1JAI

H-RAS P21 PROTEIN MUTANT G12P, COMPLEXED WITH GUANOSINE-5'-[BETA,GAMMA-METHYLENE] TRIPHOSPHATE AND MANGANESE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The role of the metal ion in the p21ras catalysed GTP-hydrolysis: Mn2+ versus Mg2+.

Schweins, T.Scheffzek, K.Assheuer, R.Wittinghofer, A.

(1997) J.Mol.Biol. 266: 847-856

  • DOI: 10.1006/jmbi.1996.0814
  • Primary Citation of Related Structures:  1JAH

  • PubMed Abstract: 
  • GTP and ATP hydrolysing proteins have an absolute requirement for a divalent cation, which is usually Mg2+, as a cofactor in the enzymatic reaction. Other phosphoryl transfer enzymes employ more than one divalent ion for the enzymatic reaction. It is ...

    GTP and ATP hydrolysing proteins have an absolute requirement for a divalent cation, which is usually Mg2+, as a cofactor in the enzymatic reaction. Other phosphoryl transfer enzymes employ more than one divalent ion for the enzymatic reaction. It is shown here for p21ras, a well studied example of GTP hydrolysing proteins, that the GTP-hydrolysis rate is significantly faster if Mg2+ is replaced by Mn2+, both in the presence or absence of its GTPase-activating protein Ras-GAP. This effect is not due to a different stoichiometry of metal ion binding, since one metal ion is sufficient for full enzymatic activity. To determine the role of the metal ion, the crystal structure of p21(G12P). GppCp complexed with Mn2+ was determined and shown to be very similar to the corresponding p21(G12P). GppCp.Mg2+ structure. Especially the coordination sphere around the metal ions is very similar, and no second metal ion binding site could be detected, consistent with the assumption that one metal ion is sufficient for GTP hydrolysis. In order to explain the biochemical differences, we analysed the GTPase reaction mechanism with a linear free energy relationships approach. The result suggests that the reaction mechanism is not changed with Mn2+ but that the transition metal ion Mn2+ shifts the pKa of the gamma-phosphate by almost half a unit and increases the reaction rate due to an increase in the basicity of GTP acting as the general base. This suggests that the intrinsic GTPase reaction could be an attractive target for anti-cancer drug design. By using Rap1A and Ran, we show that the acceleration of the GTPase by Mn2+ appears to be a general phenomenon of GTP-binding proteins.


    Related Citations: 
    • Biological Properties of Human C-Ha-Ras1 Genes Mutated at Codon 12
      Seeburg, P.H.,Colby, W.W.,Capon, D.J.,Goeddel, D.V.,Levinson, A.D.
      (1984) Nature 312: 71
    • 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


    Organizational Affiliation

    Max-Planck-Institut für molekulare Physiologie, Dortmund, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-HA-RAS
A
166Homo sapiensGene Names: HRAS (HRAS1)
Find proteins for P01112 (Homo sapiens)
Go to Gene View: HRAS
Go to UniProtKB:  P01112
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
GCP
Query on GCP

Download SDF File 
Download CCD File 
A
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.200 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 40.000α = 90.00
b = 40.000β = 90.00
c = 160.400γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORphasing
X-PLORmodel building
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-07-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance