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==PKD DOMAIN 1 FROM HUMAN POLYCYSTEIN-1==
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<StructureSection load='1b4r' size='340' side='right'caption='[[1b4r]]' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1b4r]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1B4R FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
-->
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1b4r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1b4r OCA], [https://pdbe.org/1b4r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1b4r RCSB], [https://www.ebi.ac.uk/pdbsum/1b4r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1b4r ProSAT]</span></td></tr>
{{STRUCTURE_1b4r| PDB=1b4r  | SCENE= }}
</table>
 
== Disease ==
'''PKD DOMAIN 1 FROM HUMAN POLYCYSTEIN-1'''
[https://www.uniprot.org/uniprot/PKD1_HUMAN PKD1_HUMAN] Defects in PKD1 are the cause of polycystic kidney disease 1 (PKD1) [MIM:[https://omim.org/entry/173900 173900]. PKD1 is characterized by progressive formation and enlargement of cysts in both kidneys, typically leading to end-stage renal disease in adult life. Cysts also occurs in the liver and other organs. Its prevalence is estimated at about 1/1000.<ref>PMID:12482949</ref> <ref>PMID:8554072</ref> <ref>PMID:9199561</ref> <ref>PMID:9285784</ref> <ref>PMID:9259200</ref> <ref>PMID:9521593</ref> <ref>PMID:9921908</ref> <ref>PMID:10364515</ref> <ref>PMID:10577909</ref> <ref>PMID:10987650</ref> <ref>PMID:10647901</ref> <ref>PMID:10200984</ref> <ref>PMID:10854095</ref> <ref>PMID:11216660</ref> <ref>PMID:10923040</ref> <ref>PMID:11058904</ref> <ref>PMID:11012875</ref> <ref>PMID:10729710</ref> <ref>PMID:11115377</ref> <ref>PMID:11571556</ref> <ref>PMID:11316854</ref> <ref>PMID:11558899</ref> <ref>PMID:11691639</ref> <ref>PMID:12220456</ref> <ref>PMID:11857740</ref> <ref>PMID:12007219</ref> <ref>PMID:12070253</ref> <ref>PMID:11967008</ref> <ref>PMID:11773467</ref> <ref>PMID:12842373</ref> <ref>PMID:15772804</ref> <ref>PMID:18837007</ref> <ref>PMID:21115670</ref> <ref>PMID:22508176</ref>
 
== Function ==
 
[https://www.uniprot.org/uniprot/PKD1_HUMAN PKD1_HUMAN] Involved in renal tubulogenesis. Involved in fluid-flow mechanosensation by the primary cilium in renal epithelium (By similarity). Acts as a regulator of cilium length, together with PKD2 (By similarity). The dynamic control of cilium length is essential in the regulation of mechanotransductive signaling. The cilium length response creates a negative feedback loop whereby fluid shear-mediated deflection of the primary cilium, which decreases intracellular cAMP, leads to cilium shortening and thus decreases flow-induced signaling (By similarity). May be an ion-channel regulator. Involved in adhesive protein-protein and protein-carbohydrate interactions.<ref>PMID:12482949</ref>  
==Overview==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b4/1b4r_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1b4r ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Most cases of autosomal dominant polycystic kidney disease (ADPKD) are the result of mutations in the PKD1 gene. The PKD1 gene codes for a large cell-surface glycoprotein, polycystin-1, of unknown function, which, based on its predicted domain structure, may be involved in protein-protein and protein-carbohydrate interactions. Approximately 30% of polycystin-1 consists of 16 copies of a novel protein module called the PKD domain. Here we show that this domain has a beta-sandwich fold. Although this fold is common to a number of cell-surface modules, the PKD domain represents a distinct protein family. The tenth PKD domain of human and Fugu polycystin-1 show extensive conservation of surface residues suggesting that this region could be a ligand-binding site. This structure will allow the likely effects of missense mutations in a large part of the PKD1 gene to be determined.
Most cases of autosomal dominant polycystic kidney disease (ADPKD) are the result of mutations in the PKD1 gene. The PKD1 gene codes for a large cell-surface glycoprotein, polycystin-1, of unknown function, which, based on its predicted domain structure, may be involved in protein-protein and protein-carbohydrate interactions. Approximately 30% of polycystin-1 consists of 16 copies of a novel protein module called the PKD domain. Here we show that this domain has a beta-sandwich fold. Although this fold is common to a number of cell-surface modules, the PKD domain represents a distinct protein family. The tenth PKD domain of human and Fugu polycystin-1 show extensive conservation of surface residues suggesting that this region could be a ligand-binding site. This structure will allow the likely effects of missense mutations in a large part of the PKD1 gene to be determined.


==About this Structure==
The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease.,Bycroft M, Bateman A, Clarke J, Hamill SJ, Sandford R, Thomas RL, Chothia C EMBO J. 1999 Jan 15;18(2):297-305. PMID:9889186<ref>PMID:9889186</ref>
1B4R is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1B4R OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease., Bycroft M, Bateman A, Clarke J, Hamill SJ, Sandford R, Thomas RL, Chothia C, EMBO J. 1999 Jan 15;18(2):297-305. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9889186 9889186]
</div>
<div class="pdbe-citations 1b4r" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Bycroft, M.]]
[[Category: Bycroft M]]
[[Category: Membrane protein]]
[[Category: Pkd domain 1 from human polycystein-1]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 11:04:14 2008''

Latest revision as of 11:16, 22 May 2024

PKD DOMAIN 1 FROM HUMAN POLYCYSTEIN-1PKD DOMAIN 1 FROM HUMAN POLYCYSTEIN-1

Structural highlights

1b4r is a 1 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Solution NMR
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

PKD1_HUMAN Defects in PKD1 are the cause of polycystic kidney disease 1 (PKD1) [MIM:173900. PKD1 is characterized by progressive formation and enlargement of cysts in both kidneys, typically leading to end-stage renal disease in adult life. Cysts also occurs in the liver and other organs. Its prevalence is estimated at about 1/1000.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34]

Function

PKD1_HUMAN Involved in renal tubulogenesis. Involved in fluid-flow mechanosensation by the primary cilium in renal epithelium (By similarity). Acts as a regulator of cilium length, together with PKD2 (By similarity). The dynamic control of cilium length is essential in the regulation of mechanotransductive signaling. The cilium length response creates a negative feedback loop whereby fluid shear-mediated deflection of the primary cilium, which decreases intracellular cAMP, leads to cilium shortening and thus decreases flow-induced signaling (By similarity). May be an ion-channel regulator. Involved in adhesive protein-protein and protein-carbohydrate interactions.[35]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Most cases of autosomal dominant polycystic kidney disease (ADPKD) are the result of mutations in the PKD1 gene. The PKD1 gene codes for a large cell-surface glycoprotein, polycystin-1, of unknown function, which, based on its predicted domain structure, may be involved in protein-protein and protein-carbohydrate interactions. Approximately 30% of polycystin-1 consists of 16 copies of a novel protein module called the PKD domain. Here we show that this domain has a beta-sandwich fold. Although this fold is common to a number of cell-surface modules, the PKD domain represents a distinct protein family. The tenth PKD domain of human and Fugu polycystin-1 show extensive conservation of surface residues suggesting that this region could be a ligand-binding site. This structure will allow the likely effects of missense mutations in a large part of the PKD1 gene to be determined.

The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease.,Bycroft M, Bateman A, Clarke J, Hamill SJ, Sandford R, Thomas RL, Chothia C EMBO J. 1999 Jan 15;18(2):297-305. PMID:9889186[36]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

