Molecular basis for thiocarboxylation and release of Urm1 by its E1-activating enzyme Uba4

• Published in: Nucleic acids research 2024-12, Vol.52 (22), p.13980-13995
• Main Authors: Sokołowski, Mikołaj, Kwasna, Dominika, Ravichandran, Keerthiraju E, Eggers, Cristian, Krutyhołowa, Rościsław, Kaczmarczyk, Magdalena, Skupien-Rabian, Bozena, Jaciuk, Marcin, Walczak, Marta, Dahate, Priyanka, Pabis, Marta, Jemioła-Rzemińska, Małgorzata, Jankowska, Urszula, Leidel, Sebastian A, Glatt, Sebastian
• Format: Article
• Language: English
• Subjects: Cryoelectron Microscopy; Models, Molecular; Molecular and Structural Biology; Mutation; Nucleotidyltransferases - chemistry; Nucleotidyltransferases - genetics; Nucleotidyltransferases - metabolism; Protein Binding; Protein Domains; RNA, Transfer - chemistry; RNA, Transfer - metabolism; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - metabolism; Sulfhydryl Compounds - chemistry; Sulfhydryl Compounds - metabolism; Ubiquitin-Activating Enzymes - chemistry; Ubiquitin-Activating Enzymes - genetics; Ubiquitin-Activating Enzymes - metabolism; Ubiquitins - chemistry; Ubiquitins - genetics; Ubiquitins - metabolism
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkae1111

Ubiquitin-related modifier 1 (Urm1) is a highly conserved member of the ubiquitin-like (UBL) family of proteins. Urm1 is a key component of the eukaryotic transfer RNA (tRNA) thiolation cascade, responsible for introducing sulfur at wobble uridine (U34) in several eukaryotic tRNAs. Urm1 must be thiocarboxylated (Urm1-SH) by its E1 activating enzyme UBL protein activator 4 (Uba4). Uba4 first adenylates and then thiocarboxylates the C-terminus of Urm1 using its adenyl-transferase (AD) and rhodanese (RHD) domains. However, the detailed mechanisms of Uba4, the interplay between the two domains, and the release of Urm1 remain elusive. Here, we report a cryo-EM-based structural model of the Uba4/Urm1 complex that reveals the position of its RHD domains after Urm1 binding, and by analyzing the in vitro and in vivo consequence of mutations at the interface, we show its importance for the thiocarboxylation of Urm1. Our results confirm that the formation of the Uba4-Urm1 thioester and thiocarboxylation of Urm1's C-terminus depend on conserved cysteine residues of Uba4 and that the complex avoids unwanted side-reactions of the adenylate by forming a thioester intermediate. We show how the Urm1-SH product can be released and how Urm1 interacts with upstream (Tum1) and downstream (Ncs6) components of the pathway. Our work provides a detailed mechanistic description of the reaction steps that are needed to produce Urm1-SH, which is required to thiolate tRNAs and persulfidate proteins.