Structural basis of ubiquitin modification by the Legionella effector SdeA

Yanan Dong, Yajuan Mu, Yongchao Xie, Yupeng Zhang, Youyou Han, Yu Zhou, Wenhe Wang, Zihe Liu, Mei Wu, Hao Wang, Man Pan, Ning Xu, Cong-Qiao Xu, Maojun Yang, Shilong Fan, Haiteng Deng, Tianwei Tan, Xiaoyun Liu, Lei Liu, Jun Li, Jiawei Wang, Xianyang Fang and Yue Feng ()
Additional contact information
Yanan Dong: College of Life Science and Technology, Beijing University of Chemical Technology
Yajuan Mu: College of Life Science and Technology, Beijing University of Chemical Technology
Yongchao Xie: College of Life Science and Technology, Beijing University of Chemical Technology
Yupeng Zhang: School of Life Sciences, Tsinghua University
Youyou Han: College of Life Science and Technology, Beijing University of Chemical Technology
Yu Zhou: National Institute of Biological Sciences
Wenhe Wang: College of Life Science and Technology, Beijing University of Chemical Technology
Zihe Liu: College of Life Science and Technology, Beijing University of Chemical Technology
Mei Wu: College of Chemistry and Molecular Engineering, Peking University
Hao Wang: College of Life Science and Technology, Beijing University of Chemical Technology
Man Pan: Tsinghua University
Ning Xu: School of Life Sciences, Tsinghua University
Cong-Qiao Xu: Tsinghua University
Maojun Yang: School of Life Sciences, Tsinghua University
Shilong Fan: School of Life Sciences, Tsinghua University
Haiteng Deng: School of Life Sciences, Tsinghua University
Tianwei Tan: College of Life Science and Technology, Beijing University of Chemical Technology
Xiaoyun Liu: College of Chemistry and Molecular Engineering, Peking University
Lei Liu: Tsinghua University
Jun Li: Tsinghua University
Jiawei Wang: School of Life Sciences, Tsinghua University
Xianyang Fang: School of Life Sciences, Tsinghua University
Yue Feng: College of Life Science and Technology, Beijing University of Chemical Technology

Nature, 2018, vol. 557, issue 7707, 674-678

Abstract: 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.

Date: 2018
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DOI: 10.1038/s41586-018-0146-7

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