2BVN

E. coli EF-Tu:GDPNP in complex with the antibiotic enacyloxin IIa

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Enacyloxin Iia Pinpoints a Binding Pocket of Elongation Factor TU for Development of Novel Antibiotics.

Parmeggiani, A., Krab, I.M., Watanabe, T., Nielsen, R.C., Dahlberg, C., Nyborg, J., Nissen, P.

(2006) J.Biol.Chem. 281: 2893

  • DOI: 10.1074/jbc.M505951200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Elongation factor (EF-) Tu.GTP is the carrier of aminoacyl-tRNA to the programmed ribosome. Enacyloxin IIa inhibits bacterial protein synthesis by hindering the release of EF-Tu.GDP from the ribosome. The crystal structure of the Escherichia coli EF- ...

    Elongation factor (EF-) Tu.GTP is the carrier of aminoacyl-tRNA to the programmed ribosome. Enacyloxin IIa inhibits bacterial protein synthesis by hindering the release of EF-Tu.GDP from the ribosome. The crystal structure of the Escherichia coli EF-Tu.guanylyl iminodiphosphate (GDPNP).enacyloxin IIa complex at 2.3 A resolution presented here reveals the location of the antibiotic at the interface of domains 1 and 3. The binding site overlaps that of kirromycin, an antibiotic with a structure that is unrelated to enacyloxin IIa but that also inhibits EF-Tu.GDP release. As one of the major differences, the enacyloxin IIa tail borders a hydrophobic pocket that is occupied by the longer tail of kirromycin, explaining the higher binding affinity of the latter. EF-Tu.GDPNP.enacyloxin IIa shows a disordered effector region that in the Phe-tRNAPhe.EF-Tu (Thermus aquaticus).GDPNP.enacyloxin IIa complex, solved at 3.1 A resolution, is stabilized by the interaction with tRNA. This work clarifies the structural background of the action of enacyloxin IIa and compares its properties with those of kirromycin, opening new perspectives for structure-guided design of novel antibiotics.

    Organizational Affiliation: 

    Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10 C, DK-8000 Aarhus C, Denmark. andrea@bioxray.dk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ELONGATION FACTOR TU
A, B
393Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: tufB
Find proteins for P0CE48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0CE48
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ENX
Query on ENX
Download SDF File 
Download CCD File 
A, B
ENACYLOXIN IIA
C33 H45 Cl2 N O11
IWBADCVFZDCUTN-OCXJTLLTSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP
Download SDF File 
Download CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.230 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 72.070α = 90.00
b = 72.070β = 90.00
c = 335.730γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-09-01
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-17
    Type: Data collection