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PR00500

Identifier
POLYCYSTIN1  [View Relations]  [View Alignment]  
Accession
PR00500
No. of Motifs
10
Creation Date
29-MAR-1996  (UPDATE 30-OCT-2000)
Title
Polycystic kidney disease type 1 protein (PKD1) signature
Database References
Literature References
1. WARD, C.J., TURLEY, H., ONG, A.C.M., COMLEY, M., BIDDOLPH, S.,
CHETTY, R., RATCLIFFE, P.J., GATTER, K. AND HARRIS, P.C.
Polycystin, the polycystic kidney disease 1 protein, is expressed by
epithelial cells in fetal, adult, and polycystic kidney.
PROC.NATL.ACAD.SCI.U.S.A. 93(4) 1524-1528 (1996).
 
2. WARD, C.J., PERAL, B., HUGHES, J., THOMAS, S., GAMBLE, V., 
MACCARTHY, A.B., SLOANE-STANLEY, J., BUCKLE, V.J., KEARNEY, L., HIGGS, D.R.,
RATCLIFFE, P.J., HARRIS, P.C., ROELFSEMA, J.H., SPRUIT, L.L., SARIS, J.J., 
DAUWERSE, H.G., PETERS, D.J.M., BREUNING, M.H., NELLIST, M., BROOK-CARTER,
P.T., MAHESHWAR, M.M., CORDEIRO, I., SANTOS, H., CABRAL, P., SAMPSON, J.R.,
JANSSEN, B., HESSELING-JANSSEN, A.L.W., VAN DEN OUWELAND, A.M.W., 
EUSSEN, B., VERHOEF, S., LINDHOUT, D. AND HALLEY, D.J.J. 
The polycystic kidney disease 1 gene encodes a 14 kb transcript and lies
within a duplicated region on chromosome 16. The European Polycystic Kidney
Disease Consortium.
CELL 77 881-894 (1994). 
 
3. BYCROFT, M., BATEMAN, A., CLARKE, J., HAMILL, S.J., SANDFORD, R., 
THOMAS, R.L. AND CHOTHIA, C. 
The structure of a PKD domain from polycystin-1: implications for
polycystic kidney disease.
EMBO J. 18 297-305 (1999). 
 
4. 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. AND FRISCHAUF, A.-M. 
Polycystic kidney disease: the complete structure of the PKD1 gene and its
protein. The International Polycystic Kidney Disease Consortium.
CELL 81 289-298 (1995). 

Documentation
Polycystic kidney diseases (PKD) are disorders characterised by large
numbers of cysts distributed throughout grossly-enlarged kidneys. Cyst
development is associated with impairment of kidney function, and ultimately
kidney failure and death [1,2]. Most cases of autosomal dominant PKD result
from mutations in the PKD1 gene that cause premature protein termination. 
 
PKD1 encodes a large cell-surface glycoprotein termed polycystin-1, the 
function of which is unknown [3]. The protein contains 4304 amino acid 
residues and has a composite domain architecture. The N-terminal half of
the protein consists of a mosaic of domains such as leucine-rich repeats
flanked by characteristic cysteine-rich structures, LDL-A and C-type lectin
domains, and 14 units of a novel 80-amino acid module, designated the PKD
domain [4]. The presence of these domains suggests that the PKD1 protein is
involved in adhesive protein-protein and protein-carbohydrate interactions
in the extracellular compartment [4]. 
 
The PKD domain has been shown to adopt a beta-sandwich fold, which is
characteristic of a number of cell-surface modules; nevertheless, the PKD
domain represents a distinct protein family [3]. The tenth PKD domain of 
human and Fugu polycystin-1 show extensive conservation of surface residues,
implicating this region as a potential ligand-binding site [3]. 
 
POLYCYSTIN1 is a 10-element fingerprint that provides a signature for
polycystin-1. The fingerprint was derived from an initial alignment of 4 
sequences: the motifs were drawn largely from hydrophobic segments spanning
the C-terminal half of the alignment. Two iterations on SPTR39_14f were 
required to reach convergence, at which point a true set comprising 6 
sequences was identified.
Summary Information
6 codes involving 10 elements
0 codes involving 9 elements
0 codes involving 8 elements
0 codes involving 7 elements
0 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
106666666666
90000000000
80000000000
70000000000
60000000000
50000000000
40000000000
30000000000
20000000000
12345678910
True Positives
O08852        O42181        PKD1_HUMAN    Q15140        
Q15141 Q15142
Sequence Titles
O08852      POLYCYSTIC KIDNEY DISEASE 1 PROTEIN - Mus musculus (Mouse). 
O42181 PKD1 PROTEIN - Fugu rubripes (Japanese pufferfish) (Takifugu rubripes).
PKD1_HUMAN POLYCYSTIN PRECURSOR (AUTOSOMAL DOMINANT POLYCYSTIC KIDNEY DISEASE PROTEIN 1) - Homo sapiens (Human).
Q15140 POLYCYSTIC KIDNEY DISEASE 1 PROTEIN - Homo sapiens (Human).
Q15141 POLYCYSTIC KIDNEY DISEASE 1 PROTEIN - Homo sapiens (Human).
Q15142 POLYCYSTIC KIDNEY DISEASE-ASSOCIATED PROTEIN - Homo sapiens (Human).
Scan History
SPTR39_14f 2  30   NSINGLE    
Initial Motifs
Motif 1  width=22
Element Seqn Id St Int Rpt
YIVMLTCAVCLVTYMVMAAILH Q15140 3075 3075 -
YIVMLTCAVCLVTYMVMAAILH PKD1_HUMAN 3075 3075 -
YIVLLTCVICLVTYVVMAMILR O08852 3067 3067 -
LVVLLVCVLGLMSYVVAAAILH O42181 3206 3206 -

