1ZM2

Structure of ADP-ribosylated eEF2 in complex with catalytic fragment of ETA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Exotoxin A-eEF2 complex structure indicates ADP ribosylation by ribosome mimicry.

Joergensen, R.Merrill, A.R.Yates, S.P.Marquez, V.E.Schwan, A.L.Boesen, T.Andersen, G.R.

(2005) Nature 436: 979-984

  • DOI: 10.1038/nature03871
  • Primary Citation of Related Structures:  
    1ZM9, 1ZM4, 1ZM3, 1ZM2

  • PubMed Abstract: 
  • The bacteria causing diphtheria, whooping cough, cholera and other diseases secrete mono-ADP-ribosylating toxins that modify intracellular proteins. Here, we describe four structures of a catalytically active complex between a fragment of Pseudomonas ...

    The bacteria causing diphtheria, whooping cough, cholera and other diseases secrete mono-ADP-ribosylating toxins that modify intracellular proteins. Here, we describe four structures of a catalytically active complex between a fragment of Pseudomonas aeruginosa exotoxin A (ETA) and its protein substrate, translation elongation factor 2 (eEF2). The target residue in eEF2, diphthamide (a modified histidine), spans across a cleft and faces the two phosphates and a ribose of the non-hydrolysable NAD+ analogue, betaTAD. This suggests that the diphthamide is involved in triggering NAD+ cleavage and interacting with the proposed oxacarbenium intermediate during the nucleophilic substitution reaction, explaining the requirement of diphthamide for ADP ribosylation. Diphtheria toxin may recognize eEF2 in a manner similar to ETA. Notably, the toxin-bound betaTAD phosphates mimic the phosphate backbone of two nucleotides in a conformational switch of 18S rRNA, thereby achieving universal recognition of eEF2 by ETA.


    Organizational Affiliation

    Centre for Structural Biology, Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10C, DK-8000, Denmark.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor 2ACE842Saccharomyces cerevisiaeMutation(s): 1 
Find proteins for P32324 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32324 
Go to UniProtKB:  P32324
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Exotoxin ABDF207Pseudomonas aeruginosaMutation(s): 0 
Gene Names: eta
EC: 2.4.2 (PDB Primary Data), 2.4.2.36 (UniProt)
Find proteins for P11439 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore P11439 
Go to UniProtKB:  P11439
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APR
Query on APR

Download CCD File 
E
ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DDE
Query on DDE
A,C,EL-PEPTIDE LINKINGC13 H24 N5 O3HIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.07 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 330.63α = 90
b = 67.84β = 103.3
c = 191.5γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
MOLREPphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance