1OB5

T. aquaticus elongation factor EF-Tu complexed with the antibiotic enacyloxin IIa, a GTP analog, and Phe-tRNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.280 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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: https://doi.org/10.1074/jbc.M505951200
  • Primary Citation of Related Structures:  
    1OB5, 2BVN

  • 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-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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ELONGATION FACTOR TU
A, C, E
405Thermus aquaticusMutation(s): 0 
EC: 3.6.1.48
UniProt
Find proteins for Q01698 (Thermus aquaticus)
Explore Q01698 
Go to UniProtKB:  Q01698
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01698
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
TRANSFER-RNA, PHE
B, D, F
78Saccharomyces cerevisiae
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ENX
Query on ENX

Download Ideal Coordinates CCD File 
I [auth A],
L [auth C],
O [auth E]
ENACYLOXIN IIA
C33 H45 Cl2 N O11
IWBADCVFZDCUTN-OCXJTLLTSA-N
GNP
Query on GNP

Download Ideal Coordinates CCD File 
G [auth A],
J [auth C],
M [auth E]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A],
K [auth C],
N [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PHA
Query on PHA
B, D, F
L-PEPTIDE LINKINGC9 H11 N OPHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.280 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.57α = 90
b = 122.33β = 121.3
c = 135.68γ = 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: 2005-10-13
    Type: Initial release
  • Version 1.1: 2015-08-19
    Changes: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2023-12-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description