The name of this superfamily has been modified since the most recent official CATH+ release (v4_3_0). At the point of the last release, this superfamily was: waiting to be named.
PDZ domains can occur in one or multiple copies and are nearly always found in cytoplasmic proteins. They recognise internal sequence motifs or short amino acid sequences at the C-terminus of target proteins. Structurally, they consist of 5-6 beta-strands and 2 or 3 small alpha helical structures. PDZ domains have a highly conserved fold, but secondary structures vary in length and in sequence.
Peptide binding of the ligand takes place in an elongated surface groove as an anti-parallel beta-strand interacts with a beta strand and the second helix. The structure of PDZ domains allows binding to a free carboxylate group at the end of a peptide through a carboxylate-binding loop between the beta-A and beta-B strands.
They bind either the C-terminal sequences of proteins or internal peptide sequences. In most cases, interaction between a PDZ domain and its target is constitutive, with a binding affinity of 1 to 10 microns. However, agonist-dependent activation of cell surface receptors is sometimes required to promote interaction with a PDZ protein. PDZ domain proteins are frequently associated with the plasma membrane, a compartment where high concentrations of phosphatidylinositol 4,5-bisphosphate (PIP2) are found. Direct interaction between PIP2 and a subset of class II PDZ domains (syntenin, CASK, Tiam-1) has been demonstrated.
|Domain clusters (>95% seq id):||272|
|Domain clusters (>35% seq id):||123|
|Structural Clusters (5A):||26|
|Structural Clusters (9A):||10|