3CH8

The crystal structure of PDZ-Fibronectin fusion protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for exquisite specificity of affinity clamps, synthetic binding proteins generated through directed domain-interface evolution.

Huang, J.Makabe, K.Biancalana, M.Koide, A.Koide, S.

(2009) J.Mol.Biol. 392: 1221-1231

  • DOI: 10.1016/j.jmb.2009.07.067

  • PubMed Abstract: 
  • We have established a new protein-engineering strategy termed "directed domain-interface evolution" that generates a binding site by linking two protein domains and then optimizing the interface between them. Using this strategy, we have generated sy ...

    We have established a new protein-engineering strategy termed "directed domain-interface evolution" that generates a binding site by linking two protein domains and then optimizing the interface between them. Using this strategy, we have generated synthetic two-domain "affinity clamps" using PDZ and fibronectin type III (FN3) domains as the building blocks. While these affinity clamps all had significantly higher affinity toward a target peptide than the underlying PDZ domain, two distinct types of affinity clamps were found in terms of target specificity. One type conserved the specificity of the parent PDZ domain, and the other increased the specificity dramatically. Here, we characterized their specificity profiles using peptide phage-display libraries and scanning mutagenesis, which suggested a significantly enlarged recognition site of the high-specificity affinity clamps. The crystal structure of a high-specificity affinity clamp showed extensive contacts with a portion of the peptide ligand that is not recognized by the parent PDZ domain, thus rationalizing the improvement of the specificity of the affinity clamp. A comparison with another affinity clamp structure showed that, although both had extensive contacts between PDZ and FN3 domains, they exhibited a large offset in the relative position of the two domains. Our results indicate that linked domains could rapidly fuse and evolve as a single functional module, and that the inherent plasticity of domain interfaces allows for the generation of diverse active-site topography. These attributes of directed domain-interface evolution provide facile means to generate synthetic proteins with a broad range of functions.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, 929 East 57th Street, Chicago, IL 60637, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
fusion protein PDZ-Fibronectin
A
195Homo sapiensMutation(s): 0 
Gene Names: ERBIN (ERBB2IP, KIAA1225, LAP2)
Find proteins for Q96RT1 (Homo sapiens)
Go to Gene View: ERBIN
Go to UniProtKB:  Q96RT1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
C-terminal octapeptide from protein ARVCF
P
8N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.201 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 69.008α = 90.00
b = 69.008β = 90.00
c = 46.706γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-31
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance