Crystal structure of Pelagibacterium halotolerans PE8: New insight into its substrate-binding pattern.
Crystal structure of Pelagibacterium halotolerans PE8: New insight into its substrate-binding pattern.
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Pelagibacter halotolerans PE8 的晶体结构：对其底物结合模式的新见解
DOI：
10.1038/s41598-017-04550-7
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发表时间：
2017-06-30
影响因子：
4.6
通讯作者：
Xu XW
中科院分区：
文献类型：
--
作者：
Huo YY;Li S;Huang J;Rong Z;Wang Z;Li Z;Ji R;Kuang S;Cui HL;Li J;Xu XW
溶血磷脂酶_羧酸酯酶(LPCE)在从细菌到人类的多种物种中都具有高度保守的同源物，具有重要的生物学意义和潜在的治疗意义。然而，由于缺乏结构信息，对其生物学功能和催化机理的研究还很少。在这里，我们报道了属于LPCE家族的细菌酯酶PE8的晶体结构。对PE8的晶体结构进行了解析，得到了1.66？的高分辨率。与该家族中的其他同源物相比，在氨基酸序列、三维结构和底物结合模式上存在显著差异。残基Arg79在与底物结合时发生构型转换，形成独特的壁，导致底物结合口袋中的空腔相对闭合，与其他同源物中相对开放和更长的裂隙相比。此外，突变体Met122Ala具有更强的底物亲和力和更高的催化效率，这是因为对底物的空间斥力较小。综上所述，这些结果表明，在PE8中，Arg79和Met122分别在底物结合和结合口袋形成中发挥重要作用。我们的研究为LPCE的催化机理提供了新的见解，可能会促进基于结构的疗法和其他生物催化应用的发展。
Lysophospholipase_carboxylesterase (LPCE) has highly conserved homologs in many diverse species ranging from bacteria to humans, as well as substantial biological significance and potential therapeutic implications. However, its biological function and catalytic mechanism remain minimally investigated because of the lack of structural information. Here, we report the crystal structure of a bacterial esterase PE8 belonging to the LPCE family. The crystal structure of PE8 was solved with a high resolution of 1.66 Å. Compared with other homologs in the family, significant differences were observed in the amino acid sequence, three-dimensional structure, and substrate-binding pattern. Residue Arg79 undergoes configuration switching when binding to the substrate and forms a unique wall, leading to a relatively closed cavity in the substrate-binding pocket compared with the relatively more open and longer clefts in other homologs. Moreover, the mutant Met122Ala showed much stronger substrate affinity and higher catalytic efficiency because less steric repulsion acted on the substrates. Taken together, these results showed that, in PE8, Arg79 and Met122 play important roles in substrate binding and the binding pocket shaping, respectively. Our study provides new insight into the catalytic mechanism of LPCE, which may facilitate the development of structure-based therapeutics and other biocatalytic applications.