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TitleMultisite phosphorylation dictates selective E2-E3 pairing as revealed by Ubc8/UBE2H-GID/CTLH assemblies.
Journal, issue, pagesMol Cell, Vol. 84, Issue 2, Page 293-308.e14, Year 2024
Publish dateJan 18, 2024
AuthorsJakub Chrustowicz / Dawafuti Sherpa / Jerry Li / Christine R Langlois / Eleftheria C Papadopoulou / D Tung Vu / Laura A Hehl / Özge Karayel / Viola Beier / Susanne von Gronau / Judith Müller / J Rajan Prabu / Matthias Mann / Gary Kleiger / Arno F Alpi / Brenda A Schulman /
PubMed AbstractUbiquitylation 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 ...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.
External linksMol Cell / PubMed:38113892 / PubMed Central
MethodsEM (single particle)
Resolution3.4 - 19.5 Å
Structure data

EMDB-17705: Structure of Chelator-GIDSR4 - Fbp1 - phospho-Ubc8~ubiquitin - class I
Method: EM (single particle) / Resolution: 16.0 Å

EMDB-17706: Structure of Chelator-GIDSR4 - Fbp1 - phospho-Ubc8~ubiquitin - class II
Method: EM (single particle) / Resolution: 19.5 Å

EMDB-17707: Chelator-GIDSR4 - Fbp1 - phospho-Ubc8~ubiquitin - class III
Method: EM (single particle) / Resolution: 17.6 Å

EMDB-17709: Structure of Chelator-GIDSR4 - Fbp1 - phospho-Ubc8~ubiquitin - class V
Method: EM (single particle) / Resolution: 16.7 Å

EMDB-17710: Structure of Chelator-GIDSR4 - Fbp1 - phospho-Ubc8~ubiquitin - class IV
Method: EM (single particle) / Resolution: 16.7 Å

17713

8pjn

EMDB-17713, PDB-8pjn:
Catalytic module of human CTLH E3 ligase bound to multiphosphorylated UBE2H~ubiquitin
Method: EM (single particle) / Resolution: 3.4 Å

EMDB-17715: SRS and Cat modules of human CTLHSR4 bound to multiphosphorylated UBE2H~ubiquitin
Method: EM (single particle) / Resolution: 7.4 Å

EMDB-17716: Structure of CTLHSR4 - phospho-UBE2H~ubiquitin bound to engineered VH
Method: EM (single particle) / Resolution: 11.8 Å

EMDB-17717: SRS and Cat modules of yeast Chelator-GIDSR4 bound to multiphosphorylated Ubc8~ubiquitin
Method: EM (single particle) / Resolution: 4.8 Å

17764

8pmq

EMDB-17764, PDB-8pmq:
Catalytic module of yeast GID E3 ligase bound to multiphosphorylated Ubc8~ubiquitin
Method: EM (single particle) / Resolution: 3.53 Å

Chemicals

ChemComp-ZN:
Unknown entry

Source
  • saccharomyces cerevisiae (brewer's yeast)
  • homo sapiens (human)
KeywordsLIGASE / E3 ubiquitin ligase / E2 ubiquitin-conjugating enzyme / phosphorylation / CTLH / GID / UBE2H

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