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TitleCryo-EM structures of Gid12-bound GID E3 reveal steric blockade as a mechanism inhibiting substrate ubiquitylation.
Journal, issue, pagesNat Commun, Vol. 13, Issue 1, Page 3041, Year 2022
Publish dateJun 1, 2022
AuthorsShuai Qiao / Chia-Wei Lee / Dawafuti Sherpa / Jakub Chrustowicz / Jingdong Cheng / Maximilian Duennebacke / Barbara Steigenberger / Ozge Karayel / Duc Tung Vu / Susanne von Gronau / Matthias Mann / Florian Wilfling / Brenda A Schulman /
PubMed AbstractProtein degradation, a major eukaryotic response to cellular signals, is subject to numerous layers of regulation. In yeast, the evolutionarily conserved GID E3 ligase mediates glucose-induced ...Protein degradation, a major eukaryotic response to cellular signals, is subject to numerous layers of regulation. In yeast, the evolutionarily conserved GID E3 ligase mediates glucose-induced degradation of fructose-1,6-bisphosphatase (Fbp1), malate dehydrogenase (Mdh2), and other gluconeogenic enzymes. "GID" is a collection of E3 ligase complexes; a core scaffold, RING-type catalytic core, and a supramolecular assembly module together with interchangeable substrate receptors select targets for ubiquitylation. However, knowledge of additional cellular factors directly regulating GID-type E3s remains rudimentary. Here, we structurally and biochemically characterize Gid12 as a modulator of the GID E3 ligase complex. Our collection of cryo-EM reconstructions shows that Gid12 forms an extensive interface sealing the substrate receptor Gid4 onto the scaffold, and remodeling the degron binding site. Gid12 also sterically blocks a recruited Fbp1 or Mdh2 from the ubiquitylation active sites. Our analysis of the role of Gid12 establishes principles that may more generally underlie E3 ligase regulation.
External linksNat Commun / PubMed:35650207 / PubMed Central
MethodsEM (single particle)
Resolution3.3 - 31.2 Å
Structure data

EMDB-14323: Structure of Chelator-GIDSR4 bound to Mdh2
Method: EM (single particle) / Resolution: 18.9 Å

EMDB-14324: Structure of Cage-GIDSR4 bound to PHSVTP-Fbp1
Method: EM (single particle) / Resolution: 12.0 Å

EMDB-14338: Structure of endogenous Cage-GIDAnt complex
Method: EM (single particle) / Resolution: 31.2 Å

32830

7wug

EMDB-32830, PDB-7wug:
GID subcomplex: Gid12 bound Substrate Receptor Scaffolding module
Method: EM (single particle) / Resolution: 3.3 Å

EMDB-32831: Gid12 bound GIDSR4 E3 ubiquitin ligase complex
Method: EM (single particle) / Resolution: 9.8 Å

EMDB-32833: Gid12 bound Chelator-GIDSR4
Method: EM (single particle) / Resolution: 19.4 Å

EMDB-32834: Cage assembly GID E3 ubiquitin ligase
Method: EM (single particle) / Resolution: 19.8 Å

EMDB-32835: Gid12 bound Cage-GIDSR3
Method: EM (single particle) / Resolution: 20.6 Å

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • saccharomyces cerevisiae yjm1133 (yeast)
KeywordsLIGASE / E3 ubiquitin Ligase / beta-propellor

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