1CLU

H-RAS COMPLEXED WITH DIAMINOBENZOPHENONE-BETA,GAMMA-IMIDO-GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Guanosine triphosphatase stimulation of oncogenic Ras mutants.

Ahmadian, M.R.Zor, T.Vogt, D.Kabsch, W.Selinger, Z.Wittinghofer, A.Scheffzek, K.

(1999) Proc Natl Acad Sci U S A 96: 7065-7070

  • DOI: 10.1073/pnas.96.12.7065
  • Primary Citation of Related Structures:  
    1CLU, 1RVD

  • PubMed Abstract: 
  • Interest in the guanosine triphosphatase (GTPase) reaction of Ras as a molecular drug target stems from the observation that, in a large number of human tumors, Ras is characteristically mutated at codons 12 or 61, more rarely 13. Impaired GTPase activity, even in the presence of GTPase activating proteins, has been found to be the biochemical reason behind the oncogenicity of most Gly12/Gln61 mutations, thus preventing Ras from being switched off ...

    Interest in the guanosine triphosphatase (GTPase) reaction of Ras as a molecular drug target stems from the observation that, in a large number of human tumors, Ras is characteristically mutated at codons 12 or 61, more rarely 13. Impaired GTPase activity, even in the presence of GTPase activating proteins, has been found to be the biochemical reason behind the oncogenicity of most Gly12/Gln61 mutations, thus preventing Ras from being switched off. Therefore, these oncogenic Ras mutants remain constitutively activated and contribute to the neoplastic phenotype of tumor cells. Here, we show that the guanosine 5'-triphosphate (GTP) analogue diaminobenzophenone-phosphoroamidate-GTP (DABP-GTP) is hydrolyzed by wild-type Ras but more efficiently by frequently occurring oncogenic Ras mutants, to yield guanosine 5'-diphosphate-bound inactive Ras and DABP-Pi. The reaction is independent of the presence of Gln61 and is most dramatically enhanced with Gly12 mutants. Thus, the defective GTPase reaction of the oncogenic Ras mutants can be rescued by using DABP-GTP instead of GTP, arguing that the GTPase switch of Ras is not irreversibly damaged. An exocyclic aromatic amino group of DABP-GTP is critical for the reaction and bypasses the putative rate-limiting step of the intrinsic Ras GTPase reaction. The crystal structures of Ras-bound DABP-beta,gamma-imido-GTP show a disordered switch I and identify the Gly12/Gly13 region as the hydrophobic patch to accommodate the DABP-moiety. The biochemical and structural studies help to define the requirements for the design of anti-Ras drugs aimed at the blocked GTPase reaction.


    Related Citations: 
    • GTP analogue hydrolysis by the Gs protein: implication for the role of catalytic glutamine in the GTPase reaction.
      Zor, T., Andorn, R., Sofer, I., Chorev, M., Selinger, Z.
      (1998) FEBS Lett 433: 326
    • Rescue of a mutant G-protein by substrate-assisted catalysis.
      Zor, T., Bar-Yaacov, M., Elgavish, S., Shaanan, B., Selinger, Z.
      (1997) Eur J Biochem 249: 330
    • Three-dimensional structures and properties of a transforming and a nontransforming glycine-12 mutant of p21H-ras.
      Franken, S.M., Scheidig, A.J., Krengel, U., Rensland, H., Lautwein, A., Geyer, M., Scheffzek, K., Goody, R.S., Kalbitzer, H.R., Pai, E.F.
      (1993) Biochemistry 32: 8411
    • Three-dimensional structures of H-ras p21 mutants: molecular basis for their inability to function as signal switch molecules.
      Krengel, U., Schlichting, I., Scherer, A., Schumann, R., Frech, M., John, J., Kabsch, W., Pai, E.F., Wittinghofer, A.
      (1990) Cell 62: 539

    Organizational Affiliation

    Abteilung Strukturelle Biologie, Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRANSFORMING PROTEIN P21/H-RAS-1A166Homo sapiensMutation(s): 1 
Gene Names: H-RAS-1HRASHRAS1
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
DBG
Query on DBG

Download Ideal Coordinates CCD File 
C [auth A]3-AMINOBENZOPHENONE-4-YL-AMINOHYDROXYPHOSPHINYLAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C23 H27 N8 O13 P3
MXYGEAAJPIMEHV-CIVUBGFFSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
B [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DBGKd:  5.400000095367432   nM  Binding MOAD
DBGKd :  5.400000095367432   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.203 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.2α = 90
b = 40.2β = 90
c = 161.97γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-05-28
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-03-14
    Changes: Database references
  • Version 1.4: 2019-11-27
    Changes: Database references