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: 2.7 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.4 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: 10.1016/j.str.2015.05.020
  • Primary Citation of Related Structures:  

  • 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 mo ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 D2
A
148Homo sapiensMutation(s): 1 
Gene Names: UBE2D2 (PUBC1, UBC4, UBC5B, UBCH4, UBCH5B)
EC: 2.3.2.23
Find proteins for P62837 (Homo sapiens)
Go to Gene View: UBE2D2
Go to UniProtKB:  P62837
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase LubX
B
215Legionella pneumophila (strain Paris)Mutation(s): 0 
Gene Names: lubX
EC: 2.3.2.27
Find proteins for Q5X159 (Legionella pneumophila (strain Paris))
Go to UniProtKB:  Q5X159
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 119.293α = 90.00
b = 119.293β = 90.00
c = 49.809γ = 120.00
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM094585
Department of Energy (United States)United StatesDE-AC02-06CH11357

Revision History 

  • Version 1.0: 2015-01-07
    Type: Initial release
  • Version 1.1: 2015-02-04
    Type: Derived calculations
  • Version 1.2: 2015-07-29
    Type: Database references
  • Version 1.3: 2015-08-19
    Type: Derived calculations
  • Version 1.4: 2017-09-20
    Type: Author supporting evidence, Derived calculations