5W72

Impact of IR active probes on PDZ3 and its ligand binding studied by NMR and X-ray crystallography


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 400 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Impact of Azidohomoalanine Incorporation on Protein Structure and Ligand Binding.

Lehner, F.Kudlinzki, D.Richter, C.Muller-Werkmeister, H.M.Eberl, K.B.Bredenbeck, J.Schwalbe, H.Silvers, R.

(2017) Chembiochem 18: 2340-2350

  • DOI: 10.1002/cbic.201700437
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The impact of the incorporation of a non-natural amino acid (NNAA) on protein structure, dynamics, and ligand binding has not been studied rigorously so far. NNAAs are regularly used to modify proteins post-translationally in vivo and in vitro throug ...

    The impact of the incorporation of a non-natural amino acid (NNAA) on protein structure, dynamics, and ligand binding has not been studied rigorously so far. NNAAs are regularly used to modify proteins post-translationally in vivo and in vitro through click chemistry. Herein, structural characterisation of the impact of the incorporation of azidohomoalanine (AZH) into the model protein domain PDZ3 is examined by means of NMR spectroscopy and X-ray crystallography. The structure and dynamics of the apo state of AZH-modified PDZ3 remain mostly unperturbed. Furthermore, the binding of two PDZ3 binding peptides are unchanged upon incorporation of AZH. The interface of the AZH-modified PDZ3 and an azulene-linked peptide for vibrational energy transfer studies has been mapped by means of chemical shift perturbations and NOEs between the unlabelled azulene-linked peptide and the isotopically labelled protein. Co-crystallisation and soaking failed for the peptide-bound holo complex. NMR spectroscopy, however, allowed determination of the protein-ligand interface. Although the incorporation of AZH was minimally invasive for PDZ3, structural analysis of NNAA-modified proteins through the methodology presented herein should be performed to ensure structural integrity of the studied target.


    Organizational Affiliation

    Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438, Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Disks large homolog 4
A
102Rattus norvegicusMutation(s): 0 
Gene Names: Dlg4 (Dlgh4, Psd95)
Find proteins for P31016 (Rattus norvegicus)
Go to UniProtKB:  P31016
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
AZH
Query on AZH
A
L-PEPTIDE LINKINGC4 H9 N4 O2ALA
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 400 
  • Conformers Submitted: 20 
  • Selection Criteria: target function 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
BMRZ--
HESSEN--
iNEXTEcuador--
German Research FoundationGermanySI2105/1-1

Revision History 

  • Version 1.0: 2017-12-13
    Type: Initial release