The polycystic kidney disease (PKD) domain is an 80-90 amino acid module originally found in 16 copies in the extracellular segment of polycystin-1, a large cell surface glycoprotein. Polycystin-1 is encoded by the PKD1 gene, which is mutated in autosomal dominant polycystic kidney disease (ADPKD). Although its function is unknown, it may be involved in protein-protein and protein-carbohydrate interactions based on its predicted domain structure. One or more copies of the PKD domain are also found in several other extracellular proteins from higher organisms, eubacteria, and archaebacteria. Singles copies of the PKD domain are found in the melanocytes heavily glycosylated cell-surface proteins Pmel 17, MMP and Nmp. Some bacterial collagenases and proteases also contain a single PKD domain adjacent to their catalytic domains, whereas four copies are present in the heavily glycosylated surface layer protein of archaebacteria [1,2]. The PKD modules are often observed, within a same protein sequence, in association with FnIII domains [3].

The most conserved motif is the WDFGDGS sequence that is found in the central part of many PKD domains and could play a structural role [1,2,4]. Determination of the solution structure of the first PKD domain from human polycystin-1 has shown that the module is built from two β-sheet, one of three strands and one of four strands, which are packed face-to-face [4].

Some proteins containing a PKD domain are listed below:

• Polycystin-1 (PKD1).
• Vertebrate proteins of the Pmel-17/NMB family.
• Archaeal surface-layer proteins.
• Clostridium perfringens and Vibrio alginolyticus microbial collagenases.
• Achromobacter lyticus protease I.

The profile we developed covers the entire PKD domain.