Motif 2 width=23
Element Seqn Id St Int Rpt
RATCCVLLICLFLGANAVWYGAV Q15140 3280 183 -
RATCCVLLICLFLGANAVWYGAV PKD1_HUMAN 3280 183 -
RVTCCVLLLCLFLAANAVWYGVV O08852 3272 183 -
RATCCALLLQLLLLANTLWYSIV O42181 3411 183 -

Motif 3 width=25
Element Seqn Id St Int Rpt
TVAVGLVSSVVVYPVYLAILFLFRM Q15140 3322 19 -
TVAVGLVSSVVVYPVYLAILFLFRM PKD1_HUMAN 3322 19 -
TVAIGLVSSVVVYPVYLAVLFLFRM O08852 3314 19 -
TVAVGVVTCLVAYPLYLLVFTLLRM O42181 3453 19 -

Motif 4 width=16
Element Seqn Id St Int Rpt
SLLLVAVAVAVSGWVG Q15140 3561 214 -
SLLLVAVAVAVSGWVG PKD1_HUMAN 3562 215 -
SLLLVAVAVAVSGWIG O08852 3552 213 -
SWTGIALASGVSMWAG O42181 3701 223 -

Motif 5 width=18
Element Seqn Id St Int Rpt
VSVAWLLSSSASFLASFL Q15140 3583 6 -
VSVAWLLSSSASFLASFL PKD1_HUMAN 3584 6 -
VSVMWLLSSSSSFLASFL O08852 3574 6 -
VAMLWLLSCFASFLCSCL O42181 3723 6 -

Motif 6 width=20
Element Seqn Id St Int Rpt
MLRSLLVYMLFLLVTLLASY Q15140 3669 68 -
MLRSLLVYMLFLLVTLLASY PKD1_HUMAN 3670 68 -
MLKRLLVYMLFLLVTLLANY O08852 3660 68 -
MLKNFLVYTFFLLVVLLLNY O42181 3809 68 -

Motif 7 width=19
Element Seqn Id St Int Rpt
GLSLPLLTSVCLLLFAVHF Q15140 3895 206 -
GLSLPLLTSVCLLLFAVHF PKD1_HUMAN 3896 206 -
GLSLPLLTSVCLLLFALYF O08852 3886 206 -
GLDLQLLLTIILLALVLYF O42181 4021 192 -

Motif 8 width=23
Element Seqn Id St Int Rpt
LAASLLFLLLVKAAQQLRFVRQW Q15140 3989 75 -
LAASLLFLLLVKAAQHVRFVRQW PKD1_HUMAN 3990 75 -
LAASLLFLLLVKAAQQLRFVRQW O08852 3980 75 -
ASALLLFVFVLKVSHQLRFLREW O42181 4115 75 -

Motif 9 width=22
Element Seqn Id St Int Rpt
LLGVTLGLVVLGVAYAQLAILL Q15140 4025 13 -
LLGVTLGLVVLGVAYAQLAILL PKD1_HUMAN 4026 13 -
LMGATLGLVLLGVAYAQMAILL O08852 4016 13 -
LLAVAFALLLLLLAYSHAGHLL O42181 4151 13 -

Motif 10 width=17
Element Seqn Id St Int Rpt
ALRLWGALRLGAVILRW Q15140 4091 44 -
ALRLWGALRLGAVILRW PKD1_HUMAN 4092 44 -
ALRVWGALRLGAILLRW O08852 4082 44 -
ILRLAFLWLVISVLLRN O42181 4225 52 -
Final Motifs
Motif 1  width=22
Element Seqn Id St Int Rpt
YIVMLTCAVCLVTYMVMAAILH Q15140 3075 3075 -
YIVMLTCAVCLVTYMVMAAILH Q15142 2411 2411 -
YIVMLTCAVCLVTYMVMAAILH Q15141 3065 3065 -
YIVMLTCAVCLVTYMVMAAILH PKD1_HUMAN 3075 3075 -
YIVLLTCVICLVTYVVMAMILR O08852 3067 3067 -
LVVLLVCVLGLMSYVVAAAILH O42181 3206 3206 -

