{PDOC50093}
{PS50093; PKD}
{BEGIN}
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* Polycystic kidney disease (PKD) domain profile *
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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 beta-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.

-Sequences known to belong to this class detected by the profile: ALL.
-Other sequence(s) detected in Swiss-Prot: NONE.
-Last update: December 2001 / First entry.

[ 1] Gluecksmann-Kuis M.A., Tayber O., Woolf E.A., Bougueleret L.,
     Deng N., Alperin G.D., Iris F., Hawkins F., Munro C., Lakey N.,
     Duyk G., Schneider M.C., Geng L., Zhang F., Zhao Z., Torosian S.,
     Reeders S.T., Bork P., Pohlschmidt M., Loehning C., Kraus B.,
     Nowicka U., Leung A.L.S., Frischauf A.-M.
     Cell 81:289-298(1995).
[ 2] Hughes J., Ward C.J., Peral B., Aspinwall R., Clark K.,
     San Millan J.L., Gamble V., Harris P.C.
     "The polycystic kidney disease 1 (PKD1) gene encodes a novel protein
     with multiple cell recognition domains."
     Nat. Genet. 10:151-160(1995).
     PubMed=7663510; DOI=10.1038/ng0695-151
[ 3] Callebaut I., Gilges D., Vigon I., Mornon J.-P.
     "HYR, an extracellular module involved in cellular adhesion and
     related to the immunoglobulin-like fold."
     Protein Sci. 9:1382-1390(2000).
     PubMed=10933504
[ 4] Bycroft M., Bateman A., Clarke J., Hamill S.J., Sandford R.,
     Thomas R.L., Chothia C.
     "The structure of a PKD domain from polycystin-1: implications for
     polycystic kidney disease."
     EMBO J. 18:297-305(1999).
     PubMed=9889186; DOI=10.1093/emboj/18.2.297

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