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: 3.1 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.280 

wwPDB Validation 3D Report Full Report


This is version 1.2 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, C, E
405Thermus aquaticusMutation(s): 0 
Gene Names: tuf (tufA)
Find proteins for Q01698 (Thermus aquaticus)
Go to UniProtKB:  Q01698
Entity ID: 2
MoleculeChainsLengthOrganism
TRANSFER-RNA, PHEB,D,F78Saccharomyces cerevisiae
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ENX
Query on ENX

Download SDF File 
Download CCD File 
A, C, E
ENACYLOXIN IIA
C33 H45 Cl2 N O11
IWBADCVFZDCUTN-OCXJTLLTSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

Download SDF File 
Download CCD File 
A, C, E
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Modified Residues  12 Unique
IDChainsTypeFormula2D DiagramParent
PHA
Query on PHA
B, D, F
L-PEPTIDE LINKINGC9 H11 N OPHE
PSU
Query on PSU
B, D, F
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
B, D, F
RNA LINKINGC10 H16 N3 O8 PC
M2G
Query on M2G
B, D, F
RNA LINKINGC12 H18 N5 O8 PG
1MA
Query on 1MA
B, D, F
RNA LINKINGC11 H16 N5 O7 PA
OMC
Query on OMC
B, D, F
RNA LINKINGC10 H16 N3 O8 PC
2MG
Query on 2MG
B, D, F
RNA LINKINGC11 H16 N5 O8 PG
OMG
Query on OMG
B, D, F
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
B, D, F
RNA LINKINGC11 H18 N5 O8 PG
YG
Query on YG
B, D, F
RNA LINKINGC21 H29 N6 O12 PG
5MU
Query on 5MU
B, D, F
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
B, D, F
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.280 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 212.570α = 90.00
b = 122.330β = 121.30
c = 135.680γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-13
    Type: Initial release
  • Version 1.1: 2015-08-19
    Type: Atomic model, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
  • Version 1.2: 2019-07-24
    Type: Advisory, Data collection, Derived calculations