Mechanism of phosphoribosyl-ubiquitination mediated by a single Legionella effector

• Published in: Nature (London) Vol. 557; no. 7707; pp. 729 - 733
• Main Authors: Akturk, Anil, Wasilko, David J., Wu, Xiaochun, Liu, Yao, Zhang, Yong, Qiu, Jiazhang, Luo, Zhao-Qing, Reiter, Katherine H., Brzovic, Peter S., Klevit, Rachel E., Mao, Yuxin
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01.05.2018; Nature Publishing Group
• Subjects: 101/6; 13/1; 13/106; 13/109; 631/326/41/2536; 631/45/607/1166; 631/535/1266; 631/80/458/582; 82/1; 82/16; 82/29; 82/80; 82/83; Adenosine diphosphate; Amino acids; AMP; Bacterial proteins; Binding sites; Biochemical analysis; Catalysis; Crystal structure; Eukaryotes; Future predictions; Homology; Humanities and Social Sciences; Legionella; Legionella pneumophila; Legionnaires' disease bacterium; Letter; Lysine; Molecular chains; multidisciplinary; Mutation; Phosphodiesterase; Post-translation; Post-translational modifications; Protein research; Proteins; Science; Science (multidisciplinary); Serine; Signal transduction; Substrates; Translation; Ubiquitin; Ubiquitin-proteasome system; Ubiquitination
• ISSN: 0028-0836; 1476-4687
• DOI: 10.1038/s41586-018-0147-6

Ubiquitination is a post-translational modification that regulates many cellular processes in eukaryotes 1 – 4 . The conventional ubiquitination cascade culminates in a covalent linkage between the C terminus of ubiquitin (Ub) and a target protein, usually on a lysine side chain 1 , 5 . Recent studies of the Legionella pneumophila SidE family of effector proteins revealed a ubiquitination method in which a phosphoribosyl ubiquitin (PR-Ub) is conjugated to a serine residue on substrates via a phosphodiester bond 6 – 8 . Here we present the crystal structure of a fragment of the SidE family member SdeA that retains ubiquitination activity, and determine the mechanism of this unique post-translational modification. The structure reveals that the catalytic module contains two distinct functional units: a phosphodiesterase domain and a mono-ADP-ribosyltransferase domain. Biochemical analysis shows that the mono-ADP-ribosyltransferase domain-mediated conversion of Ub to ADP-ribosylated Ub (ADPR-Ub) and the phosphodiesterase domain-mediated ligation of PR-Ub to substrates are two independent activities of SdeA. Furthermore, we present two crystal structures of a homologous phosphodiesterase domain from the SidE family member SdeD 9 in complexes with Ub and ADPR-Ub. The structures suggest a mechanism for how SdeA processes ADPR-Ub to PR-Ub and AMP, and conjugates PR-Ub to a serine residue in substrates. Our study establishes the molecular mechanism of phosphoribosyl-linked ubiquitination and will enable future studies of this unusual type of ubiquitination in eukaryotes. Crystal structures of the Legionella effectors SdeA and SdeD uncover the mechanism of a unique phosphoribosyl-ubiquitination reaction.