Analysis of the Evolutionary Relationships of the PDZ Domains

The PDZ domains are well-known globular fold module of many scaffolding proteins. The domains are involved in protein-protein interaction and play a central role in organizing diverse cell signaling assemblies [2]. Recently the motifs of their binding sites have been researched in biochemical and structural studies [1, 3], but it was pointed out the difficulty to classify the PDZ domains on the basis of the chemical characteristics of binding sites residues [4]. Another one of the specific known features is that the domain appears several times in a mature protein. The result of sequence analysis of the PDZ domain strongly suggested that the PDZ domains were derived from the domain duplication rather than the vertical conservation or the gene duplication.