Classification of PDZ domains

FEBS Lett. 2001 Dec 14;509(3):457-62. doi: 10.1016/s0014-5793(01)03214-8.


A diverse family of PDZ domains has been identified, but the rules that govern their ligand specificity are not clear. Here we propose a novel classification of PDZ domains based on the nature of amino acids in the two critical positions in the PDZ domain fold. Using these principles, we classified PDZ domains present in the SMART database. Using yeast two-hybrid, in vitro pull-down and plasmon surface resonance assays, we demonstrated that in agreement with their position in the proposed classification the Mint1-1, hINADL-5, and PAR6 PDZ domains display similar dual ligand specificity. The proposed classification helps to organize PDZ domain containing proteins.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adaptor Proteins, Signal Transducing*
  • Amino Acid Sequence
  • Animals
  • Carrier Proteins / chemistry*
  • Carrier Proteins / classification*
  • Databases, Protein
  • Discs Large Homolog 1 Protein
  • Guanylate Kinases
  • Humans
  • Ligands
  • Membrane Proteins / chemistry*
  • Mice
  • Molecular Sequence Data
  • Nerve Tissue Proteins / chemistry*
  • Phosphoproteins / chemistry*
  • Protein Binding
  • Protein Structure, Tertiary
  • Proteins / chemistry*
  • Rats
  • Sequence Homology, Amino Acid
  • Substrate Specificity
  • Surface Plasmon Resonance
  • Two-Hybrid System Techniques
  • Yeasts
  • Zonula Occludens-1 Protein


  • APBA1 protein, human
  • Adaptor Proteins, Signal Transducing
  • Apba1 protein, mouse
  • Apba1 protein, rat
  • Carrier Proteins
  • DLG1 protein, human
  • Discs Large Homolog 1 Protein
  • Dlg1 protein, mouse
  • Dlg1 protein, rat
  • Ligands
  • Membrane Proteins
  • Nerve Tissue Proteins
  • Phosphoproteins
  • Proteins
  • TJP1 protein, human
  • Tjp1 protein, mouse
  • Tjp1 protein, rat
  • Zonula Occludens-1 Protein
  • postsynaptic density proteins
  • Guanylate Kinases