8QBN

Structure of the non-canonical CTLH E3 substrate receptor WDR26 bound to YPEL5


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 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

Non-canonical substrate recognition by the human WDR26-CTLH E3 ligase regulates prodrug metabolism.

Gottemukkala, K.V.Chrustowicz, J.Sherpa, D.Sepic, S.Vu, D.T.Karayel, O.Papadopoulou, E.C.Gross, A.Schorpp, K.von Gronau, S.Hadian, K.Murray, P.J.Mann, M.Schulman, B.A.Alpi, A.F.

(2024) Mol Cell 84: 1948-1963.e11

  • DOI: https://doi.org/10.1016/j.molcel.2024.04.014
  • Primary Citation of Related Structures:  
    8QBN, 8QE8

  • PubMed Abstract: 

    The yeast glucose-induced degradation-deficient (GID) E3 ubiquitin ligase forms a suite of complexes with interchangeable receptors that selectively recruit N-terminal degron motifs of metabolic enzyme substrates. The orthologous higher eukaryotic C-terminal to LisH (CTLH) E3 complex has been proposed to also recognize substrates through an alternative subunit, WDR26, which promotes the formation of supramolecular CTLH E3 assemblies. Here, we discover that human WDR26 binds the metabolic enzyme nicotinamide/nicotinic-acid-mononucleotide-adenylyltransferase 1 (NMNAT1) and mediates its CTLH E3-dependent ubiquitylation independently of canonical GID/CTLH E3-family substrate receptors. The CTLH subunit YPEL5 inhibits NMNAT1 ubiquitylation and cellular turnover by WDR26-CTLH E3, thereby affecting NMNAT1-mediated metabolic activation and cytotoxicity of the prodrug tiazofurin. Cryoelectron microscopy (cryo-EM) structures of NMNAT1- and YPEL5-bound WDR26-CTLH E3 complexes reveal an internal basic degron motif of NMNAT1 essential for targeting by WDR26-CTLH E3 and degron mimicry by YPEL5's N terminus antagonizing substrate binding. Thus, our data provide a mechanistic understanding of how YPEL5-WDR26-CTLH E3 acts as a modulator of NMNAT1-dependent metabolism.


  • Organizational Affiliation

    Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried 82152, Germany; TUM School of Natural Sciences, Technical University, Munich 85748, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
WD repeat-containing protein 26A [auth 7],
B [auth W]
645Homo sapiensMutation(s): 0 
Gene Names: WDR26CDW2MIP2PRO0852
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7D7 (Homo sapiens)
Explore Q9H7D7 
Go to UniProtKB:  Q9H7D7
PHAROS:  Q9H7D7
GTEx:  ENSG00000162923 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H7D7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein yippee-like 5C [auth Y]121Homo sapiensMutation(s): 0 
Gene Names: YPEL5CGI-127
UniProt & NIH Common Fund Data Resources
Find proteins for P62699 (Homo sapiens)
Explore P62699 
Go to UniProtKB:  P62699
PHAROS:  P62699
GTEx:  ENSG00000119801 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62699
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



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: 2024-05-15
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references
  • Version 1.2: 2024-07-03
    Changes: Data collection, Derived calculations