PDBsum entry 2oj2

Signaling protein,transferase/inhibitor

PDB id: 2oj2

Contents

Protein chains

86 a.a. *

14 a.a. *

* Residue conservation analysis

PDB id:

2oj2

Name:

Signaling protein,transferase/inhibitor

Title:

Nmr structure analysis of the hematopoetic cell kinase sh3 domain complexed with an artificial high affinity ligand (pd1)

Structure:

Hematopoetic cell kinase, sh3 domain. Chain: a. Fragment: sh3. Synonym: tyrosine-protein kinase hck. P59-hck/p60-hck. Engineered: yes. Artificial peptide pd1. Chain: b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: hck. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Synthetic: yes. Other_details: the peptide was identified as high affinity ligand of hck-sh3 from screening a phage displayed peptide libary, acetylated

NMR struc:

20 models

Authors:

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

Key ref:

H.Schmidt et al. (2007). Solution structure of a Hck SH3 domain ligand complex reveals novel interaction modes. J Mol Biol, 365, 1517-1532. PubMed id: 17141806 DOI: 10.1016/j.jmb.2006.11.013

Date:

12-Jan-07 Release date: 30-Jan-07

Supersedes:

2a4y

Protein chain

P08631  (HCK_HUMAN) -  Tyrosine-protein kinase HCK from Homo sapiens

Seq: 526 a.a.

Struc: 86 a.a.*

Protein chain

No UniProt id for this chain

Struc: 13 a.a.

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

Enzyme reactions

• Enzyme class: Chain A: E.C.2.7.10.2 - non-specific protein-tyrosine kinase.
• Reaction: L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H⁺

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

Added reference

DOI no: 10.1016/j.jmb.2006.11.013

J Mol Biol 365:1517-1532 (2007)

PubMed id: 17141806

Solution structure of a Hck SH3 domain ligand complex reveals novel interaction modes.

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

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.

Selected figure(s)

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.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 365, 1517-1532) copyright 2007.

Figures were selected by the author.