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PDBsum entry 3dj3

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protein Protein-protein interface(s) links
Signaling protein PDB id
3dj3
Jmol
Contents
Protein chains
100 a.a. *
Waters ×103
* Residue conservation analysis
PDB id:
3dj3
Name: Signaling protein
Title: Crystal structure of c-terminal truncated tip-1 (6-113)
Structure: Tax1-binding protein 3. Chain: a, b, c, d. Fragment: c-terminal truncation, unp residues 1-112. Synonym: tax interaction protein 1, tip-1. Engineered: yes
Source: Mus musculus. Mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562
Resolution:
2.40Å     R-factor:   0.265     R-free:   0.314
Authors: Y.Shen
Key ref:
J.Zhang et al. (2008). Structural basis of beta-catenin recognition by Tax-interacting protein-1. J Mol Biol, 384, 255-263. PubMed id: 18835279 DOI: 10.1016/j.jmb.2008.09.034
Date:
21-Jun-08     Release date:   21-Oct-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9DBG9  (TX1B3_MOUSE) -  Tax1-binding protein 3
Seq:
Struc:
124 a.a.
100 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   4 terms 
  Biological process     negative regulation of protein localization at cell surface   7 terms 
  Biochemical function     protein binding     3 terms  

 

 
DOI no: 10.1016/j.jmb.2008.09.034 J Mol Biol 384:255-263 (2008)
PubMed id: 18835279  
 
 
Structural basis of beta-catenin recognition by Tax-interacting protein-1.
J.Zhang, X.Yan, C.Shi, X.Yang, Y.Guo, C.Tian, J.Long, Y.Shen.
 
  ABSTRACT  
 
Tax-interacting protein-1 (TIP-1) is an unusual signaling protein, containing a single PDZ domain. TIP-1 is able to bind beta-catenin with high affinity and thus inhibit its transcriptional activity. The high-resolution crystal structure of TIP-1 in complex with the C-terminal peptide of beta-catenin provides molecular details for the recognition of beta-catenin by TIP-1. Moreover, structural comparison of peptide-free and peptide-bound TIP-1 reveals that significant conformational changes are required in the betaB-betaC loop region of TIP-1 to avoid clashes with the incoming C-terminal beta-catenin peptide. Such conformational changes have not been observed in other structures of PDZ domains. In addition to the canonical peptide-binding pocket of the PDZ domain, TIP-1 can form a binding cavity to anchor more amino acids through a conserved hydrophobic residue pair (Trp776 of beta-catenin and Pro45 of TIP-1). Structural and biochemical data indicate that the canonical binding pocket together with the hydrophobic residue pair are presumably the major cause of the significantly higher affinity of the beta-catenin C-terminal to TIP-1 than to other PDZ domains, providing a unique binding specificity. Our results reveal the molecular mechanism of TIP-1 as an antagonist in PDZ domain signaling.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. Summary of six binding modes of PDZ domain with peptide. The following PDB files were used: 1BE9^36 for PSD-95-PDZ3/CRIPT; 1QAV^52 for nNOS/Syntrophin; 1X8S^53 for Par-6/Pals1; 1MFG^38 for Erbin/ErbB2; and 2K20^54 for Par-3/PTEN.
Figure 5.
Fig. 5. The proline-tryptophan hydrophobic pair. (a), Sequence comparison of the βB–bC loop region shows the conserved NPF motif. The Pro45 residue is labeled with an asterisk ( asterisk ). Surface representation of the proline-tryptophan interaction in the crystal structure of TIP-1 in complex with the C-terminal b-catenin peptide (b), Erbin in complex with the C-terminal ErbB2 peptide (c), and Erbin in complex with a peptide derived from phage display (d). Peptides are colored cyan and β-catenin is colored green. The surface is colored as follows: hydrophobic residues, yellow; positively charged residues, blue; and negatively charged residues, red.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 384, 255-263) copyright 2008.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20213668 R.J.Falconer, A.Penkova, I.Jelesarov, and B.M.Collins (2010).
Survey of the year 2008: applications of isothermal titration calorimetry.
  J Mol Recognit, 23, 395-413.  
19685007 M.A.Durney, G.Birrane, C.Anklin, A.Soni, and J.A.Ladias (2009).
Solution structure of the human Tax-interacting protein-1.
  J Biomol NMR, 45, 329-334.
PDB code: 2kg2
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