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: 2.70 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

  • DOI: 10.1126/science.3898365
  • Primary Citation of Related Structures:  
    1EFM

  • 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 located at the COOH-terminal end of the beta sheet and is linked to the protein via a Mg2+ ion salt bridge ...

    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: 
    • 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
    • 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
    • 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 U S A 77: 1326

    Organizational Affiliation

    Departments of Pharmacology and Neuroscience, University of Florida, Gainesville, Florida 32610-0267, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ELONGATION FACTOR TUA379Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0CE48 (Escherichia coli (strain K12))
Explore P0CE48 
Go to UniProtKB:  P0CE48
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
C [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.609α = 90
b = 100.807β = 90
c = 162.465γ = 90

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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