8GXR | pdb_00008gxr

crystal structure of UBC domain of UBE2O


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 
    0.250 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 
    0.226 (Depositor) 

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Literature

Structural insights into the biochemical mechanism of the E2/E3 hybrid enzyme UBE2O.

Huang, H.Zhu, W.Huang, B.Fu, Z.Xiong, Y.Cao, D.Ye, Y.Chang, Q.Li, W.Li, L.Zhou, H.Niu, X.Zhang, W.

(2025) Structure 33: 274-288.e4

  • DOI: https://doi.org/10.1016/j.str.2024.12.002
  • Primary Citation of Related Structures:  
    7YW1, 8GXR

  • PubMed Abstract: 

    The E2/E3 hybrid enzyme UBE2O plays important roles in key biological events, but its autoubiquitination mechanism remains largely unclear. In this study, we determined the crystal structures of full-length (FL) UBE2O from Trametes pubescens (tp) and its ubiquitin-conjugating (UBC) domain. The dimeric FL-tpUBE2O structure revealed interdomain interactions between the conserved regions (CR1-CR2) and UBC. The dimeric intermolecular and canonical ubiquitin/UBC interactions are mechanistically important for UBE2O functions in catalyzing the formation of free polyubiquitin chains and substrate ubiquitination. Beyond dimerization, autoubiquitination within the CR1-CR2 domain also regulates tpUBE2O activity. Additionally, we show that tpUBE2O catalyzes the formation of all seven types of polyubiquitin chains in vitro. The CR1-CR2/UBC and canonical ubiquitin/UBC interactions are important for the polyubiquitination of AMP-activated protein kinase α2 (AMPKα2) by human UBE2O (hUBE2O), which leads to tumorigenesis. These structural insights lay the groundwork for understanding UBE2O's mechanisms and developing structure-based therapeutics targeting UBE2O.


  • Organizational Affiliation
    • State Key Laboratory of Chemical Oncogenomics, Laboratory of Structural Biology and Drug Discovery, Laboratory of Ubiquitination and Targeted Therapy, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China; Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518132, China. Electronic address: huang.hao@pku.edu.cn.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
(E3-independent) E2 ubiquitin-conjugating enzyme UBE2O
A, B, C, D
281Trametes pubescensMutation(s): 0 
Gene Names: TRAPUB_10883
UniProt
Find proteins for A0A1M2VY70 (Trametes pubescens)
Explore A0A1M2VY70 
Go to UniProtKB:  A0A1M2VY70
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1M2VY70
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free:  0.250 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.225 (DCC) 
  • R-Value Observed: 0.226 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.39α = 90
b = 96.96β = 90
c = 207.13γ = 90
Software Package:
Software NamePurpose
xia2data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXphasing
BUCCANEERmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-27
    Type: Initial release
  • Version 1.1: 2025-02-26
    Changes: Database references, Structure summary