Structural and Functional Analysis of the Pyridoxal Phosphate Homeostasis Protein YggS from <i>Fusobacterium nucleatum</i>
Shanru He,
Yuanyuan Chen,
Lulu Wang,
Xue Bai,
Tingting Bu,
Jie Zhang,
Ming Lu,
Nam-Chul Ha,
Chunshan Quan,
Ki Hyun Nam,
Yongbin Xu
Affiliations
Shanru He
Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
Yuanyuan Chen
Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
Lulu Wang
Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
Xue Bai
Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
Tingting Bu
Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
Jie Zhang
Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
Ming Lu
Shandong Provincial Key Laboratory of Energy Genetics, Key Laboratory of Biofuel, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
Nam-Chul Ha
Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Gwanak-gu, Seoul 00826, Korea
Chunshan Quan
Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
Ki Hyun Nam
Department of Life Science, Pohang University of Science and Technology, Pohang 37673, Korea
Yongbin Xu
Department of Bioengineering, College of Life Science, Dalian Minzu University, Dalian 116600, China
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.
