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PDBsum entry 1b4r
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Membrane protein PDB id
1b4r

 

 

 

 

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Contents
Protein chain
80 a.a. *
* Residue conservation analysis
PDB id:
1b4r
Name: Membrane protein
Title: Pkd domain 1 from human polycystein-1
Structure: Protein (pkd1_human). Chain: a. Fragment: pkd domain. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
NMR struc: 20 models
Authors: M.Bycroft
Key ref:
M.Bycroft et al. (1999). The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease. EMBO J, 18, 297-305. PubMed id: 9889186 DOI: 10.1093/emboj/18.2.297
Date:
28-Dec-98     Release date:   06-Jan-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P98161  (PKD1_HUMAN) -  Polycystin-1 from Homo sapiens
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Seq:
Struc: 		4303 a.a.
80 a.a.
Key:    Secondary structure  CATH domain

 

 
DOI no: 10.1093/emboj/18.2.297 EMBO J 18:297-305 (1999)
PubMed id: 9889186  
 
 
The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease.
M.Bycroft, A.Bateman, J.Clarke, S.J.Hamill, R.Sandford, R.L.Thomas, C.Chothia.
 
  ABSTRACT  
 
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.
 
  Selected figure(s)  
 
Figure 7.
Figure 7 PKDd1 showing the conserved structurally important sequence WDFGDGS. The figure was prepared using the program Molscript (Kraulis, 1991). 		Figure 8.
Figure 8 (A) A structural alignment of the sequences of human and Fugu PKD domain 10 (PKDd10) with that of human PKDd1. (B) Schematic representation of the sequence conservation in the sheets of PKDd10. The surface residues only are shown, in a view looking at the molecule from the outside. The filled circles represent residues pointing into the interior of the protein. The C' -C -F -G sheet is shown in the same orientation as used in Figure 3. The A -B -E sheet is shown with the entire molecule rotated 180° about the y-axis. The human sequence is on the left, the Fugu sequence on the right. Residues in the A -B -E sheet that are putative glycosylation sites are shaded.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1999, 18, 297-305) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21332816 J.Li, C.Yu, Y.Tao, Y.Yang, Z.Hu, and S.Zhang (2011).
Putative mutation of PKD1 gene responsible for autosomal dominant polycystic kidney disease in a Chinese family.
  Int J Urol, 18, 240-242.  
21079243 H.C.Chapin, and M.J.Caplan (2010).
The cell biology of polycystic kidney disease.
  J Cell Biol, 191, 701-710.  
19884326 T.Hoashi, K.Tamaki, and V.J.Hearing (2010).
The secreted form of a melanocyte membrane-bound glycoprotein (Pmel17/gp100) is released by ectodomain shedding.
  FASEB J, 24, 916-930.  
20056711 T.Hoashi, S.Sato, Y.Yamaguchi, T.Passeron, K.Tamaki, and V.J.Hearing (2010).
Glycoprotein nonmetastatic melanoma protein b, a melanocytic cell marker, is a melanosome-specific and proteolytically released protein.
  FASEB J, 24, 1616-1629.  
19840945 B.Watt, G.van Niel, D.M.Fowler, I.Hurbain, K.C.Luk, S.E.Stayrook, M.A.Lemmon, G.Raposo, J.Shorter, J.W.Kelly, and M.S.Marks (2009).
N-terminal domains elicit formation of functional Pmel17 amyloid fibrils.
  J Biol Chem, 284, 35543-35555.  
  19309740 J.Pei, P.J.Lupardus, K.C.Garcia, and N.V.Grishin (2009).
CPDadh: a new peptidase family homologous to the cysteine protease domain in bacterial MARTX toxins.
  Protein Sci, 18, 856-862.  
20004162 J.R.Forman, Z.T.Yew, S.Qamar, R.N.Sandford, E.Paci, and J.Clarke (2009).
Non-native interactions are critical for mechanical strength in PKD domains.
  Structure, 17, 1582-1590.  
19350579 J.S.Chung, M.Bonkobara, M.Tomihari, P.D.Cruz, and K.Ariizumi (2009).
The DC-HIL/syndecan-4 pathway inhibits human allogeneic T-cell responses.
  Eur J Immunol, 39, 965-974.  
19759016 L.Ma, M.Xu, J.R.Forman, J.Clarke, and A.F.Oberhauser (2009).
Naturally occurring mutations alter the stability of polycystin-1 polycystic kidney disease (PKD) domains.
  J Biol Chem, 284, 32942-32949.  
19153786 M.Dori-Bachash, B.Dassa, O.Peleg, S.A.Pineiro, E.Jurkevitch, and S.Pietrokovski (2009).
Bacterial intein-like domains of predatory bacteria: a new domain type characterized in Bdellovibrio bacteriovorus.
  Funct Integr Genomics, 9, 153-166.  
19320736 M.Tomihari, S.H.Hwang, J.S.Chung, P.D.Cruz, and K.Ariizumi (2009).
Gpnmb is a melanosome-associated glycoprotein that contributes to melanocyte/keratinocyte adhesion in a RGD-dependent fashion.
  Exp Dermatol, 18, 586-595.  
18080994 F.J.Stevens (2008).
Homology versus analogy: possible evolutionary relationship of immunoglobulins, cupredoxins, and Cu,Zn-superoxide dismutase.
  J Mol Recognit, 21, 20-29.  
18977758 G.Y.Zhao, X.L.Chen, H.L.Zhao, B.B.Xie, B.C.Zhou, and Y.Z.Zhang (2008).
Hydrolysis of Insoluble Collagen by Deseasin MCP-01 from Deep-sea Pseudoalteromonas sp. SM9913: COLLAGENOLYTIC CHARACTERS, COLLAGEN-BINDING ABILITY OF C-TERMINAL POLYCYSTIC KIDNEY DISEASE DOMAIN, AND IMPLICATION FOR ITS NOVEL ROLE IN DEEP-SEA SEDIMENTARY PARTICULATE ORGANIC NITROGEN DEGRADATION.
  J Biol Chem, 283, 36100-36107.  
19019219 L.P.Tripathi, and R.Sowdhamini (2008).
Genome-wide survey of prokaryotic serine proteases: analysis of distribution and domain architectures of five serine protease families in prokaryotes.
  BMC Genomics, 9, 549.  
18681943 O.A.Karlsen, J.R.Lillehaug, and H.B.Jensen (2008).
The presence of multiple c-type cytochromes at the surface of the methanotrophic bacterium Methylococcus capsulatus (Bath) is regulated by copper.
  Mol Microbiol, 70, 15-26.  
16964280 F.Reiter, M.Hartl, A.I.Karagiannidis, and K.Bister (2007).
WS5, a direct target of oncogenic transcription factor Myc, is related to human melanoma glycoprotein genes and has oncogenic potential.
  Oncogene, 26, 1769-1779.  
17251000 J.R.Forman, and J.Clarke (2007).
Mechanical unfolding of proteins: insights into biology, structure and folding.
  Curr Opin Struct Biol, 17, 58-66.  
17284525 J.S.Chung, K.Sato, I.I.Dougherty, P.D.Cruz, and K.Ariizumi (2007).
DC-HIL is a negative regulator of T lymphocyte activation.
  Blood, 109, 4320-4327.  
17437318 K.Zhang, C.Ye, Q.Zhou, R.Zheng, X.Lv, Y.Chen, Z.Hu, H.Guo, Z.Zhang, Y.Wang, R.Tan, and Y.Liu (2007).
PKD1 inhibits cancer cells migration and invasion via Wnt signaling pathway in vitro.
  Cell Biochem Funct, 25, 767-774.  
17444811 S.Paracchini, T.Scerri, and A.P.Monaco (2007).
The genetic lexicon of dyslexia.
  Annu Rev Genomics Hum Genet, 8, 57-79.  
17437137 V.Pletnev, R.Huether, L.Habegger, W.Schultz, and W.Duax (2007).
Rational proteomics of PKD1. I. Modeling the three dimensional structure and ligand specificity of the C_lectin binding domain of Polycystin-1.
  J Mol Model, 13, 891-896.  
16516837 A.C.Theos, S.T.Truschel, D.Tenza, I.Hurbain, D.C.Harper, J.F.Berson, P.C.Thomas, G.Raposo, and M.S.Marks (2006).
A lumenal domain-dependent pathway for sorting to intralumenal vesicles of multivesicular endosomes involved in organelle morphogenesis.
  Dev Cell, 10, 343-354.  
16314409 S.Najmudin, C.I.Guerreiro, A.L.Carvalho, J.A.Prates, M.A.Correia, V.D.Alves, L.M.Ferreira, M.J.Romão, H.J.Gilbert, D.N.Bolam, and C.M.Fontes (2006).
Xyloglucan is recognized by carbohydrate-binding modules that interact with beta-glucan chains.
  J Biol Chem, 281, 8815-8828.
PDB codes: 2c24 2c26 2c4x
16682408 T.Hoashi, J.Muller, W.D.Vieira, F.Rouzaud, K.Kikuchi, K.Tamaki, and V.J.Hearing (2006).
The repeat domain of the melanosomal matrix protein PMEL17/GP100 is required for the formation of organellar fibers.
  J Biol Chem, 281, 21198-21208.  
16162173 A.C.Theos, S.T.Truschel, G.Raposo, and M.S.Marks (2005).
The Silver locus product Pmel17/gp100/Silv/ME20: controversial in name and in function.
  Pigment Cell Res, 18, 322-336.  
16336259 A.N.Zelensky, and J.E.Gready (2005).
The C-type lectin-like domain superfamily.
  FEBS J, 272, 6179-6217.  
16219758 F.Qian, W.Wei, G.Germino, and A.Oberhauser (2005).
The nanomechanics of polycystin-1 extracellular region.
  J Biol Chem, 280, 40723-40730.  
16108796 H.Orikoshi, S.Nakayama, C.Hanato, K.Miyamoto, and H.Tsujibo (2005).
Role of the N-terminal polycystic kidney disease domain in chitin degradation by chitinase A from a marine bacterium, Alteromonas sp. strain O-7.
  J Appl Microbiol, 99, 551-557.  
15812005 H.Orikoshi, S.Nakayama, K.Miyamoto, C.Hanato, M.Yasuda, Y.Inamori, and H.Tsujibo (2005).
Roles of four chitinases (chia, chib, chic, and chid) in the chitin degradation system of marine bacterium Alteromonas sp. strain O-7.
  Appl Environ Microbiol, 71, 1811-1815.  
15895248 M.Köttgen, and G.Walz (2005).
Subcellular localization and trafficking of polycystins.
  Pflugers Arch, 451, 286-293.  
15008854 B.E.Galindo, G.W.Moy, and V.D.Vacquier (2004).
A third sea urchin sperm receptor for egg jelly module protein, suREJ2, concentrates in the plasma membrane over the sperm mitochondrion.
  Dev Growth Differ, 46, 53-60.  
18629042 S.Adindla, K.K.Inampudi, K.Guruprasad, and L.Guruprasad (2004).
Identification and analysis of novel tandem repeats in the cell surface proteins of archaeal and bacterial genomes using computational tools.
  Comp Funct Genomics, 5, 2.  
14635132 F.P.Wang, Q.Li, Y.Zhou, M.G.Li, and X.Xiao (2003).
The C-terminal module of Chi1 from Aeromonas caviae CB101 has a function in substrate binding and hydrolysis.
  Proteins, 53, 908-916.  
12562783 H.Orikoshi, N.Baba, S.Nakayama, H.Kashu, K.Miyamoto, M.Yasuda, Y.Inamori, and H.Tsujibo (2003).
Molecular analysis of the gene encoding a novel cold-adapted chitinase (ChiB) from a marine bacterium, Alteromonas sp. strain O-7.
  J Bacteriol, 185, 1153-1160.  
12711809 S.Adindla, and L.Guruprasad (2003).
Sequence analysis corresponding to the PPE and PE proteins in Mycobacterium tuberculosis and other genomes.
  J Biosci, 28, 169-179.  
11872449 D.Y.Kobayashi, R.M.Reedy, J.Bick, and P.V.Oudemans (2002).
Characterization of a chitinase gene from Stenotrophomonas maltophilia strain 34S1 and its involvement in biological control.
  Appl Environ Microbiol, 68, 1047-1054.  
12377130 H.Jing, J.Takagi, J.H.Liu, S.Lindgren, R.G.Zhang, A.Joachimiak, J.H.Wang, and T.A.Springer (2002).
Archaeal surface layer proteins contain beta propeller, PKD, and beta helix domains and are related to metazoan cell surface proteins.
  Structure, 10, 1453-1464.
PDB code: 1l0q
11889092 K.Miyamoto, E.Nukui, H.Itoh, T.Sato, T.Kobayashi, C.Imada, E.Watanabe, Y.Inamori, and H.Tsujibo (2002).
Molecular analysis of the gene encoding a novel chitin-binding protease from Alteromonas sp. strain O-7 and its role in the chitinolytic system.
  J Bacteriol, 184, 1865-1872.  
12406750 K.Miyamoto, E.Nukui, M.Hirose, F.Nagai, T.Sato, Y.Inamori, and H.Tsujibo (2002).
A metalloprotease (MprIII) involved in the chitinolytic system of a marine bacterium, Alteromonas sp. strain O-7.
  Appl Environ Microbiol, 68, 5563-5570.  
11981261 P.C.Harris (2002).
Molecular basis of polycystic kidney disease: PKD1, PKD2 and PKHD1.
  Curr Opin Nephrol Hypertens, 11, 309-314.  
12377113 R.W.Pickersgill (2002).
Complex cell signaling molecules from ancient molecular glue.
  Structure, 10, 1287-1288.  
11967008 S.Rossetti, D.Chauveau, D.Walker, A.Saggar-Malik, C.G.Winearls, V.E.Torres, and P.C.Harris (2002).
A complete mutation screen of the ADPKD genes by DHPLC.
  Kidney Int, 61, 1588-1599.  
11976326 Y.Y.Chen, K.J.Cross, R.A.Paolini, J.E.Fielding, N.Slakeski, and E.C.Reynolds (2002).
CPG70 is a novel basic metallocarboxypeptidase with C-terminal polycystic kidney disease domains from Porphyromonas gingivalis.
  J Biol Chem, 277, 23433-23440.  
11416156 D.B.Donoviel, D.D.Freed, H.Vogel, D.G.Potter, E.Hawkins, J.P.Barrish, B.N.Mathur, C.A.Turner, R.Geske, C.A.Montgomery, M.Starbuck, M.Brandt, A.Gupta, R.Ramirez-Solis, B.P.Zambrowicz, and D.R.Powell (2001).
Proteinuria and perinatal lethality in mice lacking NEPH1, a novel protein with homology to NEPHRIN.
  Mol Cell Biol, 21, 4829-4836.  
11195048 G.Wu (2001).
Current advances in molecular genetics of autosomal-dominant polycystic kidney disease.
  Curr Opin Nephrol Hypertens, 10, 23-31.  
11160770 M.A.Arnaout (2001).
Molecular genetics and pathogenesis of autosomal dominant polycystic kidney disease.
  Annu Rev Med, 52, 93.  
11473631 M.Sutters, T.Yamaguchi, R.L.Maser, B.S.Magenheimer, P.L.St John, D.R.Abrahamson, J.J.Grantham, and J.P.Calvet (2001).
Polycystin-1 transforms the cAMP growth-responsive phenotype of M-1 cells.
  Kidney Int, 60, 484-494.  
11012875 B.Phakdeekitcharoen, T.J.Watnick, C.Ahn, D.Y.Whang, B.Burkhart, and G.G.Germino (2000).
Thirteen novel mutations of the replicated region of PKD1 in an Asian population.
  Kidney Int, 58, 1400-1412.  
  10933504 I.Callebaut, D.Gilgès, I.Vigon, and J.P.Mornon (2000).
HYR, an extracellular module involved in cellular adhesion and related to the immunoglobulin-like fold.
  Protein Sci, 9, 1382-1390.  
11115102 M.A.Arnaout (2000).
The vasculopathy of autosomal dominant polycystic kidney disease: insights from animal models.
  Kidney Int, 58, 2599-2610.  
10926175 S.Somlo, and G.S.Markowitz (2000).
The pathogenesis of autosomal dominant polycystic kidney disease: an update.
  Curr Opin Nephrol Hypertens, 9, 385-394.  
10364515 R.Thomas, R.McConnell, J.Whittacker, P.Kirkpatrick, J.Bradley, and R.Sandford (1999).
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, 65, 39-49.  
10577909 T.Watnick, B.Phakdeekitcharoen, A.Johnson, M.Gandolph, M.Wang, G.Briefel, K.W.Klinger, W.Kimberling, P.Gabow, and G.G.Germino (1999).
Mutation detection of PKD1 identifies a novel mutation common to three families with aneurysms and/or very-early-onset disease.
  Am J Hum Genet, 65, 1561-1571.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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