1HA3

ELONGATION FACTOR TU IN COMPLEX WITH aurodox


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conformational Change of Elongation Factor TU Induced by Antibiotic Binding: Crystal Structure of the Complex between EF-TU:Gdp and Aurodox

Vogeley, L.Palm, G.J.Mesters, J.R.Hilgenfeld, R.

(2001) J.Biol.Chem. 276: 17149

  • DOI: 10.1074/jbc.M100017200

  • PubMed Abstract: 
  • Aurodox is a member of the family of kirromycin antibiotics, which inhibit protein biosynthesis by binding to elongation factor Tu (EF-Tu). We have determined the crystal structure of the 1:1:1 complex of Thermus thermophilus EF-Tu with GDP and aurod ...

    Aurodox is a member of the family of kirromycin antibiotics, which inhibit protein biosynthesis by binding to elongation factor Tu (EF-Tu). We have determined the crystal structure of the 1:1:1 complex of Thermus thermophilus EF-Tu with GDP and aurodox to 2.0-A resolution. During its catalytic cycle, EF-Tu adopts two strikingly different conformations depending on the nucleotide bound: the GDP form and the GTP form. In the present structure, a GTP complex-like conformation of EF-Tu is observed, although GDP is bound to the nucleotide-binding site. This is consistent with previous proposals that aurodox fixes EF-Tu on the ribosome by locking it in its GTP form. Binding of EF-Tu.GDP to aminoacyl-tRNA and mutually exclusive binding of kirromycin and elongation factor Ts to EF-Tu can be explained on the basis of the structure. For many previously observed mutations that provide resistance to kirromycin, it can now be understood how they prevent interaction with the antibiotic. An unexpected feature of the structure is the reorientation of the His-85 side chain toward the nucleotide-binding site. We propose that this residue stabilizes the transition state of GTP hydrolysis, explaining the acceleration of the reaction by kirromycin-type antibiotics.


    Related Citations: 
    • Crystals of Intact Elongation Factor TU from Thermus Thermophilus Diffracting to 1.45 Angstrom Resolution
      Reshetnikova, L.,Schirmer, N.K.,Reiser, C.O.A.,Berchtold, H.,Storm, R.,Hilgenfeld, R.,Sprinzl, M.
      (1992) J.Cryst.Growth 122: 360
    • Regulatory Gtpases
      Hilgenfeld, R.
      (1995) Curr.Opin.Struct.Biol. 5: 810
    • Insights Into the Gtpase Mechanism of EF-TU from Structural Studies
      Hilgenfeld, R.,Mesters, J.,Hogg, T.
      (2000) The Ribosome: Structure, Function, Antibiotics, and Cellular Interactions --: 347
    • Crystal Structure of Active Elongation Factor TU Reveals Major Domain Rearrangements
      Berchtold, H.,Reshetnikova, L.,Reiser, C.O.A.,Schirmer, N.K.,Sprinzl, M.,Hilgenfeld, R.
      (1993) Nature 365: 126


    Organizational Affiliation

    Department of Structural Biology and Crystallography, Institute of Molecular Biotechnology, Beutenbergstrasse 11, D-07745 Jena, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ELONGATION FACTOR TU
A, B
405Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: tufA (tuf)
Find proteins for Q5SHN6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
BME
Query on BME

Download SDF File 
Download CCD File 
A, B
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
MAU
Query on MAU

Download SDF File 
Download CCD File 
A, B
N-METHYL KIRROMYCIN
AURODOX; 1-METHYLMOCIMYCIN; ANTIBIOTIC X-5108; GOLDINODOX; GOLDINOMYCIN
C44 H62 N2 O12
NTAHMPNXQOYXSX-WKSONYIQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 69.000α = 90.00
b = 101.400β = 113.60
c = 79.100γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-05-15
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance