2LXH

NMR structure of the RING domain in ubiquitin ligase gp78


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine.

Das, R.Liang, Y.H.Mariano, J.Li, J.Huang, T.King, A.Tarasov, S.G.Weissman, A.M.Ji, X.Byrd, R.A.

(2013) EMBO J 32: 2504-2516

  • DOI: https://doi.org/10.1038/emboj.2013.174
  • Primary Citation of Related Structures:  
    2LXH, 2LXP, 4LAD

  • PubMed Abstract: 

    RING finger proteins constitute the large majority of ubiquitin ligases (E3s) and function by interacting with ubiquitin-conjugating enzymes (E2s) charged with ubiquitin. How low-affinity RING-E2 interactions result in highly processive substrate ubiquitination is largely unknown. The RING E3, gp78, represents an excellent model to study this process. gp78 includes a high-affinity secondary binding region for its cognate E2, Ube2g2, the G2BR. The G2BR allosterically enhances RING:Ube2g2 binding and ubiquitination. Structural analysis of the RING:Ube2g2:G2BR complex reveals that a G2BR-induced conformational effect at the RING:Ube2g2 interface is necessary for enhanced binding of RING to Ube2g2 or Ube2g2 conjugated to Ub. This conformational effect and a key ternary interaction with conjugated ubiquitin are required for ubiquitin transfer. Moreover, RING:Ube2g2 binding induces a second allosteric effect, disrupting Ube2g2:G2BR contacts, decreasing affinity and facilitating E2 exchange. Thus, gp78 is a ubiquitination machine where multiple E2-binding sites coordinately facilitate processive ubiquitination.


  • Organizational Affiliation

    Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase AMFRA [auth C]81Homo sapiensMutation(s): 0 
Gene Names: AMFRRNF45
EC: 6.3.2 (PDB Primary Data), 2.3.2.36 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKV5 (Homo sapiens)
Explore Q9UKV5 
Go to UniProtKB:  Q9UKV5
PHAROS:  Q9UKV5
GTEx:  ENSG00000159461 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UKV5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-28
    Type: Initial release
  • Version 1.1: 2013-10-02
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references