PDBsum entry 1q7x

Hydrolase

PDB id: 1q7x

Contents

Protein chain

108 a.a. *

* Residue conservation analysis

PDB id:

1q7x

Name:

Hydrolase

Title:

Solution structure of the alternatively spliced pdz2 domain (pdz2b) of ptp-bas (hptp1e)

Structure:

Pdz2b domain of ptp-bas (hptp1e). Chain: a. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ptp1e. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

N.Kachel,K.S.Erdmann,W.Kremer,P.Wolff,W.Gronwald,R.Heumann, H.R.Kalbitzer,Structural Proteomics In Europe (Spine)

Key ref:

N.Kachel et al. (2003). Structure determination and ligand interactions of the PDZ2b domain of PTP-Bas (hPTP1E): splicing-induced modulation of ligand specificity. J Mol Biol, 334, 143-155. PubMed id: 14596806 DOI: 10.1016/j.jmb.2003.09.026

Date:

20-Aug-03 Release date: 02-Dec-03

Protein chain

Q12923  (PTN13_HUMAN) -  Tyrosine-protein phosphatase non-receptor type 13 from Homo sapiens

Seq: 2485 a.a.

Struc: 108 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.3.48 - protein-tyrosine-phosphatase.
• Reaction: O-phospho-L-tyrosyl-[protein] + H2O = L-tyrosyl-[protein] + phosphate

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

Key reference

DOI no: 10.1016/j.jmb.2003.09.026

J Mol Biol 334:143-155 (2003)

PubMed id: 14596806

Structure determination and ligand interactions of the PDZ2b domain of PTP-Bas (hPTP1E): splicing-induced modulation of ligand specificity.

N.Kachel, K.S.Erdmann, W.Kremer, P.Wolff, W.Gronwald, R.Heumann, H.R.Kalbitzer.

ABSTRACT

Two versions of the PDZ2 domain of the protein tyrosine phosphatase PTP-Bas/human PTP-BL are generated by alternative splicing. The domains differ by the insertion of five amino acid residues and their affinity to the tumour suppressor protein APC. Whereas PDZ2a is able to bind APC in the nanomolar range, PDZ2b shows no apparent interaction with APC. Here the solution structure of the splicing variant of PDZ2 with the insertion has been determined using 2D and 3D heteronuclear NMR experiments. The structural reason for the changed binding specificity is the reorientation of the loop with extra five amino acid residues, which folds back onto beta-strands two and three. In addition the side-chain of Lys32 closes the binding site of the APC binding protein and the two helices, especially alpha-helix 2, change their relative position to the protein core. Consecutively, the binding site is sterically no longer fully accessible. From the NMR-titration studies with a C-terminal APC-peptide the affinity of the peptide with the protein can be estimated as 540(+/-40)microM. The binding site encompasses part of the analogous binding site of PDZ2a as already described previously, yet specific interaction sites are abolished by the insertion of amino acids in PDZ2b. As shown by high-affinity chromatography, GST-PDZ2b and GST-PDZ2a bind to phosphatidylinositol 4,5-bisphosphate (PIP(2)) micelles with a dissociation constant K(D) of 21 microM and 55 microM, respectively. In line with these data PDZ2b binds isolated, dissolved PIP(2) and PIP(3) (phosphatidylinositol 3,4,5-trisphosphate) molecules specifically with a lower K(D) of 230(+/-20)microM as detected by NMR spectroscopy. The binding site could be located by our studies and involves the residues Ile24, Val26, Val70, Asn71, Gly77, Ala78, Glu85, Arg88, Gly91 and Gln92. PIP(2) and PIP(3) binding takes place in the groove of the PDZ domain that is normally part of the APC binding site.

Selected figure(s)

Figure 4.
Figure 4. NOE contacts per residue in PDZ2b of PTP-Bas. The secondary structure is symbolised by arrows (b-strands) and lanyards (a-helices). The position of the insertion is marked in grey.

Figure 6.
Figure 6. NMR structure of PDZ2b. (A) Ribbon representation of the lowest-energy structure of PDZ2b of PTP-Bas. The insertion is highlighted in orange. (B) Backbone representations of the 20 lowest-energy structures from the struc- ture calculation. (C) Electrostatic potential of PDZ2b; negatively charged regions are coloured red, positively charged regions are blue. All molecules are shown in the same orientation. The Figure was prepared using the program MOLMOL. 49

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 334, 143-155) copyright 2003.

Figures were selected by an automated process.