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

  • Primary Citation of Related Structures:  
    5P21

  • 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 a final R-factor of 19 ...

    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: 
    • 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
    • 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
    • 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
    • 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 U S A 86: 7687

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
C-H-RAS P21 PROTEINA166Homo sapiensMutation(s): 0 
Gene Names: HRASHRAS1
EC: 3.6.5.2
Find proteins for P01112 (Homo sapiens)
Explore P01112 
Go to UniProtKB:  P01112
NIH Common Fund Data Resources
PHAROS:  P01112
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-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: 1.35 Å
  • R-Value Work: 0.196 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.3α = 90
b = 40.3β = 90
c = 162.2γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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