4WZ0

Crystal structure of U-box 1 of LubX / LegU2 / Lpp2887 from Legionella pneumophila str. Paris


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.238 

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:  
    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 ...

    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; Midwest Center for Structural Genomics, Bioscience Division, Argonne National Laboratory, Lemont, IL 60439, USA. Electronic address: alexei.savchenko@utoronto.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase LubXA109Legionella 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSD
Query on CSD
AL-PEPTIDE LINKINGC3 H7 N O4 SCYS
MSE
Query on MSE
AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.238 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.334α = 90
b = 90.621β = 90
c = 40.562γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
PHENIXrefinement

Structure Validation

View Full Validation Report




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: 2015-01-14
    Type: Initial release
  • Version 1.1: 2015-07-29
    Changes: Database references
  • Version 1.2: 2015-08-19
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence