Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China.
Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian 116600, China.
Molecules. 2022 Jul 26;27(15):4781. doi: 10.3390/molecules27154781.
Pyridoxal 5′-phosphate (PLP) is the active form of vitamin B6, but it is highly reactive and poisonous in its free form. YggS is a PLP-binding protein found in bacteria and humans that mediates PLP homeostasis by delivering PLP to target enzymes or by performing a protective function. Several biochemical and structural studies of YggS have been reported, but the mechanism by which YggS recognizes PLP has not been fully elucidated. Here, we report a functional and structural analysis of YggS from Fusobacterium nucleatum (FnYggS). The PLP molecule could bind to native FnYggS, but no PLP binding was observed for selenomethionine (SeMet)-derivatized FnYggS. The crystal structure of FnYggS showed a type III TIM barrel fold, exhibiting structural homology with several other PLP-dependent enzymes. Although FnYggS exhibited low (<35%) amino acid sequence similarity with previously studied YggS proteins, its overall structure and PLP-binding site were highly conserved. In the PLP-binding site of FnYggS, the sulfate ion was coordinated by the conserved residues Ser201, Gly218, and Thr219, which were positioned to provide the binding moiety for the phosphate group of PLP. The mutagenesis study showed that the conserved Ser201 residue in FnYggS was the key residue for PLP binding. These results will expand the knowledge of the molecular properties and function of the YggS family.
吡哆醛 5′-磷酸（PLP）是维生素 B6 的活性形式，但在游离形式下具有很高的反应性和毒性。YggS 是一种在细菌和人类中发现的 PLP 结合蛋白，通过将 PLP 递送给靶酶或发挥保护功能来介导 PLP 动态平衡。已经报道了几项关于 YggS 的生化和结构研究，但 YggS 识别 PLP 的机制尚未完全阐明。在这里，我们报告了来自核梭杆菌（FnYggS）的 YggS 的功能和结构分析。PLP 分子可以与天然 FnYggS 结合，但未观察到硒代甲硫氨酸（SeMet）衍生的 FnYggS 结合 PLP。FnYggS 的晶体结构显示出 III 型 TIM 桶折叠，与其他几种依赖 PLP 的酶具有结构同源性。尽管 FnYggS 与先前研究的 YggS 蛋白的氨基酸序列相似性<35%，但其整体结构和 PLP 结合位点高度保守。在 FnYggS 的 PLP 结合位点中，硫酸根离子由保守残基 Ser201、Gly218 和 Thr219 配位，这些残基的位置为 PLP 的磷酸基团提供了结合部分。突变研究表明，FnYggS 中的保守 Ser201 残基是 PLP 结合的关键残基。这些结果将扩展 YggS 家族的分子性质和功能的知识。
