The PWWP domain is an around 70 amino acids domain that was named after its central core 'Pro-Trp-Trp-Pro'. The PWWP domain is found in one or, less frequently, in two copies in nuclear, often DNA-binding proteins that function as transcription factors regulating developmental processes. Due to its position, the composition of amino acids close to the PWWP motif and the pattern of other domains present, it has been proposed that the PWWP domain is involved in protein-protein interactions [1].

Conservation of the PWWP domain is concentrated on one major and two minor blocks with length differences occurring in between [1].

Some proteins known to contain a PWWP domain are listed below:

• Human WHSC1 protein, encoded by a gene located in the Wolf-Hirschorn syndrome critical region.
• Human bromodomain and PHD finger-containing protein 1 (BRPF1/Peregrin) and 3 (BRPF3). These are possible transcription activators.
• Human bromodomain-containing protein 1 (BRD1).
• Human BS69 protein, highly expressed in colon carcinoma. It interacts with E1A specifically suppressing E1A-activated transcription.
• Mammalian hepatoma-derived growth factor (HDGF), an heparin-binding protein, with mitogenic activity for fibroblasts.
• Mammalian DNA mismatch repair protein MSH6.
• Vertebrate DNA-cytosine-methyltransferase type 3 (DNMT3).

The profile we developed covers the entire PWWP domain.