8KGY

Human glutamate dehydrogenase I

  • Classification: OXIDOREDUCTASE
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2023-08-20 Released: 2023-10-25 
  • Deposition Author(s): Su, M.-Y.
  • Funding Organization(s): Other government

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of the KLHL22 E3 ligase bound to an oligomeric metabolic enzyme.

Teng, F.Wang, Y.Liu, M.Tian, S.Stjepanovic, G.Su, M.Y.

(2023) Structure 31: 1431

  • DOI: https://doi.org/10.1016/j.str.2023.09.002
  • Primary Citation of Related Structures:  
    8KGY, 8KHP, 8W4J

  • PubMed Abstract: 

    CULLIN-RING ligases constitute the largest group of E3 ubiquitin ligases. While some CULLIN family members recruit adapters before engaging further with different substrate receptors, homo-dimeric BTB-Kelch family proteins combine adapter and substrate receptor into a single polypeptide for the CULLIN3 family. However, the entire structural assembly and molecular details have not been elucidated to date. Here, we present a cryo-EM structure of the CULLIN3 RBX1 in complex with Kelch-like protein 22 (KLHL22) and a mitochondrial glutamate dehydrogenase complex I (GDH1) at 3.06 Å resolution. The structure adopts a W-shaped architecture formed by E3 ligase dimers. Three CULLIN3 KLHL22-RBX1 dimers were found to be dynamically associated with a single GDH1 hexamer. CULLIN3 KLHL22-RBX1 ligase mediated the polyubiquitination of GDH1 in vitro. Together, these results enabled the establishment of a structural model for understanding the complete assembly of BTB-Kelch proteins with CULLIN3 and how together they recognize oligomeric substrates and target them for ubiquitination.


  • Organizational Affiliation

    Department of Biochemistry, School of Medicine, Southern University of Science and Technology, Shenzhen 518055, China; Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Shenzhen 518172, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glutamate dehydrogenase 1, mitochondrial
A, B, C, D, E
A, B, C, D, E, F
558Homo sapiensMutation(s): 0 
EC: 1.4.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P00367 (Homo sapiens)
Explore P00367 
Go to UniProtKB:  P00367
PHAROS:  P00367
GTEx:  ENSG00000148672 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00367
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2023-10-25 
  • Deposition Author(s): Su, M.-Y.

Funding OrganizationLocationGrant Number
Other governmentChina2022A1515010856

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Database references