7ZS6

Crystal structure of Apis mellifera RidA

これはPDB形式変換不可エントリーです。

7ZS6 の概要

• エントリーDOI: 10.2210/pdb7zs6/pdb
• 分子名称: Reactive intermediate deaminase A, 1,2-ETHANEDIOL, MAGNESIUM ION, ... (5 entities in total)
• 機能のキーワード: deiminase, ractive intermediate deaminase, unknown function
• 由来する生物種: Apis mellifera (honey bee)
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 46338.56

構造登録者

Visentin, C.,Rizzi, G.,Ricagno, S. (登録日: 2022-05-06, 公開日: 2022-07-13, 最終更新日: 2024-01-31)

主引用文献

Visentin, C.,Rizzi, G.,Degani, G.,Digiovanni, S.,Robecchi, G.,Barbiroli, A.,Popolo, L.,Vanoni, M.A.,Ricagno, S.
Apis mellifera RidA, a novel member of the canonical YigF/YER057c/UK114 imine deiminase superfamily of enzymes pre-empting metabolic damage.
Biochem.Biophys.Res.Commun., 616:70-75, 2022

PubMed Abstract: The Reactive intermediate deiminase (Rid) protein family is a group of enzymes widely distributed in all Kingdoms of Life. RidA is one of the eight known Rid subfamilies, and its members act by preventing the accumulation of 2-aminoacrylate, a highly reactive enamine generated during the metabolism of some amino acids, by hydrolyzing the 2-iminopyruvate tautomer to pyruvate and ammonia. RidA members are homotrimers exhibiting a remarkable thermal stability. Recently, a novel subclass of RidA was identified in teleosts, which differs for stability and substrate specificity from the canonical RidA. In this study we structurally and functionally characterized RidA from Apis mellifera (RidA) as the first example of an invertebrate RidA to assess its belonging to the canonical RidA group, and to further correlate structural and functional features of this novel enzyme class. Circular dichroism revealed a spectrum typical of the RidA proteins and the high thermal stability. RidA exhibits the 2-imino acid hydrolase activity typical of RidA family members with a substrate specificity similar to that of the canonical RidA. The crystal structure confirmed the homotrimeric assembly and the presence of the typical structural features of RidA proteins, such as the proposed substrate recognition loop, and the ß-sheets ß1-ß9 and ß1-ß2. In conclusion, our data define RidA as a canonical member of the well-conserved RidA family and further clarify the diagnostic structural features of this class of enzymes.

PubMed: 35640488
DOI: 10.1016/j.bbrc.2022.05.062

実験手法

X-RAY DIFFRACTION (1.31 Å)