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: England Nature Publishing Group 01.05.2018
• Subjects: Adenosine diphosphate; Amino acids; AMP; Bacterial proteins; Binding sites; Biochemical analysis; Catalysis; Crystal structure; Eukaryotes; Future predictions; Homology; Legionella; Legionella pneumophila; Legionnaires' disease bacterium; Lysine; Molecular chains; Mutation; Phosphodiesterase; Post-translation; Post-translational modifications; Protein research; Proteins; 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 . 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 . 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 . 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 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.