1HA3

ELONGATION FACTOR TU IN COMPLEX WITH aurodox


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.6 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: https://doi.org/10.1074/jbc.M100017200
  • Primary Citation of Related Structures:  
    1HA3

  • 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 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ELONGATION FACTOR TU
A, B
405Thermus thermophilus HB8Mutation(s): 4 
Gene Names: TUFB
EC: 3.1.5.1
UniProt
Find proteins for Q5SHN6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SHN6 
Go to UniProtKB:  Q5SHN6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHN6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MAU
Query on MAU

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
N-METHYL KIRROMYCIN
C44 H62 N2 O12
NTAHMPNXQOYXSX-WKSONYIQSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
BME
Query on BME

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69α = 90
b = 101.4β = 113.6
c = 79.1γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-05-15
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.4: 2019-07-24
    Changes: Data collection
  • Version 1.5: 2019-10-23
    Changes: Data collection, Database references, Other
  • Version 1.6: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description