5P21

REFINED CRYSTAL STRUCTURE OF THE TRIPHOSPHATE CONFORMATION OF H-RAS P21 AT 1.35 ANGSTROMS RESOLUTION: IMPLICATIONS FOR THE MECHANISM OF GTP HYDROLYSIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Refined crystal structure of the triphosphate conformation of H-ras p21 at 1.35 A resolution: implications for the mechanism of GTP hydrolysis.

Pai, E.F.Krengel, U.Petsko, G.A.Goody, R.S.Kabsch, W.Wittinghofer, A.

(1990) EMBO J. 9: 2351-2359


  • PubMed Abstract: 
  • The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp has been determined at 1.35 A resolution. 211 water molecules have been built into the electron density. The structure has been refined to ...

    The crystal structure of the H-ras oncogene protein p21 complexed to the slowly hydrolysing GTP analogue GppNp has been determined at 1.35 A resolution. 211 water molecules have been built into the electron density. The structure has been refined to a final R-factor of 19.8% for all data between 6 A and 1.35 A. The binding sites of the nucleotide and the magnesium ion are revealed in high detail. For the stretch of amino acid residues 61-65, the temperature factors of backbone atoms are four times the average value of 16.1 A2 due to the multiple conformations. In one of these conformations, the side chain of Gln61 makes contact with a water molecule, which is perfectly placed to be the nucleophile attacking the gamma-phosphate of GTP. Based on this observation, we propose a mechanism for GTP hydrolysis involving mainly Gln61 and Glu63 as activating species for in-line attack of water. Nucleophilic displacement is facilitated by hydrogen bonds from residues Thr35, Gly60 and Lys16. A mechanism for rate enhancement by GAP is also proposed.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Analysis of the Human C-H-Ras-Oncogene Product P21 Complexed with GTP Analogues
      Scherer, A.,John, J.,Linke, R.,Goody, R.S.,Wittinghofer, A.,Pai, E.F.,Holmes, K.C.
      (1989) J.Mol.Biol. 206: 257
    • Biochemical and Crystallographic Characterization of a Complex of C-Ha-Ras P21 and Caged GTP with Flash Photolysis
      Schlichting, I.,Rapp, G.,John, J.,Wittinghofer, A.,Pai, E.F.,Goody, R.S.
      (1989) Proc.Natl.Acad.Sci.USA 86: 7687
    • Time-Resolved X-Ray Crystallographic Study of the Conformational Change in Ha-Ras P21 Protein on GTP Hydrolysis
      Schlichting, I.,Almo, S.C.,Rapp, G.,Wilson, K.,Petratos, K.,Lentfer, A.,Wittinghofer, A.,Kabsch, W.,Pai, E.F.,Petsko, G.A.,Goody, R.S.
      (1990) Nature 345: 309
    • Structure of the Guanine-Nucleotide-Binding Domain of the Ha-Ras Oncogene Product P21 in the Triphosphate Conformation
      Pai, E.F.,Kabsch, W.,Krengel, U.,Holmes, K.C.,John, J.,Wittinghofer, A.
      (1989) Nature 341: 209


    Organizational Affiliation

    Max-Planck-Institut für medizinische Forschung, Abteilung Biophysik, Heidelberg, FRG.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-H-RAS P21 PROTEIN
A
166Homo sapiensGene Names: HRAS (HRAS1)
Find proteins for P01112 (Homo sapiens)
Go to Gene View: HRAS
Go to UniProtKB:  P01112
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
GNP
Query on GNP

Download SDF File 
Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Work: 0.196 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 40.300α = 90.00
b = 40.300β = 90.00
c = 162.200γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1992-01-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other