PDBsum entry 1f2f

Transferase

PDB id: 1f2f

Contents

Protein chain

104 a.a. *

Ligands

PO4

Waters ×55

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structural basis for specificity switching of the src sh2 domain.

Authors

M.S.Kimber, J.Nachman, A.M.Cunningham, G.D.Gish, T.Pawson, E.F.Pai.

Ref.

Mol Cell, 2000, 5, 1043-1049. [DOI no: 10.1016/S1097-2765(00)80269-5]

PubMed id

10911998

Abstract

The Src SH2 domain binds pYEEI-containing phosphopeptides in an extended conformation with a hydrophobic pocket, which includes ThrEF1, binding Ile(pY +3). Mutating ThrEF1 to tryptophan switches specificity to an Asn(pY +2) requirement, yielding a biological mimic of the Grb2 SH2 domain. Here we show that the Src ThrEF1Trp SH2 domain mutant binds pYVNV phosphopeptides in a beta turn conformation, which, despite differing conformations of the interacting tryptophan, closely resembles the native Grb2/pYVNV cognate peptide binding mode. The ThrEF1Trp substitution therefore switches specificity by physically occluding the pTyr +3 binding pocket and by providing additional interaction surface area for Asn(pY +2). This demonstrates structurally how novel SH2 domain specificities may rapidly evolve through single amino acid substitutions and suggests how new signaling pathways may develop.

Figure 1.
Figure 1. Structure of the Ligand-Free Src TEF1W Mutant(a) Structure of the unliganded form of TEF1W Src SH2 showing the phosphate group and the residues interacting with TrpEF1. The secondary structure nomenclature indicated follows [8], which names the secondary structural elements sequentially, αA, βB, βC, etc., loops being named for the two secondary structural elements they connect, and residues then being designated by the sequential position they occupy on that secondary structural element. For the residues of the phosphotyrosylated peptide, pY 0 indicates the phosphotyrosine, and pY +n and pY-n designate residues n amino acids C- and N-terminal to it, respectively. It should be noted that packing interactions stabilize much of the BC loop in β strand conformation, but these residues are still shown as loop so as to facilitate comparison with other SH2 domains. Residues discussed in the text are displayed and labeled.(b) Stereo diagram of the σ[A] weighted 2F[obs] − F[c] electron density map for the unliganded TEF1W Src SH2 showing TrpEF1 and the phosphate group. Density is contoured at 1.0 σ. The figure is in approximately the same orientation as in (a).

Figure 2.
Figure 2. Binding of pYVNV to TEF1W Src SH2(a) Stereo ribbon diagram of TEF1W Src SH2 complexed with the phosphopeptide SpYVNVQN. A σ[A] weighted 2F[obs] − F[c] electron density map at 1.0 σ is contoured around the phosphopeptide.(b) In the same orientation as (a) but with the SH2 domain represented as van der Waals spheres and the phosphopeptide as a ball-and-stick model. The pYVNV peptide is shown with bonds in orange, Src with atoms in white except residue TrpEF1 (in magenta), TyrβD5 (in green), IleβE4 (in peach), LysβD6 (in pink), and ArgαA2 and ArgβB5 (in cyan).(c) Superposition of the TEF1W Src SH2 complexed with the SpYVNVQN structure onto the native Grb2 SH2 complexed with KRFpYVNV. For clarity, only the phosphopeptide residues resolved in both structures are shown (SpYVNV for Src TEF1W, FpYVNV for Grb2). Src TEF1W is in lighter shades (yellow, cyan, light green, and magenta for Src, the peptide, TyrβD5, and TrpEF1, respectively) while Grb2 is in darker shades (orange, blue, dark green, and purple for Grb2, the peptide, PheβD6, and TrpEF1, respectively). Coordinates for Grb2 SH2 were taken from the crystal structure of Rahuel et al. ([25]) (RCSB ID code 1tze).

The above figures are reprinted by permission from Cell Press: Mol Cell (2000, 5, 1043-1049) copyright 2000.