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• W2065881793 abstract "Autosomal dominant polycystic kidney disease (ADPKD) has a prevalence of 1 in 800 of the world's population and accounts for 10% of individuals who require renal replacement therapy, either dialysis or transplantation. Renal cyst formation occurs as part of a ‘two-hit’ process in which inactivation of both alleles of ADPKD genes leads to abnormalities of cell proliferation, apoptosis and differentiation [[1]Qian F Watnick T Onuchic L Germino G The molecular basis of focal cyst formation in human autosomal dominant polycystic kidney disease type I.Cell. 1996; 87: 979-987Abstract Full Text Full Text PDF PubMed Scopus (461) Google Scholar]. Of ADPKD cases, 85% are due to mutations in the PKD1 gene, which encodes a 4,302 amino acid protein, polycystin-1 (PKD1), of unknown function. Comparison of the PKD1 sequence with homologous sequences from mouse and Fugu predicts polycystin-1 to have a large extracellular region of 3,000 amino acid residues, a region containing 11 putative transmembrane segments and a short intracellular tail [[2]Sandford R Sgotto B Aparicio S Brenner S Vaudin M Wilson RK Chissoe S Bateman A Chothia C Hughes J et al.Comparative analysis of the polycystic kidney disease 1 (PKD1) gene reveals an integral membrane glycoprotein with multiple evolutionary conserved domains.Proc Natl Acad Sci USA. 1997; 6: 1483-1489Google Scholar]. A well-defined extracellular domain structure is apparent; the presence of amino-terminal leucine-rich repeats, a C-type-lectin domain and multiple PKD repeats suggests a role in cell–cell or cell–matrix interactions (Figure 1) [[3]Hughes J Ward CJ Peral B Aspinwall R Clark K San Millan JL Gamble V Harris PC The polycystic kidney disease 1 (PKD1) gene encodes a novel protein with multiple cell recognition domains.Nat Genet. 1995; 10: 151-160Crossref PubMed Scopus (728) Google Scholar]. So far, no extracellular ligands of polycystin-1 have been identified. Of the intracellular regions of PKD1, functional properties have been defined only for the short 198 amino acid carboxy-terminal region, which contains a predicted coiled-coil domain. These include a direct interaction with the carboxyl terminus of the protein encoded by PKD2, polycystin-2 [[4]Qian F Germino F Cai Y Zhang X Somlo S Germino G PKD1 interacts with PKD2 through a probable coiled-coil domain.Nat Genet. 1997; 16: 179-183Crossref PubMed Scopus (536) Google Scholar], activation of transcription factor AP-1 [[5]Arnould T Kim E Tsiokas L Jochimsen F Gruning W Chang J Walz G The polycystic kidney disease 1 gene product mediates protein kinase C alpha-dependent and c-Jun N-terminal kinase-dependent activation of the transcription factor AP-1.J Biol Chem. 1998; 273: 6013-6018Crossref PubMed Scopus (147) Google Scholar] and activation of heterotrimeric G proteins [[6]Parnell S Magenheimer B Maser R Rankin C Smine A Okamoto T Calvet J The polycystic kidney disease-1 protein, polycystin-1, binds and activates heterotrimeric G-proteins in vitro.Biochem Biophys Res Commun. 1998; 251: 625-631Crossref PubMed Scopus (185) Google Scholar]. The last of these occurs via a motif present in one of polycystin-1's most highly conserved regions. Polycystin-1 may therefore act as a cell-surface receptor or form part of a large membrane-associated complex that is capable of signaling by several different pathways to control cell proliferation and differentiation. To further aid the understanding of this enigmatic protein, we have surveyed all the intracellular regions for potential domains that may suggest novel functions and identify further avenues for experiment. The current model of polycystin-1 topology suggests that there are four intracellular regions that are large enough to contain a discrete protein domain. These regions are between transmembrane (TM) helices TM1 and TM2 (residues, 3,096–3,280), TM3 and TM4 (residues 3,344–3,558), TM5 and TM6 (residues 3,603–3,668) and the carboxy-terminal region after TM11 (residues 4,105–4,302). The high sequence conservation seen in these regions between the human and Fugu polycystin-1 suggest that they are functionally important. We have used each of these regions as a query for the sequence comparison program PSI-BLAST, using an expectation-value (E-value) threshold of 0.001 [[7]Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.Nucleic Acids Res. 1997; 25: 3389-3402Crossref PubMed Scopus (56917) Google Scholar]. For each of the four intracellular regions, PSI-BLAST returned the known PKD1 orthologues from human, mouse and Fugu. Only one region returned significant matches with PSI-BLAST. The first intracellular region between TM1 and TM2, which represents the most strongly conserved sequence region of PKD1 between human and Fugu[[2]Sandford R Sgotto B Aparicio S Brenner S Vaudin M Wilson RK Chissoe S Bateman A Chothia C Hughes J et al.Comparative analysis of the polycystic kidney disease 1 (PKD1) gene reveals an integral membrane glycoprotein with multiple evolutionary conserved domains.Proc Natl Acad Sci USA. 1997; 6: 1483-1489Google Scholar], was found to match to 67 other sequences in SWISS-PROT version 37 and TrEMBL version 9 [[8]Bairoch A Apweiler R The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999.Nucleic Acids Res. 1999; 27: 49-54Crossref PubMed Scopus (437) Google Scholar]. These sequences include mammalian lipoxygenases, triacylglycerol lipase and lipoprotein lipase. The common feature found in all these alignments was topological and sequence similarity to a β-sandwich domain. We call this new protein domain the PLAT domain (after polycystin-1, lipoxygenase and alpha toxin). The copy of the PLAT domain found in polycystin-1 therefore identifies an important new region of the protein. The three-dimensional structure of the PLAT domain is known for human pancreatic lipase [[9]van Tilbeurgh H Egloff MP Martinez C Rugani N Verger R Cambillau C Interfacial activation of the lipase-procolipase complex by mixed micelles revealed by X-ray crystallography.Nature. 1993; 362: 814-820Crossref PubMed Scopus (612) Google Scholar], rabbit 15-lipoxygenase [[10]Gillmor SA Villasenor A Fletterick R Sigal E Browner MF The structure of mammalian 15-lipoxygenase reveals similarity to the lipases and the determinants of substrate specificity.Nat Struct Biol. 1998; 4: 1003-1009Crossref Scopus (378) Google Scholar] and alpha toxin from Clostridium perfringens[[11]Naylor CE Eaton JT Howells A Justin N Moss DS Titball RW Basak AK Structure of the key toxin in gas gangrene.Nat Struct Biol. 1998; 5: 738-746Crossref PubMed Scopus (153) Google Scholar]. The domain is a β-sandwich composed of two sheets of four strands each. The sequence relationship of the alpha toxin to polycystin-1 can be demonstrated by using the sequence of the PLAT domain from the known structure as a query for PSI-BLAST. The search essentially converges to the same family, including the polycystin-1 PLAT domain. Soybean lipoxygenase L-1 [[12]Minor W Steczko J Stec B Otwinowski Z Bolin JT Walter R Axelrod B Crystal structure of soybean lipoxygenase L-1 at 1.4 å resolution.Biochem. 1996; 35: 10687-10701Crossref PubMed Scopus (384) Google Scholar] contains a domain structurally related to the PLAT domains. It is more distant in sequence to the rest of the family; PSI-BLAST is able to find relationships to the rest of the family for only a few sequences. Although structural similarities were noticed between these structures, it was not suggested that they share a common ancestor [[11]Naylor CE Eaton JT Howells A Justin N Moss DS Titball RW Basak AK Structure of the key toxin in gas gangrene.Nat Struct Biol. 1998; 5: 738-746Crossref PubMed Scopus (153) Google Scholar]. The most highly conserved regions in the alignment of known PLAT domains (Figure 2) coincide with the β-strands. Most of the highly conserved residues are buried residues. An exception to this is a surface lysine or arginine that occurs on the surface of the fifth β-strand of all the eukaryotic PLAT domains. In pancreatic lipase, the lysine in this position forms a salt bridge with the procolipase protein. The conservation of a charged surface residue may indicate the location of a conserved ligand-binding site within the PLAT domain. The importance of PLAT domains is underlined by mutations that lead to human disease. Mutations in lipoprotein lipase lead to chylomicronaemia and mutations in triacylglycerol lipase lead to hepatic lipase deficiency [[13]Hegele R Tu L Connelly P Human hepatic lipase mutations and polymorphisms.Hum Mutat. 1992; 1: 320-324Crossref PubMed Scopus (36) Google Scholar]. In pancreatic lipase the PLAT domain is involved in binding to the procolipase protein. This interaction is required to bring the enzymatic active site of the lipase into close contact with its lipid substrate. In 15-lipoxygenase, a protein composed of an amino-terminal β-sandwich (PLAT) and a carboxy-terminal catalytic domain, the PLAT domain may function to localise the enzyme near its membrane or lipoprotein sequestered substrates, by analogy to the lipase–procolipase protein–protein interaction. It is also possible that the PLAT domain of 5-lipoxygenase, another member of the mammalian lipoxygenase family, mediates an interaction with the 5-lipoxygenase activating protein (FLAP), an integral membrane protein. For alpha toxin and plant lipoxygenases, it has been suggested that the PLAT domain interacts directly with the membrane in a Ca2+ dependent manner. Although a Ca2+-binding region has been predicted for alpha toxin from crystallographic data and similarity to eukaryotic calcium-binding C2 domains [[11]Naylor CE Eaton JT Howells A Justin N Moss DS Titball RW Basak AK Structure of the key toxin in gas gangrene.Nat Struct Biol. 1998; 5: 738-746Crossref PubMed Scopus (153) Google Scholar], the conserved residues that form this region are not present in the PLAT domains identified in polycystin-1 or pancreatic lipase. PLAT domains may therefore be involved in protein–protein and protein–lipid interactions. The presence of the PLAT domain in the first cytoplasmic loop of polycystin-1 suggests that this region is important in mediating interactions with other membrane protein(s) involved in polycystin-1 function. A Bateman, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK. R Sandford, Cambridge Institute for Medical Research, Addenbrooke’s Hospital, Cambridge CB2 2XY, UK. E-mail: [email protected]" @default.
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• W2065881793 title "The PLAT domain: a new piece in the PKD1 puzzle" @default.
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