  1. ↑ Qian F, Boletta A, Bhunia AK, Xu H, Liu L, Ahrabi AK, Watnick TJ, Zhou F, Germino GG. Cleavage of polycystin-1 requires the receptor for egg jelly domain and is disrupted by human autosomal-dominant polycystic kidney disease 1-associated mutations. Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16981-6. Epub 2002 Dec 13. PMID:12482949 doi:10.1073/pnas.252484899
  2. ↑ Peral B, San Millan JL, Ong AC, Gamble V, Ward CJ, Strong C, Harris PC. Screening the 3' region of the polycystic kidney disease 1 (PKD1) gene reveals six novel mutations. Am J Hum Genet. 1996 Jan;58(1):86-96. PMID:8554072
  3. ↑ Peral B, Gamble V, Strong C, Ong AC, Sloane-Stanley J, Zerres K, Winearls CG, Harris PC. Identification of mutations in the duplicated region of the polycystic kidney disease 1 gene (PKD1) by a novel approach. Am J Hum Genet. 1997 Jun;60(6):1399-410. PMID:9199561 doi:10.1086/515467
  4. ↑ Watnick TJ, Piontek KB, Cordal TM, Weber H, Gandolph MA, Qian F, Lens XM, Neumann HP, Germino GG. An unusual pattern of mutation in the duplicated portion of PKD1 is revealed by use of a novel strategy for mutation detection. Hum Mol Genet. 1997 Sep;6(9):1473-81. PMID:9285784
  5. ↑ Turco AE, Rossetti S, Bresin E, Englisch S, Corra S, Pignatti PF. Three novel mutations of the PKD1 gene in Italian families with autosomal dominant polycystic kidney disease. Hum Mutat. 1997;10(2):164-7. PMID:9259200 doi:<164::AID-HUMU9>3.0.CO;2-K 10.1002/(SICI)1098-1004(1997)10:2<164::AID-HUMU9>3.0.CO;2-K
  6. ↑ Daniells C, Maheshwar M, Lazarou L, Davies F, Coles G, Ravine D. Novel and recurrent mutations in the PKD1 (polycystic kidney disease) gene. Hum Genet. 1998 Feb;102(2):216-20. PMID:9521593
  7. ↑ Koptides M, Constantinides R, Kyriakides G, Hadjigavriel M, Patsalis PC, Pierides A, Deltas CC. Loss of heterozygosity in polycystic kidney disease with a missense mutation in the repeated region of PKD1. Hum Genet. 1998 Dec;103(6):709-17. PMID:9921908
  8. ↑ Thomas R, McConnell R, Whittacker J, Kirkpatrick P, Bradley J, Sandford R. Identification of mutations in the repeated part of the autosomal dominant polycystic kidney disease type 1 gene, PKD1, by long-range PCR. Am J Hum Genet. 1999 Jul;65(1):39-49. PMID:10364515 doi:10.1086/302460
  9. ↑ Watnick T, Phakdeekitcharoen B, Johnson A, Gandolph M, Wang M, Briefel G, Klinger KW, Kimberling W, Gabow P, Germino GG. Mutation detection of PKD1 identifies a novel mutation common to three families with aneurysms and/or very-early-onset disease. Am J Hum Genet. 1999 Dec;65(6):1561-71. PMID:10577909 doi:S0002-9297(07)63575-7
  10. ↑ Perrichot RA, Mercier B, Simon PM, Whebe B, Cledes J, Ferec C. DGGE screening of PKD1 gene reveals novel mutations in a large cohort of 146 unrelated patients. Hum Genet. 1999 Sep;105(3):231-9. PMID:10987650
  11. ↑ Afzal AR, Hand M, Ternes-Pereira E, Saggar-Malik A, Taylor R, Jeffery S. Novel mutations in the 3 region of the polycystic kidney disease 1 (PKD1) gene. Hum Genet. 1999 Dec;105(6):648-53. PMID:10647901
  12. ↑ Badenas C, Torra R, San Millan JL, Lucero L, Mila M, Estivill X, Darnell A. Mutational analysis within the 3' region of the PKD1 gene. Kidney Int. 1999 Apr;55(4):1225-33. PMID:10200984 doi:10.1046/j.1523-1755.1999.00368.x
  13. ↑ Perrichot R, Mercier B, Quere I, Carre A, Simon P, Whebe B, Cledes J, Ferec C. Novel mutations in the duplicated region of PKD1 gene. Eur J Hum Genet. 2000 May;8(5):353-9. PMID:10854095 doi:10.1038/sj.ejhg.5200459
