Structure of the GDP Domain of EF-Tu and Location of the Amino Acids Homologous to ras Oncogene Proteins

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. 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.

Examination of elongation factor Tu for aluminum fluoride binding sites using fluorescence and 19F‐NMR methodologies

“…Th~s conclusson ~s also supported by the further observation that the blndlng of GTP~S, Fluorescence enhancement of the EF-Tu tryptophan has been observed m the cases of EF-Tu denaturation in 6 M guamne HCI (Hazlett and Jameson, unpubhshed) or SDS [19] and for the GTP-form of the protein [19]. Information from the crystal structure [20,21] and sequence data [22] have assigned the single tryptophan to res)due 184 withln the GDP-binding domam and near the nucleottde site Fluorescence quenching data have described the tryptophan environment as relatively in. accessible to the solvent [23] suggesting an interior fac.…”

“…The exact nature of the resulting conformational change ~s not presently known for any of the G proteins under study. Of the GTP-blnding proteins being mvestlgated, EF-Tu is probably the best understood w~th data on the crystal structure for the GDP form having been reported [20,21]. Other G proteins, with the exceptlon of the ras p21 proteins [15-I'7], have yet to be crystalhzed and little ~s known about their overall structure.…”

Proteolysis of Bacillus stearothermophilus IF2 and specific protection by fMet‐tRNA

“…During the course of trypsinolysis, the N-terminal pot- GTP/GDP binding site of IF2, in the middle of the structural elements conserved among G-proteins [14,15] but no binding of fMet-tRNA with this part of the molecule has ever been observed and under no circumstance has it been found that the binding of GTP or GDP and fMet-tRNA to IF2 may influence each other [6,16]. Thus, it is unlikely that the protection of this site by the initiator tRNA might be due to a direct interaction.…”

Kirromycin‐induced modifications facilitate the separation of EF‐Tu species and reveal intermolecular interactions

“…Ha-ras p21, with known three-dimensional structure [1][2][3][4] and one of the best characterized members of this class of proteins [5][6][7][8]. It has been the object of intensive mutagenesis by diverse procedures (for references, see [9]).…”