Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 9.77 kDa 
• Atom Count: 687 
• Residue Count: 94 
• Unique protein chains: 1

1GM1

Second PDZ Domain (PDZ2) of PTP-BL

• DOI: 10.2210/pdb1GM1/pdb
• BMRB: 6091
• BMRB: 5131
• BMRB: 6092
• BMRB: 6060

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-09-06 Released: 2002-03-08 
• Deposition Author(s): Walma, T., Tessari, M., Aelen, J., Schepens, J., Hendriks, W., Vuister, G.W.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 35 
• Selection Criteria: LOWEST ENERGY 

Literature

Structure, dynamics and binding characteristics of the second PDZ domain of PTP-BL.

Walma, T., Spronk, C.A., Tessari, M., Aelen, J., Schepens, J., Hendriks, W., Vuister, G.W.

(2002) J Mol Biol 316: 1101-1110

• PubMed: 11884147 
• DOI: 10.1006/jmbi.2002.5402
• Primary Citation of Related Structures:  
  1GM1


• PubMed Abstract: 
  

The PDZ domains of the protein tyrosine phosphatase PTP-BL mediate interactions by binding to specific amino acid sequences in target proteins. The solution structure of the second PDZ domain of PTP-BL, PDZ2, displays a compact fold with six beta strands and two alpha-helices. A unique feature of this domain compared to the canonical PDZ fold is an extended flexible loop at the base of the binding pocket, termed L1, that folds back onto the protein backbone, a feature that is shared by both the murine and human orthologues. The structure of PDZ2 differs significantly from the orthologous human structure. A comparison of structural quality indicators clearly demonstrates that the PDZ2 ensemble is statistically more reasonable than that of the human orthologue. The analysis of (15)N relaxation data for PDZ2 shows a normal pattern, with more rigid secondary structures and more flexible loop structures. Close to the binding pocket, Leu85 and Thr88 display greater mobility when compared to surrounding residues. Peptide binding studies demonstrated a lack of interaction between murine PDZ2 and the C terminus of the murine Fas/CD95 receptor, suggesting that the Fas/CD95 receptor is not an in vivo target for PDZ2. In addition, PDZ2 specifically binds the C termini of both human Fas/CD95 receptor and the RIL protein, despite RIL containing a non-canonical PDZ-interacting sequence of E-x-V. A model of PDZ2 with the RIL peptide reveals that the PDZ2 binding pocket is able to accommodate the bulkier side-chain of glutamic acid while maintaining crucial protein to peptide hydrogen bond interactions.

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Organizational Affiliation: 

NSR-RIM Center, Department of Biophysical Chemistry, University of Nijmegen, Toernooiveld 1, 6525 ED Nijmegen, The Netherlands.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN TYROSINE PHOSPHATASE	A	94	Mus musculus	Mutation(s): 0  Gene Names: Ptpn13, Ptp14 EC: 3.1.3.48
Find proteins for Q64512 (Mus musculus) Explore Q64512  Go to UniProtKB:  Q64512

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 35 
• Selection Criteria: LOWEST ENERGY 
• OLDERADO: 1GM1 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-09-06 
• Released Date: 2002-03-08 
Deposition Author(s): Walma, T., Tessari, M., Aelen, J., Schepens, J., Hendriks, W., Vuister, G.W.

Revision History 

• Version 1.0: 2002-03-08
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-03-28
  Changes: Database references, Source and taxonomy