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PDBsum entry 1zw6

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Oncoprotein PDB id
1zw6
Jmol
Contents
Protein chain
166 a.a.
Ligands
GNP
Metals
_MG ×3
_CA ×2
Waters ×167

References listed in PDB file
Key reference
Title Structure of a transient intermediate for gtp hydrolysis by ras.
Authors B.Ford, V.Hornak, H.Kleinman, N.Nassar.
Ref. Structure, 2006, 14, 427-436. [DOI no: 10.1016/j.str.2005.12.010]
PubMed id 16531227
Abstract
The flexibility of the conserved 57DTAGQ61 motif is essential for Ras proper cycling in response to growth factors. Here, we increase the flexibility of the 57DTAGQ61 motif by mutating Gln61 to Gly. The crystal structure of the RasQ61G mutant reveals a new conformation of switch 2 that bears remarkable structural homology to an intermediate for GTP hydrolysis revealed by targeted molecular dynamics simulations. The mutation increased retention of GTP and inhibited Ras binding to the catalytic site, but not to the distal site of Sos. Most importantly, the thermodynamics of RafRBD binding to Ras are altered even though the structure of switch 1 is not affected by the mutation. Our results suggest that interplay and transmission of structural information between the switch regions are important factors for Ras function. They propose that initiation of GTP hydrolysis sets off the separation of the Ras/effector complex even before the GDP conformation is reached.
Figure 2.
Figure 2. Comparison of the Switch Regions of RasQ61G with WT-Ras and RasA59G
(A) Superposition of the switch 1 (Sw 1) and switch 2 (Sw 2) regions of the GppNp bound forms of WT-Ras (yellow) (Pai et al., 1990) and RasQ61G (blue). The GppNp and Mg^2+ ions are in ball-and-stick representation in purple and green, respectively. The water molecule in WT-Ras responsible for the nucleophilic attack on the γ-phosphate (W175) is shown as a yellow sphere; the closest water molecule in the RasQ61G structure is shown as a blue sphere.
(B) Superposition of the switch regions of the GppNp bound forms of RasA59G (gold) (Hall et al., 2002) and RasQ61G (blue). Dotted lines represent hydrogen bonds. For simplicity, only a few residues in each region are shown.
This figure was prepared with Molscript (Kraulis, 1991) and Pymol (http://pymol.sourceforge.net/).
Figure 6.
Figure 6. Evolution of the Switch Regions along the Path for GTP Hydrolysis
(A–D) Backbone atoms of both switch 1 (pink, residues 25–40) and switch 2 (yellow, residues 57–75) are shown along with key side chain residues for simplicity. The guanine nucleotide (GTP/GDP) and the Mg^2+ ion are shown in a ball-and-stick model. (A) The beginning of the path (Ras•GTP) (Pai et al., 1990). (B) Transient intermediate 1 (RasQ61G). (C) Transient intermediate 2 (RasA59G) (Hall et al., 2002). (D) The end of the path (Ras•GDP) (Milburn et al., 1990). Hydrogen bonds between switch regions and other key hydrogen bonds are denoted by dotted lines.
The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 427-436) copyright 2006.
Secondary reference #1
Title The structural basis for the transition from ras-Gtp to ras-Gdp.
Authors B.E.Hall, D.Bar-Sagi, N.Nassar.
Ref. Proc Natl Acad Sci U S A, 2002, 99, 12138-12142. [DOI no: 10.1073/pnas.192453199]
PubMed id 12213964
Full text Abstract
Figure 1.
Fig 1. Structural changes induced in Ras switch regions by the glycine for alanine substitution at position 59. Close-up view of Glu-37 (switch 1) and Arg-68 (switch 2) in the crystal structures of wild-type Ras (A) (15) and RasA59G (B) in the GppNp-bound forms. Switch 1 (SwI) and switch 2 (SwII) are in magenta and yellow, respectively. Loop L4 and helix- 2 of switch 2 are labeled. The GppNp and the Mg2+-ion are in light blue, and water molecules (W) are represented by red spheres. Tyr-32 is in pink, Glu-37 in red, and Arg-68 in blue. Hydrogen bonds are represented by dashed lines and the van der Waals interactions between Glu-37 and Tyr-71 (B) are indicated by a dotted line. In wild-type Ras (A), Arg-68 stabilizes the N terminus of the switch 2 region (60-62) through direct or water-mediated hydrogen bonds. In RasA59G (B), Glu-37 makes hydrogen bonds with Arg-68 and van der Waals interactions with Tyr-71, which protects it partially from the solvent. Tyr-64, which is essential for Sos-binding by Ras, adopts a position that inhibits the docking of the two proteins. The catalytic residue Gln-61 is positioned far from W175. Tyr-32 is making a water-mediated hydrogen bond with the -phosphate, and its bulky phenol group is protecting the phosphates from the surrounding solvent. (C) Stereo representation of the superposition of the C of switch 1 and 2 regions between the structures of wild-type Ras (green) and RasA59G (gold) in the GppNp-bound form. The residues of L4 are shown, whereas only the side chains of Tyr-32, Glu-37, Gln-61, Arg-68, and Tyr-71 are shown. The two water molecules (W332 and W349) in wild-type Ras that coordinated Arg-68 and that have been exchanged with the solvent on the reorientation of the switch 2 region, are shown. Prepared with MOLSCRIPT (24) and RASTER3D (25).
Figure 2.
Fig 2. Structural changes that affect the switch 1 and switch 2 regions of Ras along the path for GTP hydrolysis. Structures proceed from the GTP-bound form (Left, PDB coordinates 5P21 [PDB] ), to the intermediate (Center) that is represented by the A59G mutant, and finally to the GDP-bound form (Right, PDB coordinates 4Q21). Water molecules are shown as red spheres; the nucleotide and the Mg2+-ion are in light blue. Switch 1 is in magenta and switch 2 in gold. Close contacts are represented by dotted lines.
PROCHECK
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