Tianjin Key Laboratory of Protein Science, College of Life Science, Nankai University, Tianjin 300071, China.
J Struct Biol. 2010 Apr;170(1):76-82. doi: 10.1016/j.jsb.2009.11.012. Epub 2009 Nov 26.
Protoporphyrinogen IX oxidase (PPO) converts protoporphyrinogen IX to protoporphyrin IX, playing an important part in the heme/chlorophyll biosynthetic pathway. Bacillus subtilis PPO (bsPPO) is unique among PPO family members in that it is a soluble monomer, is inefficiently inhibited by the herbicide acifluorfen (AF) and has broader substrate specificity than other PPO enzymes. Here, we present the crystal structure of bsPPO bound to AF. Our structure shows that the AF molecule binds to a new site outside the previously identified inhibitor binding pocket. Most importantly, the benzene ring of the 2-nitrobenzoic acid moiety of AF lies parallel to the isoalloxazine ring of FAD at a distance of less than 3.5A, providing a framework for the interaction of FAD with the substrate protoporphyrinogen IX. Furthermore, our structure reveals that the larger substrate binding chamber and predominantly positively charged chamber surface of bsPPO are more favorable for the binding of coproporphyrinogen-III. These crystallographic findings uncover biochemically unique properties of bsPPO, providing important information for further understanding the enzymatic mechanism.
原卟啉原 IX 氧化酶（PPO）将原卟啉原 IX 转化为原卟啉 IX，在血红素/叶绿素生物合成途径中发挥重要作用。枯草芽孢杆菌 PPO（bsPPO）在 PPO 家族成员中是独特的，因为它是一种可溶性单体，对除草剂三氟羧草醚（AF）的抑制效率较低，并且比其他 PPO 酶具有更广泛的底物特异性。在这里，我们展示了与 AF 结合的 bsPPO 的晶体结构。我们的结构表明，AF 分子结合到先前确定的抑制剂结合口袋之外的新位点。最重要的是，AF 的 2-硝基苯甲酸部分的苯环与 FAD 的异咯嗪环平行，距离小于 3.5A，为 FAD 与底物原卟啉原 IX 的相互作用提供了一个框架。此外，我们的结构揭示了 bsPPO 更大的底物结合腔和主要带正电荷的腔表面更有利于粪卟啉原-III 的结合。这些晶体学发现揭示了 bsPPO 的生化独特性质，为进一步了解酶的机制提供了重要信息。
