5BNB

Crystal structure of a Ube2S-ubiquitin conjugate

5BNB の概要

• エントリーDOI: 10.2210/pdb5bnb/pdb
• 分子名称: Ubiquitin-conjugating enzyme E2 S, Polyubiquitin-B (3 entities in total)
• 機能のキーワード: ubiquitin-conjugating enzyme, e2 enzyme, ubc domain, ubiquitination, cell cycle
• 由来する生物種: Homo sapiens (Human); 詳細
• 細胞内の位置: Ubiquitin: Cytoplasm : P0CG47
• タンパク質・核酸の鎖数: 8
• 化学式量合計: 104159.74

構造登録者

Lorenz, S.G.,Feiler, C.G.,Kuriyan, J. (登録日: 2015-05-25, 公開日: 2016-02-17, 最終更新日: 2024-11-13)

主引用文献

Lorenz, S.,Bhattacharyya, M.,Feiler, C.,Rape, M.,Kuriyan, J.
Crystal Structure of a Ube2S-Ubiquitin Conjugate.
Plos One, 11:e0147550-e0147550, 2016

PubMed Abstract: Protein ubiquitination occurs through the sequential formation and reorganization of specific protein-protein interfaces. Ubiquitin-conjugating (E2) enzymes, such as Ube2S, catalyze the formation of an isopeptide linkage between the C-terminus of a "donor" ubiquitin and a primary amino group of an "acceptor" ubiquitin molecule. This reaction involves an intermediate, in which the C-terminus of the donor ubiquitin is thioester-bound to the active site cysteine of the E2 and a functionally important interface is formed between the two proteins. A docked model of a Ube2S-donor ubiquitin complex was generated previously, based on chemical shift mapping by NMR, and predicted contacts were validated in functional studies. We now present the crystal structure of a covalent Ube2S-ubiquitin complex. The structure contains an interface between Ube2S and ubiquitin in trans that resembles the earlier model in general terms, but differs in detail. The crystallographic interface is more hydrophobic than the earlier model and is stable in molecular dynamics (MD) simulations. Remarkably, the docked Ube2S-donor complex converges readily to the configuration seen in the crystal structure in 3 out of 8 MD trajectories. Since the crystallographic interface is fully consistent with mutational effects, this indicates that the structure provides an energetically favorable representation of the functionally critical Ube2S-donor interface.

PubMed: 26828794
DOI: 10.1371/journal.pone.0147550

実験手法

X-RAY DIFFRACTION (2.49 Å)