8PMQ

Catalytic module of yeast GID E3 ligase bound to multiphosphorylated Ubc8~ubiquitin

Summary for 8PMQ

• Entry DOI: 10.2210/pdb8pmq/pdb
• Related: 8PJN
• EMDB information: 17705 17706 17707 17709 17710 17713 17717 17764
• Descriptor: E3 ubiquitin-protein ligase RMD5, Protein FYV10, Ubiquitin-conjugating enzyme E2-24 kDa, ... (5 entities in total)
• Functional Keywords: e3 ubiquitin ligase, e2 ubiquitin-conjugating enzyme, phosphorylation, gid, ligase
• Biological source: Saccharomyces cerevisiae (baker's yeast); More
• Total number of polymer chains: 4
• Total formula weight: 142848.12

Authors

Chrustowicz, J.,Sherpa, D.,Prabu, R.J.,Schulman, B.A. (deposition date: 2023-06-29, release date: 2024-01-03, Last modification date: 2024-10-16)

Primary citation

Chrustowicz, J.,Sherpa, D.,Li, J.,Langlois, C.R.,Papadopoulou, E.C.,Vu, D.T.,Hehl, L.A.,Karayel, O.,Beier, V.,von Gronau, S.,Muller, J.,Prabu, J.R.,Mann, M.,Kleiger, G.,Alpi, A.F.,Schulman, B.A.
Multisite phosphorylation dictates selective E2-E3 pairing as revealed by Ubc8/UBE2H-GID/CTLH assemblies.
Mol.Cell, 84:293-, 2024

PubMed Abstract: Ubiquitylation is catalyzed by coordinated actions of E3 and E2 enzymes. Molecular principles governing many important E3-E2 partnerships remain unknown, including those for RING-family GID/CTLH E3 ubiquitin ligases and their dedicated E2, Ubc8/UBE2H (yeast/human nomenclature). GID/CTLH-Ubc8/UBE2H-mediated ubiquitylation regulates biological processes ranging from yeast metabolic signaling to human development. Here, cryoelectron microscopy (cryo-EM), biochemistry, and cell biology reveal this exquisitely specific E3-E2 pairing through an unconventional catalytic assembly and auxiliary interactions 70-100 Å away, mediated by E2 multisite phosphorylation. Rather than dynamic polyelectrostatic interactions reported for other ubiquitylation complexes, multiple Ubc8/UBE2H phosphorylation sites within acidic CK2-targeted sequences specifically anchor the E2 C termini to E3 basic patches. Positions of phospho-dependent interactions relative to the catalytic domains correlate across evolution. Overall, our data show that phosphorylation-dependent multivalency establishes a specific E3-E2 partnership, is antagonistic with dephosphorylation, rigidifies the catalytic centers within a flexing GID E3-substrate assembly, and facilitates substrate collision with ubiquitylation active sites.

PubMed: 38113892
DOI: 10.1016/j.molcel.2023.11.027

Experimental method

ELECTRON MICROSCOPY (3.53 Å)