4PC6

Elongation factor Tu:Ts complex with bound GDPNP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural outline of the detailed mechanism for elongation factor Ts-mediated guanine nucleotide exchange on elongation factor Tu.

Thirup, S.S.Van, L.B.Nielsen, T.K.Knudsen, C.R.

(2015) J.Struct.Biol. 191: 10-21

  • DOI: 10.1016/j.jsb.2015.06.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Translation elongation factor EF-Tu belongs to the superfamily of guanine-nucleotide binding proteins, which play key cellular roles as regulatory switches. All G-proteins require activation via exchange of GDP for GTP to carry out their respective t ...

    Translation elongation factor EF-Tu belongs to the superfamily of guanine-nucleotide binding proteins, which play key cellular roles as regulatory switches. All G-proteins require activation via exchange of GDP for GTP to carry out their respective tasks. Often, guanine-nucleotide exchange factors are essential to this process. During translation, EF-Tu:GTP transports aminoacylated tRNA to the ribosome. GTP is hydrolyzed during this process, and subsequent reactivation of EF-Tu is catalyzed by EF-Ts. The reaction path of guanine-nucleotide exchange is structurally poorly defined for EF-Tu and EF-Ts. We have determined the crystal structures of the following reaction intermediates: two structures of EF-Tu:GDP:EF-Ts (2.2 and 1.8Å resolution), EF-Tu:PO4:EF-Ts (1.9Å resolution), EF-Tu:GDPNP:EF-Ts (2.2Å resolution) and EF-Tu:GDPNP:pulvomycin:Mg(2+):EF-Ts (3.5Å resolution). These structures provide snapshots throughout the entire exchange reaction and suggest a mechanism for the release of EF-Tu in its GTP conformation. An inferred sequence of events during the exchange reaction is presented.


    Organizational Affiliation

    Aarhus University, Department of Molecular Biology and Genetics, Center for Structural Biology, DK-8000 Aarhus C, Denmark. Electronic address: sth@mbg.au.dk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Elongation factor Tu
A, B
394Escherichia coli (strain K12 / DH10B)Mutation(s): 0 
Gene Names: tufA (tuf)
Find proteins for A0A0M3KKV1 (Escherichia coli (strain K12 / DH10B))
Go to UniProtKB:  A0A0M3KKV1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Elongation factor Ts
C, D
282Escherichia coli (strain ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1)Mutation(s): 0 
Gene Names: tsf
Find proteins for A0A0M3KKV2 (Escherichia coli (strain ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1))
Go to UniProtKB:  A0A0M3KKV2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-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: 2.2 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.969α = 90.00
b = 107.467β = 90.00
c = 193.339γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2014-04-14 
  • Released Date: 2015-05-06 
  • Deposition Author(s): Thirup, S.S.

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-07-01
    Type: Database references
  • Version 1.2: 2015-07-15
    Type: Database references