PDBsum entry 1nvx

Signaling protein

PDB id: 1nvx

Contents

Protein chains

166 a.a. *

448 a.a. *

Ligands

GTP

PO4

Metals

_MG

* Residue conservation analysis

PDB id:

1nvx

Name:

Signaling protein

Title:

Structural evidence for feedback activation by rasgtp of the ras- specific nucleotide exchange factor sos

Structure:

Transforming protein p21/h-ras-1. Chain: q, r. Fragment: residues 1-166. Synonym: c-h-ras. Engineered: yes. Mutation: yes. Son of sevenless protein homolog 1. Chain: s. Fragment: residues 566-10466, including the ras guanine nucleotide

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hras or hras1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: sos1.

Biol. unit:

Trimer (from PQS)

Resolution:

3.20Å R-factor: 0.223 R-free: 0.261

Authors:

S.M.Margarit,H.Sondermann,B.E.Hall,B.Nagar,A.Hoelz,M.Pirruccello, D.Bar-Sagi,J.Kuriyan

Key ref:

S.M.Margarit et al. (2003). Structural evidence for feedback activation by Ras.GTP of the Ras-specific nucleotide exchange factor SOS. Cell, 112, 685-695. PubMed id: 12628188 DOI: 10.1016/S0092-8674(03)00149-1

Date:

04-Feb-03 Release date: 01-Apr-03

Protein chains

P01112  (RASH_HUMAN) -  GTPase HRas from Homo sapiens

Seq: 189 a.a.

Struc: 166 a.a.*

Protein chain

Q07889  (SOS1_HUMAN) -  Son of sevenless homolog 1 from Homo sapiens

Seq: 1333 a.a.

Struc: 448 a.a.

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

Enzyme reactions

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

GTP (Bound ligand (Het Group name = GTP) corresponds exactly) + H2O = GDP + phosphate + H(+) (Bound ligand (Het Group name = PO4) corresponds exactly)

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

reference

DOI no: 10.1016/S0092-8674(03)00149-1

Cell 112:685-695 (2003)

PubMed id: 12628188

Structural evidence for feedback activation by Ras.GTP of the Ras-specific nucleotide exchange factor SOS.

S.M.Margarit, H.Sondermann, B.E.Hall, B.Nagar, A.Hoelz, M.Pirruccello, D.Bar-Sagi, J.Kuriyan.

ABSTRACT

Growth factor receptors activate Ras by recruiting the nucleotide exchange factor son of sevenless (SOS) to the cell membrane, thereby triggering the production of GTP-loaded Ras. Crystallographic analyses of Ras bound to the catalytic module of SOS have led to the unexpected discovery of a highly conserved Ras binding site on SOS that is located distal to the active site and is specific for Ras.GTP. The crystal structures suggest that Ras.GTP stabilizes the active site of SOS allosterically, and we show that Ras.GTP forms ternary complexes with SOS(cat) in solution and increases significantly the rate of SOS(cat)-stimulated nucleotide release from Ras. These results demonstrate the existence of a positive feedback mechanism for the spatial and temporal regulation of Ras.

Selected figure(s)

Figure 3.
Figure 3. Views of the Distal Ras:SOS^cat Interface(A) The binding footprint on Ras of SOS^cat (left, structure D) and PI3-kinase (right, PDB code 1HE8). The structures of Ras shown here are for the complex with the GTP analog GppNp in both cases. Residues that make contact with SOS or PI3-kinase are colored purple.(B) The molecular surface of SOS^cat, showing the binding footprint of Ras·GTP on SOS^cat. Regions of the surface of SOS that are occluded by the distal Ras·GTP molecule are colored blue. The structure shown is that of the Ras^Y64A·GppNp:SOS^cat:Ras (nucleotide-free) complex (structure D).(C) Differences between Ras·GDP (Milburn et al., 1990) and the distal Ras^Y64A·GppNp molecule. The backbone of Ras·GDP is shown in red and that of Ras^Y64A·GppNp in green. GppNp is shown in orange with Mg^2+ ion drawn as a magenta sphere. The position of the alanine residue at residue 64 of Ras^Y64A is shown by the blue sphere. Side chains of Ras^Y64A are shown with carbon atoms colored blue, while side chains of Ras·GDP are shown in purple.

Figure 4.
Figure 4. Specificity for Ras·GTP at the Distal Interface(A) Interface between Ras·GTP and the distal binding site on the REM domain. The entire ternary complex, in the view used for the expanded illustration (middle, right), is shown on the left. In the middle, some of the key residues at the distal Ras:REM domain interface are indicated. The GTP analog GppNp is shown in orange, and the Mg^2+ ion is shown as a magenta sphere. The backbone of Ras^Y64A is shown in green. Note the presence of alanine instead of tyrosine at residue 64 in Ras. The molecular surface of SOS^cat is shown at the right, colored according to the conservation in sequence between human SOS1 and SOS from Drosophila, Anopheles, and C. elegans. Sequence similarity was calculated based on the BLOSUM 62 matrix (Henikoff and Henikoff, 1993). Residues that are invariant (100% identical) between the four SOS sequences are colored red, with purple, orange, and yellow indicating sequence similarity at the 90%, 80%, and 70% levels, respectively.(B) Details of the interface between Ras·GTP and the distal binding site on the cdc25 domain. The helical hairpin of SOS and the hairpin base (see text) are colored red. The surface of SOS^cat, shown on the right in each panel is colored as in (A).

The above figures are reprinted by permission from Cell Press: Cell (2003, 112, 685-695) copyright 2003.

Figures were selected by an automated process.