Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19421.69 
• Atom Count: 1356 
• Residue Count: 166 
• Unique protein chains: 1

5P21

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

• DOI: 10.2210/pdb5P21/pdb

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


• Deposited: 1990-04-30 Released: 1992-01-15 
• Deposition Author(s): Pai, E.F., Wittinghofer, A., Kabsch, W.

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Experimental Data Snapshot

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

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: 2196171 


• 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 19.8% 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.

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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
• 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
• 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
• 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




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
C-H-RAS P21 PROTEIN	A	166	Homo sapiens	Mutation(s): 0  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
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
GNP	A	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C10 H17 N6 O13 P3 UQABYHGXWYXDTK-UUOKFMHZSA-N

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 = 40.300	α = 90.00
b = 40.300	β = 90.00
c = 162.200	γ = 120.00

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1990-04-30 
• Released Date: 1992-01-15 
• Deposition Author(s): Pai, E.F., Wittinghofer, A., Kabsch, W.

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