2C78

EF-Tu complexed with a GTP analog and the antibiotic pulvomycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis of the action of pulvomycin and GE2270 A on elongation factor Tu.

Parmeggiani, A.Krab, I.M.Okamura, S.Nielsen, R.C.Nyborg, J.Nissen, P.

(2006) Biochemistry 45: 6846-6857

  • DOI: 10.1021/bi0525122
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pulvomycin inhibits protein synthesis by preventing the formation of the ternary complex between elongation factor Tu (EF-Tu) x GTP and aa-tRNA. In this work, the crystal structure of Thermus thermophilus EF-Tu x pulvomycin in complex with the GTP an ...

    Pulvomycin inhibits protein synthesis by preventing the formation of the ternary complex between elongation factor Tu (EF-Tu) x GTP and aa-tRNA. In this work, the crystal structure of Thermus thermophilus EF-Tu x pulvomycin in complex with the GTP analogue guanylyl imino diphosphate (GDPNP) at 1.4 A resolution reveals an antibiotic binding site extending from the domain 1-3 interface to domain 2, overlapping the domain 1-2-3 junction. Pulvomycin binding interferes with the binding of the 3'-aminoacyl group, the acceptor stem, and 5' end of tRNA. Only part of pulvomycin overlaps the binding site of GE2270 A, a domain 2-bound antibiotic of a structure unrelated to pulvomycin, which also hinders aa-tRNA binding. The structure of the T. thermophilus EF-Tu x GDPNP x GE2270 A complex at 1.6 A resolution shows that GE2270 A interferes with the binding of the 3'-aminoacyl group and part of the acceptor stem of aa-tRNA but not with the 5' end. Both compounds, pulvomycin more markedly, hinder the correct positioning of domain 1 over domains 2 and 3 that characterizes the active form of EF-Tu, while they affect the domain 1 switch regions that control the EF-Tu x GDP/GTP transitions in different ways. This work reveals how two antibiotics with different structures and binding modes can employ a similar mechanism of action.


    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
A
405Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: tufA (tuf)
Find proteins for Q5SHN6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

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

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
PUL
Query on PUL

Download SDF File 
Download CCD File 
A
(1S,2S,3E,5E,7E,10S,11S,12S)-12-[(2R,4E,6E,8Z,10R,12E,14E,16Z,18S,19Z)-10,18-DIHYDROXY-12,16,19-TRIMETHYL-11,22-DIOXOOXACYCLODOCOSA-4,6,8,12,14,16,19-HEPTAEN-2-YL]-2,11-DIHYDROXY-1,10-DIMETHYL-9-OXOTRIDECA-3,5,7-TRIEN-1-YL 6-DEOXY-2,4-DI-O-METHYL-BETA-L-GALACTOPYRANOSIDE
PULVOMYCIN
C47 H66 O13
FXSFWUNCIOIMAC-VXILMCRLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.197 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 86.686α = 90.00
b = 86.686β = 90.00
c = 105.514γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-16
    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: 2018-03-28
    Type: Database references, Source and taxonomy