PDBsum entry 2oj2

Signaling protein,transferase/inhibitor

PDB id

2oj2

Contents

			Protein chains

					86 a.a.


					14 a.a.

References listed in PDB file

Key reference

Title

Solution structure of a hck sh3 domain ligand complex reveals novel interaction modes.

Authors

H.Schmidt, S.Hoffmann, T.Tran, M.Stoldt, T.Stangler, K.Wiesehan, D.Willbold.

Ref.

J Mol Biol, 2007, 365, 1517-1532. [DOI no: 10.1016/j.jmb.2006.11.013]

PubMed id

17141806

Abstract

We studied the interaction of hematopoietic cell kinase SH3 domain (HckSH3) with an artificial 12-residue proline-rich peptide PD1 (HSKYPLPPLPSL) identified as high affinity ligand (K(D)=0.2 muM). PD1 shows an unusual ligand sequence for SH3 binding in type I orientation because it lacks the typical basic anchor residue at position P(-3), but instead has a tyrosine residue at this position. A basic lysine residue, however, is present at position P(-4). The solution structure of the HckSH3:PD1 complex, which is the first HckSH3 complex structure available, clearly reveals that the P(-3) tyrosine residue of PD1 does not take the position of the typical anchor residue but rather forms additional van der Waals interactions with the HckSH3 RT loop. Instead, lysine at position P(-4) of PD1 substitutes the function of the P(-3) anchor residue. This finding expands the well known ligand consensus sequence +xxPpxP by +xxxPpxP. Thus, software tools like iSPOT fail to identify PD1 as a high-affinity HckSH3 ligand so far. In addition, a short antiparallel beta-sheet in the RT loop of HckSH3 is observed upon PD1 binding. The structure of the HckSH3:PD1 complex reveals novel features of SH3 ligand binding and yields new insights into the structural basics of SH3-ligand interactions. Consequences for computational prediction tools adressing SH3-ligand interactions as well as the biological relevance of our findings are discussed.



	Figure 2. Figure 2. (a) Ensemble of the 20 lowest energy conformers calculated for the HckSH3:PD1 complex. The backbone of the HckSH3 domain is shown in blue, that of the PD1 peptide in green. For better visualisation of the three-dimensional character of the conformers, the HckSH3 backbone is coloured by different gradations. For reasons of clarity, the flexible residues (60 to 76) of the HckSH3 construct used in the present study are not represented in the Figure. (b) Ribbon structure of a representative conformer. For the HckSH3 domain (residues 77 to 140) the elements of secondary structure are labelled. (c) Surface representation of the chemical shift perturbation mapping of the HcKSH3 complex with PD1. Red coloured regions indicate the residues with chemical shift changes Δ[total]δ ≥ 0.2 ppm according to Figure 1(d), orange colour indicates residues whose resonances could not be identified during the mapping experiment. Figure 2. (a) Ensemble of the 20 lowest energy conformers calculated for the HckSH3:PD1 complex. The backbone of the HckSH3 domain is shown in blue, that of the PD1 peptide in green. For better visualisation of the three-dimensional character of the conformers, the HckSH3 backbone is coloured by different gradations. For reasons of clarity, the flexible residues (60 to 76) of the HckSH3 construct used in the present study are not represented in the Figure. (b) Ribbon structure of a representative conformer. For the HckSH3 domain (residues 77 to 140) the elements of secondary structure are labelled. (c) Surface representation of the chemical shift perturbation mapping of the HcKSH3 complex with PD1. Red coloured regions indicate the residues with chemical shift changes Δ[total]δ ≥ 0.2 ppm according to [3]Figure 1(d), orange colour indicates residues whose resonances could not be identified during the mapping experiment.		Figure 4. Figure 4. (a) Peptide binding region of the HckSH3:PD1 complex. HckSH3 backbone, hydrophobic and aromatic side-chains are coloured in blue, charged side-chains of HckSH3 are coloured in red. PD1 peptide backbone, hydrophobic and aromatic side-chains are coloured in green and Lys3 is highlighted in purple. Polar amino acid side-chains of PD1 are coloured in grey. The PD1 amino acid sequence, numbering and SH3 binding positions are shown below. (b) A focus on the anchor residues binding pocket shows the positions of the peptide residue Lys3 in different conformers calculated for the HckSH3:PD1 complex. Side-chains of different PD1 Lys3 conformers are coloured in purple. The Lys3 side-chain position upon structure calculation employing additional constraints describing a salt-bridge between Lys3 and D95 is highlighted in orange. (c) View on the RT loop regions of the HckSH3:PD1 and the FynSH3:3BP2 (PDB code 1FYN^59) complexes. Superposition is based on optimal fitting of the C^α coordinates within the β-sheets. The conserved tryptophan (HckSH3 residue W113) and proline side-chains as well as the tyrosine side-chain within the 3[10] helix (HckSH3 residue Y131) are coloured in blue and orange for HckSH3 and FynSH3, respectively. The conserved tryptophan residue in the FynSH3 complex structure (W119) is known to adopt a SH3-I orientation.^58 Compared to Fyn W119, the plane of the HckSH3 W113 side-chain is tilted by about 12° towards the conserved proline residue, indicating a SH3-II orientation for W113 in the HckSH3:PD1 complex structure. Figure 4. (a) Peptide binding region of the HckSH3:PD1 complex. HckSH3 backbone, hydrophobic and aromatic side-chains are coloured in blue, charged side-chains of HckSH3 are coloured in red. PD1 peptide backbone, hydrophobic and aromatic side-chains are coloured in green and Lys3 is highlighted in purple. Polar amino acid side-chains of PD1 are coloured in grey. The PD1 amino acid sequence, numbering and SH3 binding positions are shown below. (b) A focus on the anchor residues binding pocket shows the positions of the peptide residue Lys3 in different conformers calculated for the HckSH3:PD1 complex. Side-chains of different PD1 Lys3 conformers are coloured in purple. The Lys3 side-chain position upon structure calculation employing additional constraints describing a salt-bridge between Lys3 and D95 is highlighted in orange. (c) View on the RT loop regions of the HckSH3:PD1 and the FynSH3:3BP2 (PDB code 1FYN[3]^59) complexes. Superposition is based on optimal fitting of the C^α coordinates within the β-sheets. The conserved tryptophan (HckSH3 residue W113) and proline side-chains as well as the tyrosine side-chain within the 3[10] helix (HckSH3 residue Y131) are coloured in blue and orange for HckSH3 and FynSH3, respectively. The conserved tryptophan residue in the FynSH3 complex structure (W119) is known to adopt a SH3-I orientation.[4]^58 Compared to Fyn W119, the plane of the HckSH3 W113 side-chain is tilted by about 12° towards the conserved proline residue, indicating a SH3-II orientation for W113 in the HckSH3:PD1 complex structure.

PROCHECK

	Headers