Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.48 kDa 
• Atom Count: 1399 
• Modelled Residue Count: 166 
• Deposited Residue Count: 166 
• Unique protein chains: 1

1AGP

THREE-DIMENSIONAL STRUCTURES AND PROPERTIES OF A TRANSFORMING AND A NONTRANSFORMING GLY-12 MUTANT OF P21-H-RAS

• PDB DOI: 10.2210/pdb1AGP/pdb

• Classification: ONCOGENE PROTEIN
• Organism(s): Homo sapiens
• Mutation(s): Yes 


• Deposited: 1993-03-29 Released: 1994-04-30 
• Deposition Author(s): Franken, S.M., Scheidig, A.J., Wittinghofer, A., Goody, R.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work: 0.177 
• R-Value Observed: 0.177 

Literature

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., Wittinghofer, A.

(1993) Biochemistry 32: 8411-8420

• PubMed: 8357792 
• DOI: 10.1021/bi00084a005
• Primary Citation of Related Structures:  
  1AGP, 821P


• PubMed Abstract: 
  

The three-dimensional structures and biochemical properties of two mutants of the G-domain (residues 1-166) of p21H-ras, p21 (G12D) and p21 (G12P), have been determined in the triphosphate-bound form using guanosine 5'-(beta,gamma-imido)triphosphate (GppNHp). They correspond to the most frequent oncogenic and the only nononcogenic mutation of Gly-12, respectively. The G12D mutation is the only mutant analyzed so far that crystallizes in a space group different from wild type, and the atomic model of the protein shows the most drastic changes of structure around the active site as compared to wild-type p21. This is due to the interactions of the aspartic acid side chain with Tyr-32, Gln-61, and the gamma-phosphate, which result in reduced mobility of these structural elements. The interaction between the carboxylate group of Asp-12 and the gamma-phosphate is mediated by a shared proton, which we show by 31P NMR measurements to exist in solution as well. The structure of p21 (G12P) is remarkably similar to that of wild-type p21 in the active site, including the position of the nucleophilic water. The pyrrolidine ring of Pro-12 points outward and seems to be responsible for the weaker affinity toward GAP (GTPase-activating protein) and the failure of GAP to stimulate GTP hydrolysis.

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Related Citations: 

• 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

• Refined Crystal Structure of the Triphosphate Conformation of H-Ras P21 at 1.35 Angstroms 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

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Organizational Affiliation: 

Abteilung Biophysik, Max-Planck-Institut für Medizinische Forschung, Heidelberg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-H-RAS P21 PROTEIN	A	166	Homo sapiens	Mutation(s): 1  Gene Names: HRAS, HRAS1 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01112 (Homo sapiens) Explore P01112  Go to UniProtKB:  P01112
PHAROS:  P01112

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GNP	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work: 0.177 
• R-Value Observed: 0.177 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.91	α = 90
b = 39.81	β = 107.4
c = 56.1	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1993-03-29 
• Released Date: 1994-04-30 
Deposition Author(s): Franken, S.M., Scheidig, A.J., Wittinghofer, A., Goody, R.S.

Revision History  

• Version 1.0: 1994-04-30
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-02-22
  Changes: Database references
• Version 1.4: 2012-03-07
  Changes: Database references
• Version 1.5: 2017-11-29
  Changes: Derived calculations, Other