PDBsum entry 2etz

Transferase

PDB id: 2etz

Contents

Protein chain

109 a.a. *

Ligands

ACE-ALA-ASP-PTR-GLU-PRO-PRO-NH2

* Residue conservation analysis

PDB id:

2etz

Name:

Transferase

Title:

The nmr minimized average structure of the itk sh2 domain bound to a phosphopeptide

Structure:

Tyrosine-protein kinase itk/tsk. Chain: a. Fragment: sh2 domain. Synonym: t-cell-specific kinase, il-2-inducible t-cell kinase, kinase emt, kinase tlk, itk. Engineered: yes. Lymphocyte cytosolic protein 2 phosphopeptide fragment. Chain: b. Fragment: phosphopeptide fragment sequence database residues 143-148.

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Gene: itk, emt, tlk, tsk. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: the sequence of the peptide is naturally found in mus musculus (mouse).

NMR struc:

1 models

Authors:

M.Sundd,E.V.Pletneva,D.B.Fulton,A.H.Andreotti

Key ref:

E.V.Pletneva et al. (2006). Molecular details of Itk activation by prolyl isomerization and phospholigand binding: the NMR structure of the Itk SH2 domain bound to a phosphopeptide. J Mol Biol, 357, 550-561. PubMed id: 16436281 DOI: 10.1016/j.jmb.2005.12.073

Date:

27-Oct-05 Release date: 07-Feb-06

Protein chain

Q03526  (ITK_MOUSE) -  Tyrosine-protein kinase ITK/TSK from Mus musculus

Seq: 625 a.a.

Struc: 108 a.a.*

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

Enzyme reactions

• Enzyme class: 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.2005.12.073

J Mol Biol 357:550-561 (2006)

PubMed id: 16436281

Molecular details of Itk activation by prolyl isomerization and phospholigand binding: the NMR structure of the Itk SH2 domain bound to a phosphopeptide.

E.V.Pletneva, M.Sundd, D.B.Fulton, A.H.Andreotti.

ABSTRACT

The Src homology 2 (SH2) domain of interleukin-2 tyrosine kinase (Itk) is a critical component of the regulatory apparatus controlling the activity of this immunologically important enzyme. To gain insight into the structural features associated with the activated form of Itk, we have solved the NMR structure of the SH2 domain bound to a phosphotyrosine-containing peptide (pY) and analyzed changes in trans-hydrogen bond scalar couplings ((3h)J(NC')) that result from pY binding. Isomerization of a single prolyl imide bond in this domain is responsible for simultaneous existence of two distinct SH2 conformers. Prolyl isomerization directs ligand recognition: the trans conformer preferentially binds pY. The structure of the SH2/pY complex provides insight into the ligand specificity; the BG loop in the ligand-free trans SH2 conformer is pre-arranged for optimal contacts with the pY+3 residue of the ligand. Analysis of (3h)J(NC') couplings arising from hydrogen bonds has revealed propagation of structural changes from the pY binding pocket to the CD loop containing conformationally heterogeneous proline as well as to the alphaB helix, on the opposite site of the domain. These findings offer a structural framework for understanding the roles of prolyl isomerization and pY binding in Itk regulation.

Selected figure(s)

Figure 2.
Figure 2. NMR structure of the Itk SH2 domain bound to the Ac-ADpYEPP-NH[2] phosphopeptide. (a) The 20 lowest energy structures of the Itk SH2/ADpYEPP complex. The peptide ligand is shown in red and the SH2 domain in turquoise. Backbone heavy atoms within the secondary structural elements over the entire SH2 sequence were used for superpositions. (b) Ribbon diagram of the energy minimized average structure of the Itk SH2/phosphopeptide complex. (The view is identical with that shown in (a).) Regular secondary structural elements and loop regions are labeled. The location of Pro287 within the CD loop is indicated. The phosphopeptide ligand (Ac-ADpYEPP-NH[2]) is red and the phosphotyrosine (pY) and proline residue three positions C-terminal (pY+3) are labeled. In both (a) and (b) the first two residues of the phosphopeptide (AD) are not included for clarity. No NOEs are observed between this region of the peptide and the Itk SH2 domain.

Figure 3.
Figure 3. (a) Superposition of the minimized average structures of the cis SH2 domain (orange), the trans SH2 domain (light blue) and the phospholigand-bound SH2 domain (dark blue). The phospholigand is shown in red and the pY and pY+3 residues are labeled. The BG loop is indicated and the arrow shows the shift in position of the alpha carbon atom of Leu329 that accompanies isomerization of Pro287 from the cis to trans conformations. The structure of the BG loop for the phospholigand-bound SH2 domain (dark blue) is similar to that of BG loop in the ligand-free trans domain (light blue). (b) Superposition of the lowest energy structures of the Itk cis SH2 domain (20 structures), the trans SH2 domain (20 structures) and the SH2/phosphopeptide complex (20 structures). Colors correspond to those in (a). The ensemble of structures indicates that the BG loop in the cis SH2 structure (orange) adopts a range of conformations that differ from the conformational preferences of both the trans SH2 domain and the phospholigand bound SH2 domain. For both (a) and (b) backbone heavy atoms within the secondary structural elements were used for superpositions.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 357, 550-561) copyright 2006.

Figures were selected by an automated process.