5YIJ

Structure of a Legionella effector with substrates

5YIJ の概要

• エントリーDOI: 10.2210/pdb5yij/pdb
• 分子名称: SdeA, Ubiquitin, 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE (3 entities in total)
• 機能のキーワード: transferase, complex, alpha-helical domain, transferase-protein binding complex, transferase/protein binding
• 由来する生物種: Legionella pneumophila; 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 136859.55

構造登録者

Feng, Y.,Mu, Y.,Wang, H. (登録日: 2017-10-05, 公開日: 2018-05-30, 最終更新日: 2023-11-22)

主引用文献

Dong, Y.,Mu, Y.,Xie, Y.,Zhang, Y.,Han, Y.,Zhou, Y.,Wang, W.,Liu, Z.,Wu, M.,Wang, H.,Pan, M.,Xu, N.,Xu, C.Q.,Yang, M.,Fan, S.,Deng, H.,Tan, T.,Liu, X.,Liu, L.,Li, J.,Wang, J.,Fang, X.,Feng, Y.
Structural basis of ubiquitin modification by the Legionella effector SdeA.
Nature, 557:674-678, 2018

PubMed Abstract: Protein ubiquitination is a multifaceted post-translational modification that controls almost every process in eukaryotic cells. Recently, the Legionella effector SdeA was reported to mediate a unique phosphoribosyl-linked ubiquitination through successive modifications of the Arg42 of ubiquitin (Ub) by its mono-ADP-ribosyltransferase (mART) and phosphodiesterase (PDE) domains. However, the mechanisms of SdeA-mediated Ub modification and phosphoribosyl-linked ubiquitination remain unknown. Here we report the structures of SdeA in its ligand-free, Ub-bound and Ub-NADH-bound states. The structures reveal that the mART and PDE domains of SdeA form a catalytic domain over its C-terminal region. Upon Ub binding, the canonical ADP-ribosyltransferase toxin turn-turn (ARTT) and phosphate-nicotinamide (PN) loops in the mART domain of SdeA undergo marked conformational changes. The Ub Arg72 might act as a 'probe' that interacts with the mART domain first, and then movements may occur in the side chains of Arg72 and Arg42 during the ADP-ribosylation of Ub. Our study reveals the mechanism of SdeA-mediated Ub modification and provides a framework for further investigations into the phosphoribosyl-linked ubiquitination process.

PubMed: 29795342
DOI: 10.1038/s41586-018-0146-7

実験手法

X-RAY DIFFRACTION (3.18 Å)