title: Crystal structures of RidA, an important enzyme for the prevention of toxic side products.
abstract: The YjgF/YER057c/UK114 family proteins are highly conserved across all three domains of life, and most of them currently have no clearly defined biological roles. In vitro, these proteins were found to hydrolyze the enamine/imine intermediates generated from serine or threonine, and were renamed Reactive Intermediate Deaminase A (RidA). RidA was recently discovered in Arabidopsis thaliana, and by deaminating the toxic enamine/imine intermediates, it prevents the inactivation of many functionally important pyridoxal 5'-phosphate (PLP)-containing enzymes in plants such as branched-chain aminotransferase BCAT (IlvE). In this study, we determined the crystal structure of Arabidopsis thaliana RidA in the apo form, as well as RidA complexed with the ligand pyruvate. RidA forms the trimeric, barrel-like quaternary structure and inter-subunit cavities, and resembles most RidA family members. Each pyruvate molecule binds to the interface between two subunits, and the recognition of pyruvate is achieved by the interactions with R165 and T167. From sequence alignment and structural superposition, we identified a series of key residues responsible for the trimer assembly, whose importance was confirmed by enzymatic assays. This study provides structural insight into RidA functions in plants.
authors.affiliation: State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, 135 W. Xingang Rd., Guangzhou, Guangdong 510275, People's Republic of China.|Center for Cellular &Structural biology, The Sun Yat-Sen University, 132 E. Circle Rd., University City, Guangzhou, Guangdong 510006, People's Republic of China.
authors.forename: Xiwen
authors.initials: X
authors.lastname: Liu
authors.affiliation: State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, 135 W. Xingang Rd., Guangzhou, Guangdong 510275, People's Republic of China.|Center for Cellular &Structural biology, The Sun Yat-Sen University, 132 E. Circle Rd., University City, Guangzhou, Guangdong 510006, People's Republic of China.
authors.forename: Jianhua
authors.initials: J
authors.lastname: Zeng
authors.affiliation: State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, 135 W. Xingang Rd., Guangzhou, Guangdong 510275, People's Republic of China.|Center for Cellular &Structural biology, The Sun Yat-Sen University, 132 E. Circle Rd., University City, Guangzhou, Guangdong 510006, People's Republic of China.
authors.forename: Xiaolei
authors.initials: X
authors.lastname: Chen
authors.affiliation: State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, 135 W. Xingang Rd., Guangzhou, Guangdong 510275, People's Republic of China.|Center for Cellular &Structural biology, The Sun Yat-Sen University, 132 E. Circle Rd., University City, Guangzhou, Guangdong 510006, People's Republic of China.
authors.forename: Wei
authors.initials: W
authors.lastname: Xie
mesh_terms: D000595:Amino Acid Sequence; D000619:Aminohydrolases / Q000737:chemistry* / Q000378:metabolism*; D001051:Apoenzymes / Q000737:chemistry; D017360:Arabidopsis / Q000201:enzymology*; D029681:Arabidopsis Proteins / Q000737:chemistry* / Q000378:metabolism*; D018360:Crystallography, X-Ray; D057075:Enzyme Assays; D008024:Ligands; D050505:Mutant Proteins / Q000737:chemistry / Q000378:metabolism; D055503:Protein Multimerization; D019289:Pyruvic Acid / Q000378:metabolism; D040681:Structural Homology, Protein; D014118:Toxins, Biological / Q000378:metabolism*
chemical_list: D001051:Apoenzymes; D029681:Arabidopsis Proteins; D008024:Ligands; D050505:Mutant Proteins; D014118:Toxins, Biological; D019289:Pyruvic Acid; D000619:Aminohydrolases; C000599350:RidA protein, Arabidopsis