4NRI

Crystal Structure of a human Mms2/Ubc13 A122G mutant

4NRI の概要

• エントリーDOI: 10.2210/pdb4nri/pdb
• 関連するPDBエントリー: 4NR3 4NRG
• 分子名称: Ubiquitin-conjugating enzyme E2 variant 2, Ubiquitin-conjugating enzyme E2 N, GLYCEROL, ... (4 entities in total)
• 機能のキーワード: ubc13, mms2, e2, ubiquitin conjugating enzyme, ligase
• 由来する生物種: Homo sapiens (human); 詳細
• 細胞内の位置: Nucleus : P61088
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 34267.16

構造登録者

Hodge, C.D.,Edwards, R.A.,Glover, J.N.M. (登録日: 2013-11-26, 公開日: 2014-12-10, 最終更新日: 2023-09-20)

主引用文献

Rout, M.K.,Hodge, C.D.,Markin, C.J.,Xu, X.,Glover, J.N.,Xiao, W.,Spyracopoulos, L.
Stochastic gate dynamics regulate the catalytic activity of ubiquitination enzymes.
J.Am.Chem.Soc., 136:17446-17458, 2014

PubMed Abstract: Initiation of the DNA damage and innate immune responses is dependent upon the flow of chemical information through coupled protein-protein interaction networks and driven by the synthesis and recognition of Lys 63 linked polyubiquitin (polyUb) chains on adaptor proteins. The central chemical step in Lys 63-linked protein ubiquitination involves the reaction of a specific lysine on a target protein with Ub that is covalently attached as a thioester conjugate to the Ub conjugating enzyme (E2) Ubc13. The active site cysteine of Ubc13, and E2 enzymes in general, is buttressed by a flexible loop. The role of loop dynamics in catalysis was investigated by mutating the central and hinge residues to glycine. The loop dynamics were experimentally characterized through measurement of enzyme kinetics, main chain NMR relaxation, X-ray crystallographic studies, and in vivo studies in yeast. The experimental data were complemented by analysis of MD simulations of the dynamics and kinetics for the loop motion. The results show that fast pico- to nanosecond time scale active site loop fluctuations play a crucial role in regulating the catalytic activity of Ubc13 by functioning as a stochastic active site gate, which is characterized by precisely balanced rates of opening and closing. In vivo functional complementation assays in yeast demonstrate that defects within this regulatory mechanism can have profound biological consequences, given that Ubc13 is the only E2 dedicated to synthesizing Lys 63-linked polyUb chains.

PubMed: 25423605
DOI: 10.1021/ja505440b

実験手法

X-RAY DIFFRACTION (2.3 Å)