8PMQ

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Multisite phosphorylation dictates selective E2-E3 pairing as revealed by Ubc8/UBE2H-GID/CTLH assemblies.

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.

(2024) Mol Cell 84: 293

  • DOI: https://doi.org/10.1016/j.molcel.2023.11.027
  • Primary Citation of Related Structures:  
    8PJN, 8PMQ

  • 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.


  • Organizational Affiliation

    Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RMD5A [auth 2]421Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RMD5GID2YDR255CYD9320A.05c
EC: 2.3.2.27
UniProt
Find proteins for Q12508 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  Q12508
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UniProt GroupQ12508
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein FYV10B [auth 9]516Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: FYV10GID9YIL097W
EC: 2.3.2.27
UniProt
Find proteins for P40492 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP40492
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2-24 kDaC [auth E]218Saccharomyces cerevisiaeMutation(s): 1 
Gene Names: UBC8GID3YEL012W
EC: 2.3.2.23
UniProt
Find proteins for P28263 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP28263
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
UbiquitinD [auth U]76Homo sapiensMutation(s): 0 
Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
GTEx:  ENSG00000150991 
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UniProt GroupP0CG48
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
C [auth E]L-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
European Research Council (ERC)European UnionH2020 789016-NEDD8Activate
German Research Foundation (DFG)GermanySCHU 3196/1-1

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-03
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Database references
  • Version 1.2: 2024-02-21
    Changes: Derived calculations