• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of pnasPNASInfo for AuthorsSubscriptionsAboutThis Article
Proc Natl Acad Sci U S A. Jun 15, 1991; 88(12): 5443–5447.
PMCID: PMC51889

GTPase domains of ras p21 oncogene protein and elongation factor Tu: analysis of three-dimensional structures, sequence families, and functional sites.

Abstract

GTPase domains are functional and structural units employed as molecular switches in a variety of important cellular functions, such as growth control, protein biosynthesis, and membrane traffic. Amino acid sequences of more than 100 members of different subfamilies are known, but crystal structures of only mammalian ras p21 and bacterial elongation factor Tu have been determined. After optimal superposition of these remarkably similar structures, careful multiple sequence alignment, and calculation of residue-residue interactions, we analyzed the two subfamilies in terms of structural conservation, sequence conservation, and residue contact strength. There are three main results. (i) A structure-based alignment of p21 and elongation factor Tu. (ii) The definition of a common conserved structural core that may be useful as the basis of model building by homology of the three-dimensional structure of any GTPase domain. (iii) Identification of sequence regions, other than the effector loop and the nucleotide binding site, that may be involved in the functional cycle: they are loop L4, known to change conformation after GTP hydrolysis; helix alpha 2, especially Arg-73 and Met-67 in ras p21; loops L8 and L10, including ras p21 Arg-123, Lys-147, and Leu-120; and residues located spatially near the N and C termini. These regions are candidate sites for interaction either with the GTP/GDP exchange factor, with a GTPase-affected function, or with a molecule delivered to a destination site with the aid of the GTPase domain.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (1.3M), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Images in this article

