5P21: Refined Crystal Structure of the Triphosphate Conformation of H-ras P21 at 1.35 Angstroms Resolution: Implications for the Mechanism of GTP Hydrolysis

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.
PDB ID: 5P21Download
MMDB ID: 58508
PDB Deposition Date: 1990/4/30
Updated in MMDB: 2012/12 
Experimental Method:
x-ray diffraction
Resolution: 1.35  Å
Source Organism:
Similar Structures:
Biological Unit for 5P21: dimeric; determined by author
Molecular Components in 5P21
Label Count Molecule
Proteins (2 molecules)
C-h-ras P21 Protein
Molecule annotation
Chemicals (4 molecules)
* Click molecule labels to explore molecular sequence information.

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