Crystal structures of an E1–E2–ubiquitin thioester mimetic reveal molecular mechanisms of transthioesterification

• Published in: Nature communications 2021-04, Vol.12 (1), p.2370-2370, Article 2370
• Main Authors: Yuan, Lingmin, Lv, Zongyang, Adams, Melanie J., Olsen, Shaun K.
• Format: Article
• Language: English
• Subjects: 631/337/458/582; 631/45/173; 631/45/535/1266; Affinity; BASIC BIOLOGICAL SCIENCES; Catalysis; Catalytic Domain; Complex formation; Conformation; Crystal structure; Crystallography, X-Ray; enzyme mechanisms; Enzymes; Esterification - physiology; Humanities and Social Sciences; Models, Molecular; Molecular modelling; multidisciplinary; Recombinant Proteins - chemistry; Recombinant Proteins - genetics; Recombinant Proteins - isolation & purification; Recombinant Proteins - metabolism; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - isolation & purification; Saccharomyces cerevisiae Proteins - metabolism; Science; Science (multidisciplinary); Thioesters; Ubiquitin - chemistry; Ubiquitin - metabolism; Ubiquitin thiolesterase; Ubiquitin-Activating Enzymes - chemistry; Ubiquitin-Activating Enzymes - genetics; Ubiquitin-Activating Enzymes - isolation & purification; Ubiquitin-Activating Enzymes - metabolism; Ubiquitin-Conjugating Enzymes - chemistry; Ubiquitin-Conjugating Enzymes - genetics; Ubiquitin-Conjugating Enzymes - isolation & purification; Ubiquitin-Conjugating Enzymes - metabolism; Ubiquitination - physiology; ubiquitylation; x-ray crystallography
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-22598-y

E1 enzymes function as gatekeepers of ubiquitin (Ub) signaling by catalyzing activation and transfer of Ub to tens of cognate E2 conjugating enzymes in a process called E1–E2 transthioesterification. The molecular mechanisms of transthioesterification and the overall architecture of the E1–E2–Ub complex during catalysis are unknown. Here, we determine the structure of a covalently trapped E1–E2–ubiquitin thioester mimetic. Two distinct architectures of the complex are observed, one in which the Ub thioester (Ub(t)) contacts E1 in an open conformation and another in which Ub(t) instead contacts E2 in a drastically different, closed conformation. Altogether our structural and biochemical data suggest that these two conformational states represent snapshots of the E1–E2–Ub complex pre- and post-thioester transfer, and are consistent with a model in which catalysis is enhanced by a Ub(t)-mediated affinity switch that drives the reaction forward by promoting productive complex formation or product release depending on the conformational state. The molecular mechanism of ubiquitin transfer from E1 to E2 enzymes is still unclear. By solving the crystal structure of a covalently trapped E1–E2–ubiquitin thioester mimetic, the authors identify two conformations of this complex which suggest an affinity switch mechanism for thioester transfer.