7K5J

Structure of an E1-E2-ubiquitin thioester mimetic

Summary for 7K5J

• Entry DOI: 10.2210/pdb7k5j/pdb
• Descriptor: Ubiquitin, Ubiquitin-activating enzyme E1 1, Ubiquitin-conjugating enzyme E2-34 kDa, ... (4 entities in total)
• Functional Keywords: conformational change, adenylation, thioester transfer, transthioesterification, atp-binding, ubiquitin e2-binding, ubiquitination, signaling protein
• Biological source: Triticum aestivum (Wheat); More
• Total number of polymer chains: 24
• Total formula weight: 1169489.80

Authors

Yuan, L.,Lv, Z.,Olsen, S.K. (deposition date: 2020-09-16, release date: 2021-04-28, Last modification date: 2024-12-25)

Primary citation

Yuan, L.,Lv, Z.,Adams, M.J.,Olsen, S.K.
Crystal structures of an E1-E2-ubiquitin thioester mimetic reveal molecular mechanisms of transthioesterification.
Nat Commun, 12:2370-2370, 2021

PubMed Abstract: 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.

PubMed: 33888705
DOI: 10.1038/s41467-021-22598-y

Experimental method

X-RAY DIFFRACTION (3.42 Å)