1GNR

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

DOI: 10.2210/pdb1GNR/pdb

Classification: GTP BINDING PROTEIN
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 1995-05-11 Released: 1995-07-31
Deposition Author(s): Scheidig, A., Franken, S.M., Corrie, J.E.T., Reid, G.P., Wittinghofer, A., Pai, E.F., Goody, R.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.257
R-Value Work: 0.206
R-Value Observed: 0.206

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

PubMed: 7473708 Search on PubMed
DOI: 10.1006/jmbi.1995.0541
Primary Citation of Related Structures:
1GNR, 1GNQ, 1GNP

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'-(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 D Biol Crystallogr 50: 512

Organizational Affiliation:

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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
Find proteins for P01112 (Homo sapiens) Explore P01112 Go to UniProtKB: P01112
NIH Common Fund Data Resources
PHAROS: P01112 GTEx: ENSG00000174775
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAG Query on CAG Download Ideal Coordinates CCD File SDF format, chain C [A] MOL2 format, chain C [A]	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 Ideal Coordinates CCD File SDF format, chain B [A] MOL2 format, chain B [A]	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction