2H3L

Crystal Structure of ERBIN PDZ


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.148 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Comparative structural analysis of the Erbin PDZ domain and the first PDZ domain of ZO-1. Insights into determinants of PDZ domain specificity.

Appleton, B.A.Zhang, Y.Wu, P.Yin, J.P.Hunziker, W.Skelton, N.J.Sidhu, S.S.Wiesmann, C.

(2006) J.Biol.Chem. 281: 22312-22320

  • DOI: 10.1074/jbc.M602901200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report a structural comparison of the first PDZ domain of ZO-1 (ZO1-PDZ1) and the PDZ domain of Erbin (Erbin-PDZ). Although the binding profile of Erbin-PDZ is extremely specific ([D/E][T/S]WV(COOH)), that of ZO1-PDZ1 is similar ([R/K/S/T][T/S][W/ ...

    We report a structural comparison of the first PDZ domain of ZO-1 (ZO1-PDZ1) and the PDZ domain of Erbin (Erbin-PDZ). Although the binding profile of Erbin-PDZ is extremely specific ([D/E][T/S]WV(COOH)), that of ZO1-PDZ1 is similar ([R/K/S/T][T/S][W/Y][V/I/L](COOH)) but broadened by increased promiscuity for three of the last four ligand residues. Consequently, the biological function of ZO-1 is also broadened, as it interacts with both tight and adherens junction proteins, whereas Erbin is restricted to adherens junctions. Structural analyses reveal that the differences in specificity can be accounted for by two key differences in primary sequence. A reduction in the size of the hydrophobic residue at the base of the site(0) pocket enables ZO1-PDZ1 to accommodate larger C-terminal residues. A single additional difference alters the specificity of both site(-1) and site(-3). In ZO1-PDZ1, an Asp residue makes favorable interactions with both Tyr(-1) and Lys/Arg(-3). In contrast, Erbin-PDZ contains an Arg at the equivalent position, and this side chain cannot accommodate either Tyr(-1) or Lys/Arg(-3) but, instead, interacts favorably with Glu/Asp(-3). We propose a model for ligand recognition that accounts for interactions extending across the entire binding site but that highlights several key specificity switches within the PDZ domain fold.


    Related Citations: 
    • Convergent and Divergent Ligand Specificity Amongst the PDZ Domains of the LAP and ZO Families
      Zhang, Y.,Yeh, S.,Appleton, B.A.,Held, H.A.,Kausalya, J.P.,Phua, D.C.Y.,Wong, W.L.,Lasky, L.A.,Wiesmann, C.,Hunziker, W.,Sidhu, S.S.
      (2006) J.Biol.Chem. 281: 22299


    Organizational Affiliation

    Department of Protein Engineering, Genentech, Inc., South San Francisco, California 94080, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LAP2 protein
A, B
103Homo sapiensMutation(s): 0 
Gene Names: ERBIN (ERBB2IP, KIAA1225, LAP2)
Find proteins for Q96RT1 (Homo sapiens)
Go to Gene View: ERBIN
Go to UniProtKB:  Q96RT1
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.148 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 38.864α = 90.00
b = 44.032β = 106.18
c = 57.265γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-13
    Type: Initial release
  • Version 1.1: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description
  • Version 1.4: 2018-01-24
    Type: Database references