Motif 2 width=23
Element Seqn Id St Int Rpt
RATCCVLLICLFLGANAVWYGAV Q15140 3280 183 -
RATCCVLLICLFLGANAVWYGAV Q15142 2616 183 -
RATCCVLLICLFLGANAVWYGAV Q15141 3270 183 -
RATCCVLLICLFLGANAVWYGAV PKD1_HUMAN 3280 183 -
RVTCCVLLLCLFLAANAVWYGVV O08852 3272 183 -
RATCCALLLQLLLLANTLWYSIV O42181 3411 183 -

Motif 3 width=25
Element Seqn Id St Int Rpt
TVAVGLVSSVVVYPVYLAILFLFRM Q15140 3322 19 -
TVAVGLVSSVVVYPVYLAILFLFRM Q15142 2658 19 -
TVAVGLVSSVVVYPVYLAILFLFRM Q15141 3312 19 -
TVAVGLVSSVVVYPVYLAILFLFRM PKD1_HUMAN 3322 19 -
TVAIGLVSSVVVYPVYLAVLFLFRM O08852 3314 19 -
TVAVGVVTCLVAYPLYLLVFTLLRM O42181 3453 19 -

Motif 4 width=16
Element Seqn Id St Int Rpt
SLLLVAVAVAVSGWVG Q15140 3561 214 -
SLLLVAVAVAVSGWVG Q15142 2897 214 -
SLLLVAVAVAVSGWVG Q15141 3551 214 -
SLLLVAVAVAVSGWVG PKD1_HUMAN 3562 215 -
SLLLVAVAVAVSGWIG O08852 3552 213 -
SWTGIALASGVSMWAG O42181 3701 223 -

Motif 5 width=18
Element Seqn Id St Int Rpt
VSVAWLLSSSASFLASFL Q15140 3583 6 -
VSVAWLLSSSASFLASFL Q15142 2919 6 -
VSVAWLLSSSASFLASFL Q15141 3573 6 -
VSVAWLLSSSASFLASFL PKD1_HUMAN 3584 6 -
VSVMWLLSSSSSFLASFL O08852 3574 6 -
VAMLWLLSCFASFLCSCL O42181 3723 6 -

Motif 6 width=20
Element Seqn Id St Int Rpt
MLRSLLVYMLFLLVTLLASY Q15140 3669 68 -
MLRSLLVYMLFLLVTLLASY Q15142 3005 68 -
MLRSLLVYMLFLLVTLLASY Q15141 3659 68 -
MLRSLLVYMLFLLVTLLASY PKD1_HUMAN 3670 68 -
MLKRLLVYMLFLLVTLLANY O08852 3660 68 -
MLKNFLVYTFFLLVVLLLNY O42181 3809 68 -

Motif 7 width=19
Element Seqn Id St Int Rpt
GLSLPLLTSVCLLLFAVHF Q15140 3895 206 -
GLSLPLLTSVCLLLFAVHF Q15142 3231 206 -
GLSLPLLTSVCLLLFAVHF Q15141 3885 206 -
GLSLPLLTSVCLLLFAVHF PKD1_HUMAN 3896 206 -
GLSLPLLTSVCLLLFALYF O08852 3886 206 -
GLDLQLLLTIILLALVLYF O42181 4021 192 -

Motif 8 width=23
Element Seqn Id St Int Rpt
LAASLLFLLLVKAAQQLRFVRQW Q15140 3989 75 -
LAASLLFLLLVKAAQQLRFVRQW Q15142 3325 75 -
LAASLLFLLLVKAAQQLRFVRQW Q15141 3979 75 -
LAASLLFLLLVKAAQHVRFVRQW PKD1_HUMAN 3990 75 -
LAASLLFLLLVKAAQQLRFVRQW O08852 3980 75 -
ASALLLFVFVLKVSHQLRFLREW O42181 4115 75 -

Motif 9 width=22
Element Seqn Id St Int Rpt
LLGVTLGLVVLGVAYAQLAILL Q15140 4025 13 -
LLGVTLGLVVLGVAYAQLAILL Q15142 3361 13 -
LLGVTLGLVVLGVAYAQLAILL Q15141 4015 13 -
LLGVTLGLVVLGVAYAQLAILL PKD1_HUMAN 4026 13 -
LMGATLGLVLLGVAYAQMAILL O08852 4016 13 -
LLAVAFALLLLLLAYSHAGHLL O42181 4151 13 -

Motif 10 width=17
Element Seqn Id St Int Rpt
ALRLWGALRLGAVILRW Q15140 4091 44 -
ALRLWGALRLGAVILRW Q15142 3427 44 -
ALRLWGALRLGAVILRW Q15141 4081 44 -
ALRLWGALRLGAVILRW PKD1_HUMAN 4092 44 -
ALRVWGALRLGAILLRW O08852 4082 44 -
ILRLAFLWLVISVLLRN O42181 4225 52 -