1EFM

STRUCTURE OF THE GDP DOMAIN OF EF-TU AND LOCATION OF THE AMINO ACIDS HOMOLOGOUS TO RAS ONCOGENE PROTEINS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the GDP domain of EF-Tu and location of the amino acids homologous to ras oncogene proteins.

Jurnak, F.

(1985) Science 230: 32-36


  • PubMed Abstract: 
  • A 2.7 angstrom resolution x-ray diffraction analysis of a trypsin-modified form of the Escherichia coli elongation factor Tu reveals that the GDP-binding domain has a structure similar to that of other nucleotide-binding proteins. The GDP ligand is l ...

    A 2.7 angstrom resolution x-ray diffraction analysis of a trypsin-modified form of the Escherichia coli elongation factor Tu reveals that the GDP-binding domain has a structure similar to that of other nucleotide-binding proteins. The GDP ligand is located at the COOH-terminal end of the beta sheet and is linked to the protein via a Mg2+ ion salt bridge. The location of the guanine ring is unusual; the purine ring is located on the outer edge of the domain, not deep within a hydrophobic pocket. The amino acids from Pro10 to Arg44 and from Gly59 to Glu190 have been assigned to the electron density with computer graphic techniques, and the resulting model is consistent with all known biochemical data. An analysis of the structure reveals that four regions of the amino acid sequence that are homologous with the family of ras oncogene proteins, termed p21, are located in the vicinity of the GDP-binding site, and most of the invariant amino acids shared by the proteins interact directly with the GDP ligand.


    Related Citations: 
    • Preliminary X-Ray Diffraction Data for Tetragonal Crystals of Trypsinized Escherichia Coli Elongation Factor
      Jurnak, F.,Rich, A.,Miller, D.
      (1977) J.Mol.Biol. 115: 103
    • Biochemical and Structural Studies of the Tetragonal Crystalline Modification of the Escherichia Coli Elongation Factor TU
      Jurnak, F.,McPherson, A.,Wang, A.H.J.,Rich, A.
      (1980) J.Biol.Chem. 255: 6751
    • Primary Structure of Elongation Factor TU from Escherichia Coli
      Arai, K.,Clark, B.F.C.,Duffy, L.,Jones, M.D.,Kaziro, Y.,Laursen, R.A.,L'Italien, J.,Miller, D.L.,Nagarkatti, S.,Nakamura, S.,Nielsen, K.M.,Petersen, T.E.,Takahashi, K.,Wade, M.
      (1980) Proc.Natl.Acad.Sci.USA 77: 1326



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ELONGATION FACTOR TU
A
379Escherichia coli (strain K12)Gene Names: tufB
Find proteins for P0CE48 (Escherichia coli (strain K12))
Go to UniProtKB:  P0CE48
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 98.609α = 90.00
b = 100.807β = 90.00
c = 162.465γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1987-05-29 
  • Released Date: 1987-07-16 
  • Deposition Author(s): Jurnak, F.

Revision History 

  • Version 1.0: 1987-07-16
    Type: Initial release
  • Version 1.1: 2008-03-10
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance