PDBsum entry 2ije

Signaling protein

PDB id: 2ije

Contents

Protein chain

237 a.a. *

Ligands

GOL

Waters ×163

* Residue conservation analysis

PDB id:

2ije

Name:

Signaling protein

Title:

Crystal structure of the cdc25 domain of rasgrf1

Structure:

Guanine nucleotide-releasing protein. Chain: s. Fragment: cdc25 domain (residues 1028-1262). Synonym: gnrp, ras-specific nucleotide exchange factor cdc25, cdc25mm. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Gene: 19417. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.20Å R-factor: 0.200 R-free: 0.242

Authors:

T.S.Freedman,J.Kuriyan

Key ref:

T.S.Freedman et al. (2006). A Ras-induced conformational switch in the Ras activator Son of sevenless. Proc Natl Acad Sci U S A, 103, 16692-16697. PubMed id: 17075039 DOI: 10.1073/pnas.0608127103

Date:

29-Sep-06 Release date: 31-Oct-06

Protein chain

P27671  (RGRF1_MOUSE) -  Ras-specific guanine nucleotide-releasing factor 1 from Mus musculus

Seq: 1262 a.a.

Struc: 237 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1073/pnas.0608127103

Proc Natl Acad Sci U S A 103:16692-16697 (2006)

PubMed id: 17075039

A Ras-induced conformational switch in the Ras activator Son of sevenless.

T.S.Freedman, H.Sondermann, G.D.Friedland, T.Kortemme, D.Bar-Sagi, S.Marqusee, J.Kuriyan.

ABSTRACT

The Ras-specific guanine nucleotide-exchange factors Son of sevenless (Sos) and Ras guanine nucleotide-releasing factor 1 (RasGRF1) transduce extracellular stimuli into Ras activation by catalyzing the exchange of Ras-bound GDP for GTP. A truncated form of RasGRF1 containing only the core catalytic Cdc25 domain is sufficient for stimulating Ras nucleotide exchange, whereas the isolated Cdc25 domain of Sos is inactive. At a site distal to the catalytic site, nucleotide-bound Ras binds to Sos, making contacts with the Cdc25 domain and with a Ras exchanger motif (Rem) domain. This allosteric Ras binding stimulates nucleotide exchange by Sos, but the mechanism by which this stimulation occurs has not been defined. We present a crystal structure of the Rem and Cdc25 domains of Sos determined at 2.0-A resolution in the absence of Ras. Differences between this structure and that of Sos bound to two Ras molecules show that allosteric activation of Sos by Ras occurs through a rotation of the Rem domain that is coupled to a rotation of a helical hairpin at the Sos catalytic site. This motion relieves steric occlusion of the catalytic site, allowing substrate Ras binding and nucleotide exchange. A structure of the isolated RasGRF1 Cdc25 domain determined at 2.2-A resolution, combined with computational analyses, suggests that the Cdc25 domain of RasGRF1 is able to maintain an active conformation in isolation because the helical hairpin has strengthened interactions with the Cdc25 domain core. These results indicate that RasGRF1 lacks the allosteric activation switch that is crucial for Sos activity.

Selected figure(s)

Figure 5.
Fig. 5. The clamping of the helical hairpin. (a) View of RasGRF1 showing the helical hairpin (red), flap1, and flap2 (both gray). (b) A cutaway view through the catalytic Ras binding site of RasGRF1. A tight interface between flap1 and the helical hairpin of RasGRF1 is formed by bulky, hydrophobic residues (Phe-1052, Phe-1051, and Tyr-1048 in flap1, Ile-1214, and Ile-1210 in the helical hairpin). A salt-bridge network and hydrophobic interactions connect the helical hairpin with flap2 (Met-1181 and Phe-1188 bury Asp-1185 in the helical hairpin, bridging to Arg-1160 and Arg-1165 in flap2). (c) In the active conformation of Sos, the helical hairpin (dark blue) is similar in position to that of RasGRF1, but the interface with flap1 is not well packed (Val-805, Leu-804, and Pro-801 in flap1, Thr-964 and Val-968 in the helical hairpin). (d) In the absence of allosteric Ras binding, the helical hairpin of uncomplexed Sos (light blue) collapses inward to interact more closely with flap1. Neither active nor inactive Sos helical hairpins form close interactions with flap2 (Lys-939, Ile-932, and Asn-936 in the helical hairpin do not form contacts with His-911 and Leu-916 in flap2).

Figure 6.
Fig. 6. Computational study of the effects of swapping residues from RasGRF1 and Sos. The number of times a given residue accumulated a conformation-stabilizing mutation in low-energy sequences from 100 separate Monte Carlo simulations is described by the substitution frequency. (a and b) C[ ]positions for buried residues that are swapped with high frequency are indicated (spheres) for Sos (a) and RasGRF1 (b). (c and d) Several Sos residues that substitute with high frequency are located in the flap1-helical hairpin interface (see also Fig. 5). (c) Wild-type Sos. (d) Substitutions from RasGRF1.

Figures were selected by an automated process.