Click on the image to see a larger version.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Bourne HR, Sanders DA, McCormick F. The GTPase superfamily: a conserved switch for diverse cell functions. Nature. 1990 Nov 8;348(6297):125–132. [PubMed]
  • Bourne HR, Sanders DA, McCormick F. The GTPase superfamily: conserved structure and molecular mechanism. Nature. 1991 Jan 10;349(6305):117–127. [PubMed]
  • Barbacid M. ras genes. Annu Rev Biochem. 1987;56:779–827. [PubMed]
  • Pai EF, Kabsch W, Krengel U, Holmes KC, John J, Wittinghofer A. Structure of the guanine-nucleotide-binding domain of the Ha-ras oncogene product p21 in the triphosphate conformation. Nature. 1989 Sep 21;341(6239):209–214. [PubMed]
  • Pai EF, Krengel U, Petsko GA, Goody RS, Kabsch W, Wittinghofer A. Refined crystal structure of the triphosphate conformation of H-ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis. EMBO J. 1990 Aug;9(8):2351–2359. [PMC free article] [PubMed]
  • Krengel U, Schlichting I, Scherer A, Schumann R, Frech M, John J, Kabsch W, Pai EF, Wittinghofer A. Three-dimensional structures of H-ras p21 mutants: molecular basis for their inability to function as signal switch molecules. Cell. 1990 Aug 10;62(3):539–548. [PubMed]
  • Milburn MV, Tong L, deVos AM, Brünger A, Yamaizumi Z, Nishimura S, Kim SH. Molecular switch for signal transduction: structural differences between active and inactive forms of protooncogenic ras proteins. Science. 1990 Feb 23;247(4945):939–945. [PubMed]
  • Schlichting I, Almo SC, Rapp G, Wilson K, Petratos K, Lentfer A, Wittinghofer A, Kabsch W, Pai EF, Petsko GA, et al. Time-resolved X-ray crystallographic study of the conformational change in Ha-Ras p21 protein on GTP hydrolysis. Nature. 1990 May 24;345(6273):309–315. [PubMed]
  • McCormick F, Adari H, Trahey M, Halenbeck R, Koths K, Martin GA, Crosier WJ, Watt K, Rubinfeld B, Wong G. Interaction of ras p21 proteins with GTPase activating protein. Cold Spring Harb Symp Quant Biol. 1988;53(Pt 2):849–854. [PubMed]
  • Broek D, Toda T, Michaeli T, Levin L, Birchmeier C, Zoller M, Powers S, Wigler M. The S. cerevisiae CDC25 gene product regulates the RAS/adenylate cyclase pathway. Cell. 1987 Mar 13;48(5):789–799. [PubMed]
  • Wolfman A, Macara IG. A cytosolic protein catalyzes the release of GDP from p21ras. Science. 1990 Apr 6;248(4951):67–69. [PubMed]
  • Downward J, Riehl R, Wu L, Weinberg RA. Identification of a nucleotide exchange-promoting activity for p21ras. Proc Natl Acad Sci U S A. 1990 Aug;87(15):5998–6002. [PMC free article] [PubMed]
  • Huang YK, Kung HF, Kamata T. Purification of a factor capable of stimulating the guanine nucleotide exchange reaction of ras proteins and its effect on ras-related small molecular mass G proteins. Proc Natl Acad Sci U S A. 1990 Oct;87(20):8008–8012. [PMC free article] [PubMed]
  • Riis B, Rattan SI, Clark BF, Merrick WC. Eukaryotic protein elongation factors. Trends Biochem Sci. 1990 Nov;15(11):420–424. [PubMed]
  • Kaziro Y. The role of guanosine 5'-triphosphate in polypeptide chain elongation. Biochim Biophys Acta. 1978 Sep 21;505(1):95–127. [PubMed]
  • Panniers R, Rowlands AG, Henshaw EC. The effect of Mg2+ and guanine nucleotide exchange factor on the binding of guanine nucleotides to eukaryotic initiation factor 2. J Biol Chem. 1988 Apr 25;263(12):5519–5525. [PubMed]
  • Clark BF, Kjeldgaard M, la Cour TF, Thirup S, Nyborg J. Structural determination of the functional sites of E. coli elongation factor Tu. Biochim Biophys Acta. 1990 Aug 27;1050(1-3):203–208. [PubMed]
  • Jurnak F. Structure of the GDP domain of EF-Tu and location of the amino acids homologous to ras oncogene proteins. Science. 1985 Oct 4;230(4721):32–36. [PubMed]
  • Parmeggiani A, Swart GW, Mortensen KK, Jensen M, Clark BF, Dente L, Cortese R. Properties of a genetically engineered G domain of elongation factor Tu. Proc Natl Acad Sci U S A. 1987 May;84(10):3141–3145. [PMC free article] [PubMed]
  • McCormick F, Clark BF, la Cour TF, Kjeldgaard M, Norskov-Lauritsen L, Nyborg J. A model for the tertiary structure of p21, the product of the ras oncogene. Science. 1985 Oct 4;230(4721):78–82. [PubMed]
  • Chen JM, Lee G, Murphy RB, Carty RP, Brandt-Rauf PW, Friedman E, Pincus MR. Comparison of the computed structures for the phosphate-binding loop of the p21 protein containing the oncogenic site Gly 12 with the X-ray crystallographic structures for this region in the p21 protein and EFtu. A model for the structure of the p21 protein in its oncogenic form. J Biomol Struct Dyn. 1989 Apr;6(5):859–875. [PubMed]
  • Chen JM, Lee G, Murphy RB, Brandt-Rauf PW, Pincus MR. Comparisons between the three-dimensional structures of the chemotactic protein CheY and the normal Gly 12-p21 protein. Int J Pept Protein Res. 1990 Jul;36(1):1–6. [PubMed]
  • Chen JM, Lee G, Brandt-Rauf PW, Murphy RB, Gibson KD, Scheraga HA, Rackovsky S, Pincus MR. Conformations of the central transforming region (Ile 55-Met 67) of the p21 protein and their relationship to activation of the protein. Int J Pept Protein Res. 1990 Sep;36(3):247–254. [PubMed]
  • Sander C, Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins. 1991;9(1):56–68. [PubMed]
  • Taylor WR, Orengo CA. Protein structure alignment. J Mol Biol. 1989 Jul 5;208(1):1–22. [PubMed]
  • Chothia C, Lesk AM. The relation between the divergence of sequence and structure in proteins. EMBO J. 1986 Apr;5(4):823–826. [PMC free article] [PubMed]
  • Hubbard TJ, Blundell TL. Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling. Protein Eng. 1987 Jun;1(3):159–171. [PubMed]
  • Willumsen BM, Papageorge AG, Kung HF, Bekesi E, Robins T, Johnsen M, Vass WC, Lowy DR. Mutational analysis of a ras catalytic domain. Mol Cell Biol. 1986 Jul;6(7):2646–2654. [PMC free article] [PubMed]
  • Sigal IS, Gibbs JB, D'Alonzo JS, Scolnick EM. Identification of effector residues and a neutralizing epitope of Ha-ras-encoded p21. Proc Natl Acad Sci U S A. 1986 Jul;83(13):4725–4729. [PMC free article] [PubMed]
  • Hattori S, Clanton DJ, Satoh T, Nakamura S, Kaziro Y, Kawakita M, Shih TY. Neutralizing monoclonal antibody against ras oncogene product p21 which impairs guanine nucleotide exchange. Mol Cell Biol. 1987 May;7(5):1999–2002. [PMC free article] [PubMed]
  • Hwang YW, Sanchez A, Miller DL. Mutagenesis of bacterial elongation factor Tu at lysine 136. A conserved amino acid in GTP regulatory proteins. J Biol Chem. 1989 May 15;264(14):8304–8309. [PubMed]
  • Clanton DJ, Hattori S, Shih TY. Mutations of the ras gene product p21 that abolish guanine nucleotide binding. Proc Natl Acad Sci U S A. 1986 Jul;83(14):5076–5080. [PMC free article] [PubMed]
  • Reinstein J, Vetter IR, Schlichting I, Rösch P, Wittinghofer A, Goody RS. Fluorescence and NMR investigations on the ligand binding properties of adenylate kinases. Biochemistry. 1990 Aug 14;29(32):7440–7450. [PubMed]
  • Feuerstein J, Goody RS, Wittinghofer A. Preparation and characterization of nucleotide-free and metal ion-free p21 "apoprotein". J Biol Chem. 1987 Jun 25;262(18):8455–8458. [PubMed]
  • Créchet JB, Poullet P, Mistou MY, Parmeggiani A, Camonis J, Boy-Marcotte E, Damak F, Jacquet M. Enhancement of the GDP-GTP exchange of RAS proteins by the carboxyl-terminal domain of SCD25. Science. 1990 May 18;248(4957):866–868. [PubMed]
  • Créchet JB, Poullet P, Camonis J, Jacquet M, Parmeggiani A. Different kinetic properties of the two mutants, RAS2Ile152 and RAS2Val19, that suppress the CDC25 requirement in RAS/adenylate cyclase pathway in Saccharomyces cerevisiae. J Biol Chem. 1990 Jan 25;265(3):1563–1568. [PubMed]
  • Fasano O, Crechet JB, De Vendittis E, Zahn R, Feger G, Vitelli A, Parmeggiani A. Yeast mutants temperature-sensitive for growth after random mutagenesis of the chromosomal RAS2 gene and deletion of the RAS1 gene. EMBO J. 1988 Nov;7(11):3375–3383. [PMC free article] [PubMed]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

  • Conserved Domains
    Conserved Domains
    Link to related CDD entry
  • MedGen
    MedGen
    Related information in MedGen
  • PubMed
    PubMed
    PubMed citations for these articles

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...