PDBsum entry: 1ozi

Hydrolase

PDB-id: 1ozi

Contents

Description

Header details

Header records

References

PROCHECK

Protein chain

99 a.a. *

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1ozi

Name:

Hydrolase

Title:

The alternatively spliced pdz2 domain of ptp-bl

Structure:

Protein tyrosine phosphatase. Chain: a. Fragment: pdz2 of ptp-bl. Synonym: nonreceptor-type, 13, protein-tyrosine phosphatase rip, phosphoprotein phosphatase, protein- tyrosine-phosphatase, phosphotyrosine phosphatase, ptpase, ptp36, bas-like. Engineered: yes. Mutation: yes.

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Gene: ptp-bl. Expressed in: escherichia coli. Expression_system_taxid: 562. (De3) ril competent.

UniProt:

Q64512 (PTN13_MOUSE)

Seq:

Struc:

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Struc:

Seq:

2453 a.a.

Struc:

99 a.a.*

Key:	PfamA domain	PfamB domain
Secondary structure	CATH domain

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

Enzyme class:

E.C.3.1.3.48   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Protein tyrosine phosphate + H₂O = protein tyrosine + phosphate (see diagram below)

Resolution:

not givenÅ

NMR structure:

30 models

Authors:

T.Walma,J.Aelen,M.Oostendorp,L.Van Den Berk,W.Hendriks, G.W.Vuister

Key ref:

T.Walma et al. (2004). A closed binding pocket and global destabilization modify the binding properties of an alternatively spliced form of the second PDZ domain of PTP-BL.. Structure, 12, 11-20. [PubMed id: 14725761] [DOI: 10.1016/j.str.2003.11.023]

Date:

09-Apr-03

Release date:

27-Jan-04

Related entries:

5762 related db: bmrb
chemical shift and j coupling information
1gm1
pdz2 of ptp-bl
5131 related db: bmrb
chemical shift and j coupling information for pdz2 of ptp-b

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1016/j.str.2003.11.023

Structure 12:11-20 (2004)

PubMed id: 14725761

A closed binding pocket and global destabilization modify the binding properties of an alternatively spliced form of the second PDZ domain of PTP-BL.

T.Walma, J.Aelen, S.B.Nabuurs, M.Oostendorp, L.van den Berk, W.Hendriks, G.W.Vuister.

ABSTRACT

PTP-BL is a large phosphatase that is implicated in cellular processes as diverse as cytokinesis, actin-cytoskeletal rearrangement, and apoptosis. Five PDZ domains mediate its cellular role by binding to the C termini of target proteins, forming multiprotein complexes. The second PDZ domain (PDZ2) binds to the C termini of the tumor suppressor protein APC and the LIM domain-containing protein RIL; however, in one splice variant, PDZ2as, a 5 residue insertion abrogates this binding. The insert causes distinct structural and dynamical changes in the alternatively spliced PDZ2: enlarging the L1 loop between beta2 and beta3, both lengthening and changing the orientation of the alpha2 helix, giving the base of the binding pocket less flexibility to accommodate ligands, and destabilizing the entire domain. These changes render the binding pocket incapable of binding C termini, possibly having implications in the functional role of PTP-BL.

Selected figure(s)

Figure 1.
Figure 1. Structural Ensemble and Sequence Alignment of PD22as(A) Structural ensemble of PDZ2as (stereo diagram); secondary structures are indicated by cyan (b strand) and pink (a helix).(B) Protection of amides from H/D exchange. Amides are depicted as spheres; red spheres indicate amides with high protection factors, orange spheres, those with intermediate protection factors, and yellow spheres represent amide with low protection factors. Gray spheres indicate amides with complete solvent exchange within the experimental dead time of 20 min.(C and D) Structural superposition of PDZ2as (blue) with PDZ2 (red). The orientation of the a2 helices differ by vert, similar 20° (shown as cylinders) while that of the b2 strands remain the same (shown as arrows).(E) PDZ2as (PDB code 1ozi) sequentially aligned with GRIP (1m5z), CASK (1kwa), PSD-95 (1bfe), and DglA (1pdr). The alignments were performed on each domain with a maximal displacement of 7 Å for each pair of C^a atoms and a global RMS limit of 4 Å. Protein regions that are structurally similar to PDZ2as are indicated by underlining. Secondary structures of both PDZ2 and PDZ2as complexes are colored as in (A). The 5 residue insertion is boxed in gray. Numbering schemes are given for PDZ2as (blue) and, for reference, PDZ2 (red).

The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 11-20) copyright 2004.

Figure was selected by the author.