4WZ3

Crystal structure of the complex between LubX/LegU2/Lpp2887 U-box 1 and Homo sapiens UBE2D2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.7 of the entry. See complete history


Literature

Molecular Characterization of LubX: Functional Divergence of the U-Box Fold by Legionella pneumophila.

Quaile, A.T.Urbanus, M.L.Stogios, P.J.Nocek, B.Skarina, T.Ensminger, A.W.Savchenko, A.

(2015) Structure 23: 1459-1469

  • DOI: https://doi.org/10.1016/j.str.2015.05.020
  • Primary Citation of Related Structures:  
    4WZ0, 4WZ2, 4WZ3, 4XI1

  • PubMed Abstract: 

    LubX is part of the large arsenal of effectors in Legionella pneumophila that are translocated into the host cytosol during infection. Despite such unique features as the presence of two U-box motifs and its targeting of another effector SidH, the molecular basis of LubX activity remains poorly understood. Here we show that the N terminus of LubX is able to activate an extended number of ubiquitin-conjugating (E2) enzymes including UBE2W, UBEL6, and all tested members of UBE2D and UBE2E families. Crystal structures of LubX alone and in complex with UBE2D2 revealed drastic molecular diversification between the two U-box domains, with only the N-terminal U-box retaining E2 recognition features typical for its eukaryotic counterparts. Extensive mutagenesis followed by functional screening in a yeast model system captured functionally important LubX residues including Arg121, critical for interactions with SidH. Combined, these data provide a new molecular insight into the function of this unique pathogenic factor.


  • Organizational Affiliation

    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D2148Homo sapiensMutation(s): 1 
Gene Names: UBE2D2PUBC1UBC4UBC5BUBCH4UBCH5B
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.24 (UniProt), 2.3.2.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P62837 (Homo sapiens)
Explore P62837 
Go to UniProtKB:  P62837
PHAROS:  P62837
GTEx:  ENSG00000131508 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62837
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase LubX215Legionella pneumophila str. ParisMutation(s): 0 
Gene Names: lubXlpp2887
EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt
Find proteins for Q5X159 (Legionella pneumophila (strain Paris))
Explore Q5X159 
Go to UniProtKB:  Q5X159
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5X159
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 
  • Space Group: P 61
  • Diffraction Data: https://doi.org/10.18430/M34WZ3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.293α = 90
b = 119.293β = 90
c = 49.809γ = 120
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXphasing
PHENIXmodel building
Cootmodel building
PHENIXrefinement
HKL-3000data scaling

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM094585
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-07
    Type: Initial release
  • Version 1.1: 2015-02-04
    Changes: Derived calculations
  • Version 1.2: 2015-07-29
    Changes: Database references
  • Version 1.3: 2015-08-19
    Changes: Derived calculations
  • Version 1.4: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.5: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.6: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.7: 2023-11-15
    Changes: Data collection