1GNQ

X-RAY CRYSTAL STRUCTURE ANALYSIS OF THE CATALYTIC DOMAIN OF THE ONCOGENE PRODUCT P21H-RAS COMPLEXED WITH CAGED GTP AND MANT DGPPNHP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray crystal structure analysis of the catalytic domain of the oncogene product p21H-ras complexed with caged GTP and mant dGppNHp.

Scheidig, A.J.Franken, S.M.Corrie, J.E.Reid, G.P.Wittinghofer, A.Pai, E.F.Goody, R.S.

(1995) J.Mol.Biol. 253: 132-150

  • DOI: 10.1006/jmbi.1995.0541
  • Primary Citation of Related Structures:  1GNP, 1GNR

  • PubMed Abstract: 
  • The X-ray structures of the 1:1 complexes formed between p21H-ras (residues 1 to 166) and the nucleotides P3-1-(2-nitrophenyl)ethyl guanosine triphosphate ("caged GTP"; pure R- and S-diastereomers) and 3'-O-(N-methylanthraniloyl)-2'-deoxyguanosine 5' ...

    The X-ray structures of the 1:1 complexes formed between p21H-ras (residues 1 to 166) and the nucleotides P3-1-(2-nitrophenyl)ethyl guanosine triphosphate ("caged GTP"; pure R- and S-diastereomers) and 3'-O-(N-methylanthraniloyl)-2'-deoxyguanosine 5'-(beta, gamma-imido)-triphosphate ("mant dG-ppNHp"), have been refined to an R-factor of 21.4% (R-caged GTP, 1.85 A resolution), 18.9% (S-caged GTP, 2.5 A resolution) and 17.6% (mant dGppNHp, 2.7 A resolution), respectively. Details of the structure determination, refinement and the structures themselves are presented. The overall structures of the complexes are identical in terms of the general organization of their secondary structure elements and are also identical to that reported for the analogous complex of p21H-ras with GppNHp. The binding of the GTP part is not significantly affected by the additional aromatic group (cage and mant, respectively) in contrast to the original observation on p21:caged GTP using the racemic mixture of R- and S-caged GTP. The main differences in the structures are observed in the region of loop L2 (residues Glu31 to Thr35) where the additional aromatic group attached to the nucleotide comes very close to the side-chain of Tyr32, including backbone displacements of 2.6 A, 2.2 A and 0.3 A for the residues from Glu31 to Thr35 for R-caged, S-caged GTP and mant dGppNHp, respectively. The refined structures provide additional data for the design of new nucleotide analogs and the importance of their stereochemistry as well as for the design of new mutant forms of p21H-ras for further biochemical investigations. The binding mode of mant dGppNHp reveals significant features for the understanding of the fluorescence signals observed in solution.


    Related Citations: 
    • Crystallographic Studies on P21H-Ras Using Synchrotron Laue Method: Improvement of Crystal Quality and Monitoring of the Gtpase Reaction at Different Time Points
      Scheidig, A.J.,Sanchez-Llorente, A.,Lautwein, A.,Pai, E.F.,Corrie, J.E.T.,Reid, G.P.,Wittinghofer, A.,Goody, R.S.
      (1994) Acta Crystallogr.,Sect.D 50: 512


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
C-H-RAS P21 PROTEIN
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
CAG
Query on CAG

Download SDF File 
Download CCD File 
A
GUANOSINE 5'-TRIPHOSPHATE P3-[1-(2-NITROPHENYL)ETHYL ESTER]
C18 H23 N6 O16 P3
NYWDUFBXCCSYMK-JPDTYCKISA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.207 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 40.800α = 90.00
b = 40.800β = 90.00
c = 158.200γ = 120.00
Software Package:
Software NamePurpose
X-PLORphasing
XDSdata reduction
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-07-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance