PKD

Repeats in polycystic kidney disease 1 (PKD1) and other proteins

• SMART accession number: SM00089
• Description: Polycystic kidney disease 1 protein contains 14 repeats, present elsewhere such as in microbial collagenases.
• Interpro abstract (IPR000601):

  The PKD domain was first identified in the Polycystic kidney disease protein, polycystin-1 (PDK1 gene), and contains an Ig-like fold consisting of a beta-sandwich of seven strands in two sheets with a Greek key topology, although some members have additional strands (PUBMED:9889186). Polycystin-1 is a large cell-surface glycoprotein involved in adhesive protein-protein and protein-carbohydrate interactions; however it is not clear if the PKD domain mediates any of these interactions.

  PKD domains are also found in other proteins, usually in the extracellular parts of proteins involved in interactions with other proteins. For example, domains with a PKD-type fold are found in archaeal surface layer proteins that protect the cell from extreme environments (PUBMED:12377130), and in the human VPS10 domain-containing receptor SorCS2 (PUBMED:11499680).

There are 3449 PKD domains in 1368 proteins in SMART's nrdb database.

Literature (relevant references for this domain)

Primary literature is listed below; Automatically-derived, secondary literature is also avaliable.

• Bateman A, Sandford R
• The PLAT domain: a new piece in the PKD1 puzzle.
• Curr Biol. 1999; 9: 58890-58890

• Sandford R et al.
• Comparative analysis of the polycystic kidney disease 1 (PKD1) gene reveals an integral membrane glycoprotein with multiple evolutionary conserved domains.
• Hum Mol Genet. 1997; 6: 1483-9

PKD1 is the major locus of the common genetic disorder autosomal dominant polycystic kidney disease (ADPKD). Analysis of the predicted protein sequence of the human PKD1 gene, polycystin, shows a large molecule with a unique arrangement of extracellular domains and multiple putative transmembrane regions. The precise function of polycystin remains unclear with a paucity of mutations to define key structural and functional domains. To refine the structure of this protein we have cloned the genomic region encoding the Fugu PKD1 gene. Fugu PKD1 spans 36 kb of genomic DNA and has greater complexity with 54 exons compared with 46 in man. Comparative analysis of the predicted protein sequences shows a lower level of homology than in similar studies with identity of 40 and 59% similarity. However key structural motifs including leucine rich repeats (LRR), a C-type lectin and LDL-A like domains and 16 PKD repeats are maintained. A region of homology with the sea urchin REJ protein was also confirmed in Fugu but found to extend over 1000 amino acids. Several highly conserved intra- and extra-cellular regions, with no known sequence homologies, that are likely to be of functional importance were detected. The likely structure of the membrane associated region has been refined with similarity to the PKD2 protein and voltage gated Ca2+ and Na+ channels highlighted over part of this area. The overall protein structure has therefore been clarified and this comparative analysis derived structure will form the basis for the functional study of polycystin and its individual domains.

• Burn TC et al.
• Analysis of the genomic sequence for the autosomal dominant polycystic kidney disease (PKD1) gene predicts the presence of a leucine-rich repeat. The American PKD1 Consortium (APKD1 Consortium).
• Hum Mol Genet. 1995; 4: 575-82

The complete genomic sequence of the gene responsible for the predominant form of polycystic kidney disease, PKD1, was determined to provide a framework for understanding the biology and evolution of the gene, and to aid in the development of molecular diagnostics. The DNA sequence of a 54 kb interval immediately upstream of the poly(A) addition signal sequence of the PKD1 transcript was determined, and then analyzed using computer methods. A leucine-rich repeat (LRR) motif was identified within the resulting predicted protein sequence of the PKD1 gene. By analogy with other LRR-containing proteins, this may explain some of the disease-related renal alterations such as mislocalization of membrane protein constituents and changes in the extracellular matrix organization. Finally, comparison of the genomic sequence and the published partial cDNA sequence showed several differences between the two sequences. The most significant difference detected predicts a novel carboxy-terminus for the PKD1 gene product.

• Hughes J et al.
• The polycystic kidney disease 1 (PKD1) gene encodes a novel protein with multiple cell recognition domains.
• Nat Genet. 1995; 10: 151-60

Characterization of the polycystic kidney disease 1 (PKD1) gene has been complicated by genomic rearrangements on chromosome 16. We have used an exon linking strategy, taking RNA from a cell line containing PKD1 but not the duplicate loci, to clone a cDNA contig of the entire transcript. The transcript consists of 14,148 bp (including a correction to the previously described C terminus), distributed among 46 exons spanning 52 kb. The predicted PKD1 protein, polycystin, is a glycoprotein with multiple transmembrane domains and a cytoplasmic C-tail. The N-terminal extracellular region of over 2,500 aa contains leucine-rich repeats, a C-type lectin, 16 immunoglobulin-like repeats and four type III fibronectin-related domains. Our results indicate that polycystin is an integral membrane protein involved in cell-cell/matrix interactions.

Metabolism (metabolic pathways involving proteins which contain this domain)

% proteins involved	KEGG pathway ID	Description
72.97	map00530	Aminosugars metabolism
5.41	map00500	Starch and sucrose metabolism
2.70	map00511	N-Glycan degradation
2.70	map00780	Biotin metabolism
2.70	map00860	Porphyrin and chlorophyll metabolism
2.70	map00310	Lysine degradation
2.70	map00561	Glycerolipid metabolism
2.70	map00051	Fructose and mannose metabolism
2.70	map02010	ABC transporters - General
2.70	map01032	Glycan structures - degradation

This information is based on mapping of SMART genomic protein database to KEGG orthologous groups. Percentage points are related to the number of proteins with PKD domain which could be assigned to a KEGG orthologous group, and not all proteins containing PKD domain. Please note that proteins can be included in multiple pathways, ie. the numbers above will not always add up to 100%.

Structure (3D structures containing this domain)

3D Structures of PKD domains in PDB

PDB code	Title
1b4r	Pkd domain 1 from human polycystein-1
1ctn	Crystal structure of a bacterial chitinase at 2.3 angstroms resolution
1edq	Crystal structure of chitinase a from s. marcescens at 1.55 angstroms
1ehn	Crystal structure of chitinase a mutant e315q complexed with octa-n-acetylchitooctaose (nag)8.
1eib	Crystal structure of chitinase a mutant d313a complexed with octa-n-acetylchitooctaose (nag)8.
1ffq	Crystal structure of chitinase a complexed with allosamidin
1ffr	Crystal structure of chitinase a mutant y390f complexed with hexa-n-acetylchitohexaose (nag)6
1k9t	Chitinase a complexed with tetra-n-acetylchitotriose
1l0q	Tandem yvtn beta-propeller and pkd domains from an archaeal surface layer protein
1nh6	Structure of s. marcescens chitinase a, e315l, complex with hexasaccharide
1rd6	Crystal structure of s. marcescens chitinase a mutant w167a
1wgo	Solution structure of the pkd domain from human vps10 domain-containing receptor sorcs2
1x6l	Crystal structure of s. marcescens chitinase a mutant w167a
1x6n	Crystal structure of s. marcescens chitinase a mutant w167a in complex with allosamidin
2c26	Structural basis for the promiscuous specificity of the carbohydrate-binding modules from the beta-sandwich super family
2c4x	Structural basis for the promiscuous specificity of the carbohydrate-binding modules from the beta-sandwich super family
2yrl	Solution structure of the pkd domain from kiaa 1837 protein
3b8s	Crystal structure of wild-type chitinase a from vibrio harveyi
3b9a	Crystal structure of vibrio harveyi chitinase a complexed with hexasaccharide
3b9d	Crystal structure of vibrio harveyi chitinase a complexed with pentasaccharide
3b9e	Crystal structure of inactive mutant e315m chitinase a from vibrio harveyi

Links (links to other resources describing this domain)

• PFAM: PKD
• INTERPRO: IPR000601