieve a viable industrial process an optimised engineered enzyme needs to be developed.

In order to understand the detailed enzymatic mechanism of catalysis structures of different cofactor and substrate complexes of the FDH from the thermophilic filamentous fungus, Chaetomium thermophilum have been determined to 1.2–1.3 Å resolution. The substrate formate is shown to be held by four hydrogen bonds in the FDH catalytic site within the ternary complex with substrate and NAD+and a secondary formate binding site is observed in crystals soaked with substrate. Water molecules are excluded from the FDH catalytic site when the substrate is bound. The angle between the plane of the NAD+ cofactor pyridine ring and the plane of the formate molecule is around 27°. Additionally, structures of a FDH mutant enzyme, N120C, in complex with the reduced form of the cofactor have also been determined both in the presence and absence of formate bound at the secondary site. These structures provide further understanding of the catalytic mechanism of this fungal enzyme.



中文翻译:

从 NADH 复合物和嗜热毛壳菌酶的甲酸 NAD+ 三元复合物揭示的 NAD+ 依赖性甲酸脱氢酶机制的结构见解

从工业过程的废物流中去除二氧化碳是创建可持续循环经济的主要挑战。这使得通过 NAD +依赖性甲酸脱氢酶 (FDH)从 CO 2合成甲酸成为为此目的的有吸引力的过程。然而,该反应的效率很低,为了实现可行的工业过程,需要开发优化的工程酶。

为了了解来自嗜热丝状真菌的 FDH 的不同辅因子和底物复合物的催化结构的详细酶促机制,嗜热毛壳菌已被确定为 1.2-1.3 Å 分辨率。底物甲酸盐显示由与底物和 NAD +的三元复合物中的 FDH 催化位点中的四个氢键保持,并且在用底物浸泡的晶体中观察到二级甲酸盐结合位点。当底物被结合时,水分子被排除在 FDH 催化位点之外。NAD +平面之间的角度辅因子吡啶环与甲酸盐分子的平面大约为 27°。此外,在二级位点结合的甲酸存在和不存在的情况下,还确​​定了与辅因子的还原形式复合的 FDH 突变酶 N120C 的结构。这些结构有助于进一步了解这种真菌酶的催化机制。

更新日期:2020-11-02
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