2RSU

Alternative structure of Ubiquitin

2RSU の概要

• エントリーDOI: 10.2210/pdb2rsu/pdb
• 関連するPDBエントリー: 1V80 1V81
• NMR情報: BMRB: 11505
• 分子名称: Ubiquitin (1 entity in total)
• 機能のキーワード: ubiquitin, q41n, high energy, n2, protein binding
• 由来する生物種: Homo sapiens (human)
• 細胞内の位置: Ubiquitin: Cytoplasm (By similarity): P0CG48
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 8562.81

構造登録者

Kitazawa, S.,Kameda, T.,Yagi-Utsumi, M.,Kato, K.,Kitahara, R. (登録日: 2012-06-15, 公開日: 2013-03-27, 最終更新日: 2024-05-15)

主引用文献

Kitazawa, S.,Kameda, T.,Yagi-Utsumi, M.,Sugase, K.,Baxter, N.J.,Kato, K.,Williamson, M.P.,Kitahara, R.
Solution Structure of the Q41N Variant of Ubiquitin as a Model for the Alternatively Folded N2 State of Ubiquitin
Biochemistry, 52:1874-1885, 2013

PubMed Abstract: It is becoming increasingly clear that proteins transiently populate high-energy excited states as a necessary requirement for function. Here, we demonstrate that rational mutation based on the characteristics of the structure and dynamics of proteins obtained from pressure experiments is a new strategy for amplifying particular fluctuations in proteins. We have previously shown that ubiquitin populates a high-energy conformer, N2, at high pressures. Here, we show that the Q41N mutation favors N2: high-pressure nuclear magnetic resonance (NMR) shows that N2 is ∼70% populated in Q41N but only ∼20% populated in the wild type at ambient pressure. This allows us to characterize the structure of N2, in which α1-helix, the following loop, β3-strand, and β5-strand change their orientations relative to the remaining regions. Conformational fluctuation on the microsecond time scale, characterized by (15)N spin relaxation NMR analysis, is markedly increased for these regions of the mutant. The N2 conformers produced by high pressure and by the Q41N mutation are quite similar in both structure and dynamics. The conformational change to produce N2 is proposed to be a novel dynamic feature beyond the known recognition dynamics of the protein. Indeed, it is orthogonal to that seen when proteins containing a ubiquitin-interacting motif bind at the hydrophobic patch of ubiquitin but matches changes seen on binding to the E2 conjugating enzyme. More generally, structural and dynamic effects of hydrodynamic pressure are shown to be useful for characterizing functionally important intermediates.

PubMed: 23421577
DOI: 10.1021/bi301420m

実験手法

SOLUTION NMR