  14. ↑ Afzal AR, Florencio RN, Taylor R, Patton MA, Saggar-Malik A, Jeffery S. Novel mutations in the duplicated region of the polycystic kidney disease 1 (PKD1) gene provides supporting evidence for gene conversion. Genet Test. 2000;4(4):365-70. PMID:11216660 doi:10.1089/109065700750065108
  15. ↑ Koptides M, Mean R, Demetriou K, Constantinides R, Pierides A, Harris PC, Deltas CC. Screening of the PKD1 duplicated region reveals multiple single nucleotide polymorphisms and a de novo mutation in Hellenic polycystic kidney disease families. Hum Mutat. 2000 Aug;16(2):176. PMID:10923040 doi:<176::AID-HUMU11>3.0.CO;2-H 10.1002/1098-1004(200008)16:2<176::AID-HUMU11>3.0.CO;2-H
  16. ↑ Aguiari G, Savelli S, Garbo M, Bozza A, Augello G, Penolazzi L, De Paoli Vitali E, La Torre C, Cappelli G, Piva R, del Senno L. Novel splicing and missense mutations in autosomal dominant polycystic kidney disease 1 (PKD1) gene: expression of mutated genes. Hum Mutat. 2000 Nov;16(5):444-5. PMID:11058904 doi:<444::AID-HUMU11>3.0.CO;2-C 10.1002/1098-1004(200011)16:5<444::AID-HUMU11>3.0.CO;2-C
  17. ↑ Phakdeekitcharoen B, Watnick TJ, Ahn C, Whang DY, Burkhart B, Germino GG. Thirteen novel mutations of the replicated region of PKD1 in an Asian population. Kidney Int. 2000 Oct;58(4):1400-12. PMID:11012875 doi:kid302
  18. ↑ Kim UK, Jin DK, Ahn C, Shin JH, Lee KB, Kim SH, Chae JJ, Hwang DY, Lee JG, Namkoong Y, Lee CC. Novel mutations of the PKD1 gene in Korean patients with autosomal dominant polycystic kidney disease. Mutat Res. 2000 Feb;432(1-2):39-45. PMID:10729710
  19. ↑ Rossetti S, Strmecki L, Gamble V, Burton S, Sneddon V, Peral B, Roy S, Bakkaloglu A, Komel R, Winearls CG, Harris PC. Mutation analysis of the entire PKD1 gene: genetic and diagnostic implications. Am J Hum Genet. 2001 Jan;68(1):46-63. Epub 2000 Dec 12. PMID:11115377 doi:S0002-9297(07)62471-9
  20. ↑ Bouba I, Koptides M, Mean R, Costi CE, Demetriou K, Georgiou I, Pierides A, Siamopoulos K, Deltas CC. Novel PKD1 deletions and missense variants in a cohort of Hellenic polycystic kidney disease families. Eur J Hum Genet. 2001 Sep;9(9):677-84. PMID:11571556 doi:10.1038/sj.ejhg.5200696
  21. ↑ Phakdeekitcharoen B, Watnick TJ, Germino GG. Mutation analysis of the entire replicated portion of PKD1 using genomic DNA samples. J Am Soc Nephrol. 2001 May;12(5):955-63. PMID:11316854
  22. ↑ Mizoguchi M, Tamura T, Yamaki A, Higashihara E, Shimizu Y. Mutations of the PKD1 gene among Japanese autosomal dominant polycystic kidney disease patients, including one heterozygous mutation identified in members of the same family. J Hum Genet. 2001;46(9):511-7. PMID:11558899 doi:10.1007/s100380170032
  23. ↑ Tsuchiya K, Komeda M, Takahashi M, Yamashita N, Cigira M, Suzuki T, Suzuki K, Nihei H, Mochizuki T. Mutational analysis within the 3' region of the PKD1 gene in Japanese families. Mutat Res. 2001 Dec;458(3-4):77-84. PMID:11691639
  24. ↑ Eo HS, Lee JG, Ahn C, Cho JT, Hwang DY, Hwang YH, Lee EJ, Kim YS, Han JS, Kim S, Lee JS, Jeoung DI, Lee SE, Kim UK. Three novel mutations of the PKD1 gene in Korean patients with autosomal dominant polycystic kidney disease. Clin Genet. 2002 Aug;62(2):169-74. PMID:12220456
  25. ↑ McCluskey M, Schiavello T, Hunter M, Hantke J, Angelicheva D, Bogdanova N, Markoff A, Thomas M, Dworniczak B, Horst J, Kalaydjieva L. Mutation detection in the duplicated region of the polycystic kidney disease 1 (PKD1) gene in PKD1-linked Australian families. Hum Mutat. 2002 Mar;19(3):240-50. PMID:11857740 doi:10.1002/humu.10045
  26. ↑ Inoue S, Inoue K, Utsunomiya M, Nozaki J, Yamada Y, Iwasa T, Mori E, Yoshinaga T, Koizumi A. Mutation analysis in PKD1 of Japanese autosomal dominant polycystic kidney disease patients. Hum Mutat. 2002 Jun;19(6):622-8. PMID:12007219 doi:10.1002/humu.10080
  27. ↑ Burtey S, Lossi AM, Bayle J, Berland Y, Fontes M. Mutation screening of the PKD1 transcript by RT-PCR. J Med Genet. 2002 Jun;39(6):422-9. PMID:12070253
  28. ↑ Rossetti S, Chauveau D, Walker D, Saggar-Malik A, Winearls CG, Torres VE, Harris PC. A complete mutation screen of the ADPKD genes by DHPLC. Kidney Int. 2002 May;61(5):1588-99. PMID:11967008 doi:10.1046/j.1523-1755.2002.00326.x
  29. ↑ Ding L, Zhang S, Qiu W, Xiao C, Wu S, Zhang G, Cheng L, Zhang S. Novel mutations of PKD1 gene in Chinese patients with autosomal dominant polycystic kidney disease. Nephrol Dial Transplant. 2002 Jan;17(1):75-80. PMID:11773467
  30. ↑ Rossetti S, Chauveau D, Kubly V, Slezak JM, Saggar-Malik AK, Pei Y, Ong AC, Stewart F, Watson ML, Bergstralh EJ, Winearls CG, Torres VE, Harris PC. Association of mutation position in polycystic kidney disease 1 (PKD1) gene and development of a vascular phenotype. Lancet. 2003 Jun 28;361(9376):2196-201. PMID:12842373 doi:10.1016/S0140-6736(03)13773-7
  31. ↑ Peltola P, Lumiaho A, Miettinen R, Pihlajamaki J, Sandford R, Laakso M. Genetics and phenotypic characteristics of autosomal dominant polycystic kidney disease in Finns. J Mol Med (Berl). 2005 Aug;83(8):638-46. Epub 2005 Mar 17. PMID:15772804 doi:10.1007/s00109-005-0644-6
  32. ↑ Tan YC, Blumenfeld JD, Anghel R, Donahue S, Belenkaya R, Balina M, Parker T, Levine D, Leonard DG, Rennert H. Novel method for genomic analysis of PKD1 and PKD2 mutations in autosomal dominant polycystic kidney disease. Hum Mutat. 2009 Feb;30(2):264-73. doi: 10.1002/humu.20842. PMID:18837007 doi:10.1002/humu.20842
  33. ↑ Hoefele J, Mayer K, Scholz M, Klein HG. Novel PKD1 and PKD2 mutations in autosomal dominant polycystic kidney disease (ADPKD). Nephrol Dial Transplant. 2011 Jul;26(7):2181-8. doi: 10.1093/ndt/gfq720. Epub, 2010 Nov 29. PMID:21115670 doi:10.1093/ndt/gfq720
  34. ↑ Audrezet MP, Cornec-Le Gall E, Chen JM, Redon S, Quere I, Creff J, Benech C, Maestri S, Le Meur Y, Ferec C. Autosomal dominant polycystic kidney disease: comprehensive mutation analysis of PKD1 and PKD2 in 700 unrelated patients. Hum Mutat. 2012 Aug;33(8):1239-50. doi: 10.1002/humu.22103. Epub 2012 May 24. PMID:22508176 doi:10.1002/humu.22103
  35. ↑ Qian F, Boletta A, Bhunia AK, Xu H, Liu L, Ahrabi AK, Watnick TJ, Zhou F, Germino GG. Cleavage of polycystin-1 requires the receptor for egg jelly domain and is disrupted by human autosomal-dominant polycystic kidney disease 1-associated mutations. Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16981-6. Epub 2002 Dec 13. PMID:12482949 doi:10.1073/pnas.252484899
  36. ↑ Bycroft M, Bateman A, Clarke J, Hamill SJ, Sandford R, Thomas RL, Chothia C. The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease. EMBO J. 1999 Jan 15;18(2):297-305. PMID:9889186 doi:10.1093/emboj/18.2.297
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