1U2R

Crystal Structure of ADP-ribosylated Ribosomal Translocase from Saccharomyces cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 

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This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of ADP-ribosylated Ribosomal Translocase from Saccharomyces cerevisiae

Jorgensen, R.Yates, S.P.Teal, D.J.Nilsson, J.Prentice, G.A.Merrill, A.R.Andersen, G.R.

(2004) J Biol Chem 279: 45919-45925

  • DOI: 10.1074/jbc.M406218200
  • Primary Citation of Related Structures:  
    1U2R

  • PubMed Abstract: 
  • The crystal structure of ADP-ribosylated yeast elongation factor 2 in the presence of sordarin and GDP has been determined at 2.6 A resolution. The diphthamide at the tip of domain IV, which is the target for diphtheria toxin and Pseudomonas aeruginosa exotoxin A, contains a covalently attached ADP-ribose that functions as a very potent inhibitor of the factor ...

    The crystal structure of ADP-ribosylated yeast elongation factor 2 in the presence of sordarin and GDP has been determined at 2.6 A resolution. The diphthamide at the tip of domain IV, which is the target for diphtheria toxin and Pseudomonas aeruginosa exotoxin A, contains a covalently attached ADP-ribose that functions as a very potent inhibitor of the factor. We have obtained an electron density map of ADP-ribosylated translation factor 2 revealing both the ADP-ribosylation and the diphthamide. This is the first structure showing the conformation of an ADP-ribosylated residue and confirms the inversion of configuration at the glycosidic linkage. Binding experiments show that the ADP-ribosylation has limited effect on nucleotide binding affinity, on ribosome binding, and on association with exotoxin A. These results provide insight to the inhibitory mechanism and suggest that inhibition may be caused by erroneous interaction of the translation factor with the codon-anticodon area in the P-site of the ribosome.


    Organizational Affiliation

    Macromolecular Crystallography, Department of Molecular Biology, University of Aarhus, Gustav Wieds vej 10C, DK8000 Aarhus, Denmark.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor 2A842Saccharomyces cerevisiaeMutation(s): 1 
UniProt
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
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APR (Subject of Investigation/LOI)
Query on APR

Download Ideal Coordinates CCD File 
C [auth A]ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N
 Ligand Interaction
SO1 (Subject of Investigation/LOI)
Query on SO1

Download Ideal Coordinates CCD File 
D [auth A][1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID
C27 H42 O8
DIBGPTPYRVEPSP-OHFCZZTFSA-N
 Ligand Interaction
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
E [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
DDE
Query on DDE
AL-PEPTIDE LINKINGC13 H24 N5 O3HIS
Binding Affinity Annotations 
IDSourceBinding Affinity
GDP PDBBind:  1U2R Kd: 3900 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.725α = 90
b = 151.002β = 90
c = 65.172γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-09-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance