4KG3

Crystal structure of Saccharomyces cerevisiae Dcp2 Nudix domain in complex with Mg (E153Q mutation)

4KG3 の概要

• エントリーDOI: 10.2210/pdb4kg3/pdb
• 関連するPDBエントリー: 4K6E 4KG4
• 分子名称: mRNA-decapping enzyme subunit 2, MAGNESIUM ION (3 entities in total)
• 機能のキーワード: nudix, mrna decay, mrna decapping, hydrolase
• 由来する生物種: Saccharomyces cerevisiae (Baker's yeast)
• 細胞内の位置: Cytoplasm, P-body: P53550
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 52206.69

構造登録者

Aglietti, R.A.,Floor, S.N.,Gross, J.D. (登録日: 2013-04-28, 公開日: 2013-08-21, 最終更新日: 2024-02-28)

主引用文献

Aglietti, R.A.,Floor, S.N.,McClendon, C.L.,Jacobson, M.P.,Gross, J.D.
Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme dcp2.
Structure, 21:1571-1580, 2013

PubMed Abstract: Removal of the 5' cap structure by Dcp2 is a major step in several 5'-3' mRNA decay pathways. The activity of Dcp2 is enhanced by Dcp1 and bound coactivators, yet the details of how these interactions are linked to chemistry are poorly understood. Here, we report three crystal structures of the catalytic Nudix hydrolase domain of Dcp2 that demonstrate binding of a catalytically essential metal ion, and enzyme kinetics are used to identify several key active site residues involved in acid/base chemistry of decapping. Using nuclear magnetic resonance and molecular dynamics, we find that a conserved metal binding loop on the catalytic domain undergoes conformational changes during the catalytic cycle. These findings describe key events during the chemical step of decapping, suggest local active site conformational changes are important for activity, and provide a framework to explain stimulation of catalysis by the regulatory domain of Dcp2 and associated coactivators.

PubMed: 23911090
DOI: 10.1016/j.str.2013.06.021

実験手法

X-RAY DIFFRACTION (1.7 Å)