2QHO

Crystal structure of the UBA domain from EDD ubiquitin ligase in complex with ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of ubiquitin recognition by the ubiquitin-associated (UBA) domain of the ubiquitin ligase EDD.

Kozlov, G.Nguyen, L.Lin, T.De Crescenzo, G.Park, M.Gehring, K.

(2007) J Biol Chem 282: 35787-35795

  • DOI: 10.1074/jbc.M705655200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • EDD (or HYD) is an E3 ubiquitin ligase in the family of HECT (homologous to E6-AP C terminus) ligases. EDD contains an N-terminal ubiquitin-associated (UBA) domain, which is present in a variety of proteins involved in ubiquitin-mediated processes. H ...

    EDD (or HYD) is an E3 ubiquitin ligase in the family of HECT (homologous to E6-AP C terminus) ligases. EDD contains an N-terminal ubiquitin-associated (UBA) domain, which is present in a variety of proteins involved in ubiquitin-mediated processes. Here, we use isothermal titration calorimetry (ITC), NMR titrations, and pull-down assays to show that the EDD UBA domain binds ubiquitin. The 1.85 A crystal structure of the complex with ubiquitin reveals the structural basis of ubiquitin recognition by UBA helices alpha1 and alpha3. The structure shows a larger number of intermolecular hydrogen bonds than observed in previous UBA/ubiquitin complexes. Two of these involve ordered water molecules. The functional importance of residues at the UBA/ubiquitin interface was confirmed using site-directed mutagenesis. Surface plasmon resonance (SPR) measurements show that the EDD UBA domain does not have a strong preference for polyubiquitin chains over monoubiquitin. This suggests that EDD binds to monoubiquitinated proteins, which is consistent with its involvement in DNA damage repair pathways.


    Organizational Affiliation

    Department of Biochemistry, McGill University, Montréal, Québec H3G 1Y6, Canada.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
A, C, E, G
76Bos taurusMutation(s): 0 
Gene Names: UBC
Find proteins for P0CH28 (Bos taurus)
Go to UniProtKB:  P0CH28

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase EDD1
B, D, F, H
53Homo sapiensMutation(s): 0 
Gene Names: EDD1EDDHYDKIAA0896UBR5
EC: 6.3.2 (PDB Primary Data), 2.3.2.26 (UniProt)
Find proteins for O95071 (Homo sapiens)
Go to UniProtKB:  O95071
NIH Common Fund Data Resources
PHAROS  O95071
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.849α = 90
b = 59.333β = 90
c = 246.672γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-09-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance