3SQV

Crystal Structure of E. coli O157:H7 E3 ubiquitin ligase, NleL, with a human E2, UbcH7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.266 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of two bacterial HECT-like E3 ligases in complex with a human E2 reveal atomic details of pathogen-host interactions.

Lin, D.Y.Diao, J.Chen, J.

(2012) Proc.Natl.Acad.Sci.USA 109: 1925-1930

  • DOI: 10.1073/pnas.1115025109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In eukaryotes, ubiquitination is an important posttranslational process achieved through a cascade of ubiquitin-activating (E1), conjugating (E2), and ligase (E3) enzymes. Many pathogenic bacteria deliver virulence factors into the host cell that fun ...

    In eukaryotes, ubiquitination is an important posttranslational process achieved through a cascade of ubiquitin-activating (E1), conjugating (E2), and ligase (E3) enzymes. Many pathogenic bacteria deliver virulence factors into the host cell that function as E3 ligases. How these bacterial "Trojan horses" integrate into the eukaryotic ubiquitin system has remained a mystery. Here we report crystal structures of two bacterial E3s, Salmonella SopA and Escherichia coli NleL, both in complex with human E2 UbcH7. These structures represent two distinct conformational states of the bacterial E3s, supporting the necessary structural rearrangements associated with ubiquitin transfer. The E2-interacting surface of SopA and NleL has little similarity to those of eukaryotic E3s. However, both bacterial E3s bind to the canonical surface of E2 that normally interacts with eukaryotic E3s. Furthermore, we show that a glutamate residue on E3 is involved in catalyzing ubiquitin transfer from E3 to the substrate, but not from E2 to E3. Together, these results provide mechanistic insights into the ubiquitin pathway and a framework for understanding molecular mimicry in bacterial pathogenesis.


    Organizational Affiliation

    Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
secreted effector protein
A, B
616Escherichia coli O157:H7Mutation(s): 0 
Gene Names: espX7
Find proteins for A0A0H3JDV8 (Escherichia coli O157:H7)
Go to UniProtKB:  A0A0H3JDV8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 L3
C, D
156Homo sapiensMutation(s): 0 
Gene Names: UBE2L3 (UBCE7, UBCH7)
EC: 2.3.2.23
Find proteins for P68036 (Homo sapiens)
Go to Gene View: UBE2L3
Go to UniProtKB:  P68036
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.266 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 302.313α = 90.00
b = 72.012β = 109.22
c = 125.669γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
Blu-Icedata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-07-06 
  • Released Date: 2012-01-25 
  • Deposition Author(s): Lin, D.Y., Chen, J.

Revision History 

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2012-02-22
    Type: Database references