5HP7

Crystal structures of RidA in the apo form

5HP7 の概要

• エントリーDOI: 10.2210/pdb5hp7/pdb
• 関連するPDBエントリー: 5HP8
• 分子名称: Reactive Intermediate Deaminase A, chloroplastic (2 entities in total)
• 機能のキーワード: rida, enamine/imine, deamination, hydrolase
• 由来する生物種: Arabidopsis thaliana (Mouse-ear cress)
• 細胞内の位置: Plastid, chloroplast : Q94JQ4
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 13231.14

構造登録者

Xie, W.,Liu, X. (登録日: 2016-01-20, 公開日: 2016-10-12, 最終更新日: 2023-11-08)

主引用文献

Liu, X.,Zeng, J.,Chen, X.,Xie, W.
Crystal structures of RidA, an important enzyme for the prevention of toxic side products
Sci Rep, 6:30494-30494, 2016

PubMed 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.

PubMed: 27458092
DOI: 10.1038/srep30494

実験手法

X-RAY DIFFRACTION (2 Å)