9EWP

Crystal structure of yeast E2 Ubiquitin-conjugating enzyme Ubc6 UBC domain

Summary for 9EWP

• Entry DOI: 10.2210/pdb9ewp/pdb
• Related: 9EN5
• Descriptor: Ubiquitin-conjugating enzyme E2 6, 1,2-ETHANEDIOL, CADMIUM ION, ... (6 entities in total)
• Functional Keywords: ubiquitin, endoplasmic reticulum, non-canonical ubiquitination, transferase
• Biological source: Saccharomyces cerevisiae (brewer's yeast)
• Total number of polymer chains: 1
• Total formula weight: 21135.20

Authors

Swarnkar, A.,Stein, A. (deposition date: 2024-04-04, release date: 2024-11-20, Last modification date: 2024-12-25)

Primary citation

Swarnkar, A.,Leidner, F.,Rout, A.K.,Ainatzi, S.,Schmidt, C.C.,Becker, S.,Urlaub, H.,Griesinger, C.,Grubmuller, H.,Stein, A.
Determinants of chemoselectivity in ubiquitination by the J2 family of ubiquitin-conjugating enzymes.
Embo J., 43:6705-6739, 2024

PubMed Abstract: Ubiquitin-conjugating enzymes (E2) play a crucial role in the attachment of ubiquitin to proteins. Together with ubiquitin ligases (E3), they catalyze the transfer of ubiquitin (Ub) onto lysines with high chemoselectivity. A subfamily of E2s, including yeast Ubc6 and human Ube2J2, also mediates noncanonical modification of serines, but the structural determinants for this chemical versatility remain unknown. Using a combination of X-ray crystallography, molecular dynamics (MD) simulations, and reconstitution approaches, we have uncovered a two-layered mechanism that underlies this unique reactivity. A rearrangement of the Ubc6/Ube2J2 active site enhances the reactivity of the E2-Ub thioester, facilitating attack by weaker nucleophiles. Moreover, a conserved histidine in Ubc6/Ube2J2 activates a substrate serine by general base catalysis. Binding of RING-type E3 ligases further increases the serine selectivity inherent to Ubc6/Ube2J2, via an allosteric mechanism that requires specific positioning of the ubiquitin tail at the E2 active site. Our results elucidate how subtle structural modifications to the highly conserved E2 fold yield distinct enzymatic activity.

PubMed: 39533056
DOI: 10.1038/s44318-024-00301-3

Experimental method

X-RAY DIFFRACTION (1.21 Å)