Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19655.99 
• Atom Count: 1296 
• Residue Count: 166 
• Unique protein chains: 1

1CLU

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

• DOI: 10.2210/pdb1CLU/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Mutation(s): 1 


• Deposited: 1999-05-03 Released: 1999-05-28 
• Deposition Author(s): Ahmadian, M.R., Zor, T., Vogt, D., Kabsch, W., Selinger, Z., Wittinghofer, A., Scheffzek, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.261 
• R-Value Work: 0.203 

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.USA 96: 7065-7070

• PubMed: 10359839 
• DOI: 10.1073/pnas.96.12.7065
• Primary Citation of Related Structures:  
  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. 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.

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Related Citations: 

• Rescue of a Mutantg-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 Gly-12 Mutant of P21-H-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.,Wittinghofer, A.
  (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
• GTP Analogue Hydrolysis by the Gs Protein-Implication for the Role of Catalytic Glutamine in Thegtpase Reaction
  Zor, T.,Andorn, R.,Sofer, I.,Chorev, M.,Selinger, Z.
  (1998) FEBS Lett. 433: 326




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
TRANSFORMING PROTEIN P21/H-RAS-1	A	166	Homo sapiens	Mutation(s): 1  Gene Names: HRAS (HRAS1)
Find proteins for P01112 (Homo sapiens) Go to Gene View: HRAS Go to UniProtKB:  P01112

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
DBG	A	3-AMINOBENZOPHENONE-4-YL-AMINOHYDROXYPHOSPHINYLAMINOPHOSPHONIC ACID-GUANYLATE ESTER DABP-GPPNHP C23 H27 N8 O13 P3 MXYGEAAJPIMEHV-CIVUBGFFSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DBG	Kd: 5.4 nM BINDINGMOAD
DBG	Kd: 5.4 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.261 
• R-Value Work: 0.203 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 40.200	α = 90.00
b = 40.200	β = 90.00
c = 161.970	γ = 120.00

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-05-03 
• Released Date: 1999-05-28 
• Deposition Author(s): Ahmadian, M.R., Zor, T., Vogt, D., Kabsch, W., Selinger, Z., Wittinghofer, A., Scheffzek, K.

Revision History 

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