5P21

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

PDB DOI: 10.2210/pdb5P21/pdb

Classification: ONCOGENE PROTEIN
Organism(s): Homo sapiens
Mutation(s): No

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

Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

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 Search on PubMedSearch on PubMed Central
Primary Citation of Related Structures:
5P21

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.

Related Citations:

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

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

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 U S A 86: 7687

Organizational Affiliation:

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
C-H-RAS P21 PROTEIN	A	166	Homo sapiens	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01112
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP Query on GNP Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction