PDBsum entry 1wq1

Complex (gtp-binding/gtpase activation)

PDB id: 1wq1

Contents

Protein chains

166 a.a. *

320 a.a. *

Ligands

GDP-AF3

Metals

_MG

Waters ×35

* Residue conservation analysis

References listed in PDB file

Key reference

Title

The ras-Rasgap complex: structural basis for gtpase activation and its loss in oncogenic ras mutants.

Authors

K.Scheffzek, M.R.Ahmadian, W.Kabsch, L.Wiesmüller, A.Lautwein, F.Schmitz, A.Wittinghofer.

Ref.

Science, 1997, 277, 333-338. [DOI no: 10.1126/science.277.5324.333]

PubMed id

9219684

Abstract

The three-dimensional structure of the complex between human H-Ras bound to guanosine diphosphate and the guanosine triphosphatase (GTPase)-activating domain of the human GTPase-activating protein p120GAP (GAP-334) in the presence of aluminum fluoride was solved at a resolution of 2.5 angstroms. The structure shows the partly hydrophilic and partly hydrophobic nature of the communication between the two molecules, which explains the sensitivity of the interaction toward both salts and lipids. An arginine side chain (arginine-789) of GAP-334 is supplied into the active site of Ras to neutralize developing charges in the transition state. The switch II region of Ras is stabilized by GAP-334, thus allowing glutamine-61 of Ras, mutation of which activates the oncogenic potential, to participate in catalysis. The structural arrangement in the active site is consistent with a mostly associative mechanism of phosphoryl transfer and provides an explanation for the activation of Ras by glycine-12 and glutamine-61 mutations. Glycine-12 in the transition state mimic is within van der Waals distance of both arginine-789 of GAP-334 and glutamine-61 of Ras, and even its mutation to alanine would disturb the arrangements of residues in the transition state.

Figure 1.
Fig. 1. Stereo view of a segment of the 2F[o] F[c] electron density map (contoured at 1.2 ) covering the active site region in the^ complex, with Ras in blue, GAP-334 in red, and waters in light blue.

Figure 2.
Fig. 2. The complex between GAP-334 and Ras. (A) Ribbon representation of the complex model drawn with Molscript (52) and^ Raster3D (53) according to the assignment of secondary structure^ elements obtained with the program DSSP (54). The extra and^ catalytic domains of GAP-334 are shown in green and red (respectively), regions of GAP contacting Ras in light brown, Ras in yellow, and^ GDP and AlF[3] as ball-and-stick models. Regions involved in the^ interface are labeled, Sw I and Sw II indicating the switch regions, C the COOH-terminal, and N the NH[2]-terminal. (B) Schematic^ drawing with selected interactions. Polar interactions between individual residues of GAP-334 and Ras are shown as red lines for interactions of side chains, and as red arrows for contacts from side chain to main chain atoms, where the arrowhead marks the residue contributing the main chain group. Yellow lines indicate^ van der Waals or hydrophobic interactions. Some water molecules (marked W) from the interface region are included. Residues belonging to the interacting regions of Ras indicated in (A) are denoted^ with specified boxes, as indicated. Interaction between Lys88 and Thr791 is shown by a dashed arrow, because the electron density in this region is presently not of sufficient quality to unambiguously define the contact. Amino acid abbreviations are in (55).

The above figures are reprinted by permission from the AAAs: Science (1997, 277, 333-338) copyright 1997.

Secondary reference #1

Title

The interaction of ras with gtpase-Activating proteins.

Authors

A.Wittinghofer, K.Scheffzek, M.R.Ahmadian.

Ref.

Febs Lett, 1997, 410, 63-67. [DOI no: 10.1016/S0014-5793(97)00321-9]

PubMed id

9247124

Figure 1.
Fig. 1. Minimal scheme for the GTPase reaction of Ras with a hypothetical isomerization reaction preceding GTP hydrolysis. The binding of GTP is very fast and the affinity to GTP very high such that the protein is always saturated with nucleotide (GDP or GTP). GTP hydrolysis and release of inorganic phosphate have so far not been shown to be reversible reactions. Which of the individual reaction steps is rate-limiting and thus catalyzed by GAP is discussed in the text.

Figure 2.
Fig. 2. Ribbon plot (drawn with MOLSCRIPT, see ref. [60]) of the structure of a catalytic fragment of p120GAP. It shows the position of the invariant and highly conserved residues as black and gray dots, respectively. The invariant arginines, one or both of which are believed to participate in the GTPase reaction, are shown as ball and stick models.

The above figures are reproduced from the cited reference with permission from the Federation of European Biochemical Societies

Secondary reference #2

Title

Formation of a transition-State analog of the ras gtpase reaction by ras-Gdp, Tetrafluoroaluminate, And gtpase-Activating proteins.

Authors

R.Mittal, M.R.Ahmadian, R.S.Goody, A.Wittinghofer.

Ref.

Science, 1996, 273, 115-117. [DOI no: 10.1126/science.273.5271.115]

PubMed id

8658179

Secondary reference #3

Title

Crystal structure of the gtpase-Activating domain of human p120gap and implications for the interaction with ras.

Authors

K.Scheffzek, A.Lautwein, W.Kabsch, M.R.Ahmadian, A.Wittinghofer.

Ref.

Nature, 1996, 384, 591-596.

PubMed id

8955277

Secondary reference #4

Title

Refined crystal structure of the triphosphate conformation of h-Ras p21 at 1.35 a resolution: implications for the mechanism of gtp hydrolysis.

Authors

E.F.Pai, U.Krengel, G.A.Petsko, R.S.Goody, W.Kabsch, A.Wittinghofer.

Ref.

Embo J, 1990, 9, 2351-2359.

PubMed id

2196171

Secondary reference #5

Title

A cytoplasmic protein stimulates normal n-Ras p21 gtpase, But does not affect oncogenic mutants.

Authors

M.Trahey, F.Mccormick.

Ref.

Science, 1987, 238, 542-545. [DOI no: 10.1126/science.2821624]

PubMed id

2821624

Secondary reference #6

Title

Biological and biochemical properties of human rash genes mutated at codon 61.

Authors

C.J.Der, T.Finkel, G.M.Cooper.

Ref.

Cell, 1986, 44, 167-176. [DOI no: 10.1016/0092-8674(86)90495-2]

PubMed id

3510078

Secondary reference #7

Title

Biological properties of human c-Ha-Ras1 genes mutated at codon 12.

Authors

P.H.Seeburg, W.W.Colby, D.J.Capon, D.V.Goeddel, A.D.Levinson.

Ref.

Nature, 1984, 312, 71-75.

PubMed id

6092966