1VJ6

PDZ2 from PTP-BL in complex with the C-terminal ligand from the APC protein


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 35 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Demonstration of long-range interactions in a PDZ domain by NMR, kinetics, and protein engineering.

Gianni, S.Walma, T.Arcovito, A.Calosci, N.Bellelli, A.Engstrom, A.Travaglini-Allocatelli, C.Brunori, M.Jemth, P.Vuister, G.W.

(2006) Structure 14: 1801-1809

  • DOI: 10.1016/j.str.2006.10.010

  • PubMed Abstract: 
  • Understanding the basis of communication within protein domains is a major challenge in structural biology. We present structural and dynamical evidence for allosteric effects in a PDZ domain, PDZ2 from the tyrosine phosphatase PTP-BL, upon binding t ...

    Understanding the basis of communication within protein domains is a major challenge in structural biology. We present structural and dynamical evidence for allosteric effects in a PDZ domain, PDZ2 from the tyrosine phosphatase PTP-BL, upon binding to a target peptide. The NMR structures of its free and peptide-bound states differ in the orientation of helix alpha2 with respect to the remainder of the molecule, concomitant with a readjustment of the hydrophobic core. Using an ultrafast mixing instrument, we detected a deviation from simple bimolecular kinetics for the association with peptide that is consistent with a rate-limiting conformational change in the protein (k(obs) approximately 7 x 10(3) s(-1)) and an induced-fit model. Furthermore, the binding kinetics of 15 mutants revealed that binding is regulated by long-range interactions, which can be correlated with the structural rearrangements resulting from peptide binding. The homologous protein PSD-95 PDZ3 did not display a similar ligand-induced conformational change.


    Organizational Affiliation

    Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche A. Rossi Fanelli, Università di Roma La Sapienza, Piazzale A. Moro 5, 00185 Rome, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
protein-tyrosine-phosphatase (nonreceptor type 13)
A
102Mus musculusMutation(s): 0 
Gene Names: Ptpn13 (Ptp14)
EC: 3.1.3.48
Find proteins for Q64512 (Mus musculus)
Go to UniProtKB:  Q64512
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Adenomatous polyposis coli protein
B
12Mus musculusMutation(s): 0 
Gene Names: Apc
Find proteins for Q61315 (Mus musculus)
Go to UniProtKB:  Q61315
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 35 
  • Selection Criteria: structures with the lowest energy 
  • Olderado: 1VJ6 Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-11-01
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance