PDBsum entry 1zvq

Oncoprotein

PDB id: 1zvq

Contents

Protein chain

166 a.a. *

Ligands

GDP

Metals

_MG ×2

Waters ×79

* Residue conservation analysis

PDB id:

1zvq

Name:

Oncoprotein

Title:

Structure of the q61g mutant of ras in the gdp-bound form

Structure:

Transforming protein p21/h-ras-1. Chain: a. Synonym: c-h-ras. Engineered: yes. Mutation: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hras, hras1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.00Å R-factor: 0.188 R-free: 0.229

Authors:

B.Ford,N.Nassar

Key ref:

B.Ford et al. (2006). Structure of a transient intermediate for GTP hydrolysis by ras. Structure, 14, 427-436. PubMed id: 16531227 DOI: 10.1016/j.str.2005.12.010

Date:

02-Jun-05 Release date: 14-Mar-06

Protein chain

P01112  (RASH_HUMAN) -  GTPase HRas from Homo sapiens

Seq: 189 a.a.

Struc: 166 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.6.5.2 - small monomeric GTPase.
• Reaction: GTP + H2O = GDP + phosphate + H⁺

GTP + H2O = GDP (Bound ligand (Het Group name = GDP) corresponds exactly) + phosphate + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.str.2005.12.010

Structure 14:427-436 (2006)

PubMed id: 16531227

Structure of a transient intermediate for GTP hydrolysis by ras.

B.Ford, V.Hornak, H.Kleinman, N.Nassar.

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.

Selected figure(s)

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.

Figures were selected by the author.