GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme

Mol Cell. 2021 Jun 3;81(11):2445-2459.e13. doi: 10.1016/j.molcel.2021.03.025. Epub 2021 Apr 26.

Abstract

How are E3 ubiquitin ligases configured to match substrate quaternary structures? Here, by studying the yeast GID complex (mutation of which causes deficiency in glucose-induced degradation of gluconeogenic enzymes), we discover supramolecular chelate assembly as an E3 ligase strategy for targeting an oligomeric substrate. Cryoelectron microscopy (cryo-EM) structures show that, to bind the tetrameric substrate fructose-1,6-bisphosphatase (Fbp1), two minimally functional GID E3s assemble into the 20-protein Chelator-GIDSR4, which resembles an organometallic supramolecular chelate. The Chelator-GIDSR4 assembly avidly binds multiple Fbp1 degrons so that multiple Fbp1 protomers are simultaneously ubiquitylated at lysines near the allosteric and substrate binding sites. Importantly, key structural and biochemical features, including capacity for supramolecular assembly, are preserved in the human ortholog, the CTLH E3. Based on our integrative structural, biochemical, and cell biological data, we propose that higher-order E3 ligase assembly generally enables multipronged targeting, capable of simultaneously incapacitating multiple protomers and functionalities of oligomeric substrates.

Keywords: CTLH; E3; GID; RING; cryo-EM; gluconeogenesis; metabolic regulation; supramolecular assembly; ubiquitin; ubiquitin ligase.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptor Proteins, Signal Transducing / chemistry*
  • Adaptor Proteins, Signal Transducing / genetics
  • Adaptor Proteins, Signal Transducing / metabolism
  • Animals
  • Binding Sites
  • Cell Adhesion Molecules / chemistry*
  • Cell Adhesion Molecules / genetics
  • Cell Adhesion Molecules / metabolism
  • Cryoelectron Microscopy
  • Fructose-Bisphosphatase / chemistry*
  • Fructose-Bisphosphatase / genetics
  • Fructose-Bisphosphatase / metabolism
  • Gene Expression
  • Gluconeogenesis / genetics
  • Humans
  • Intracellular Signaling Peptides and Proteins / chemistry*
  • Intracellular Signaling Peptides and Proteins / genetics
  • Intracellular Signaling Peptides and Proteins / metabolism
  • K562 Cells
  • Kinetics
  • Models, Molecular
  • Multienzyme Complexes / chemistry*
  • Multienzyme Complexes / genetics
  • Multienzyme Complexes / metabolism
  • Promoter Regions, Genetic
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Conformation, beta-Strand
  • Protein Interaction Domains and Motifs
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / genetics
  • Recombinant Proteins / metabolism
  • Saccharomyces cerevisiae
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism
  • Sf9 Cells
  • Spodoptera
  • Structural Homology, Protein
  • Substrate Specificity
  • Ubiquitin / chemistry*
  • Ubiquitin / genetics
  • Ubiquitin / metabolism
  • Ubiquitin-Conjugating Enzymes / chemistry*
  • Ubiquitin-Conjugating Enzymes / genetics
  • Ubiquitin-Conjugating Enzymes / metabolism
  • Ubiquitination

Substances

  • Adaptor Proteins, Signal Transducing
  • Cell Adhesion Molecules
  • Intracellular Signaling Peptides and Proteins
  • MKLN1 protein, human
  • Multienzyme Complexes
  • Recombinant Proteins
  • Saccharomyces cerevisiae Proteins
  • Ubiquitin
  • WDR26 protein, human
  • Ubiquitin-Conjugating Enzymes
  • ubiquitin-conjugating enzyme UBC8
  • FBP1 protein, S cerevisiae
  • Fructose-Bisphosphatase