Cysteine-rich domains related to Frizzled receptors and Hedgehog-interacting proteins

Protein Science

Volumn 21, Issue 8, 2012, Pages 1172-1184

  Pei, Jimin ^a   Grishin, Nick V ^a,b  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

Frizzled; FZ CRD; Glypican; Hedgehog interacting protein; HFN CRD; Mid1; RECK

Indexed keywords

CALCIUM CHANNEL; CYSTEINE; FRIZZLED PROTEIN; PROTEOHEPARAN SULFATE; SONIC HEDGEHOG PROTEIN;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CHROMALVEOLATA; DICTYOSTELIUM; EUKARYOTE; FUNGUS; GENE DUPLICATION; HUMAN; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION;

AMINO ACID SEQUENCE; ANIMALS; CARRIER PROTEINS; CYSTEINE; FRIZZLED RECEPTORS; GPI-LINKED PROTEINS; HEDGEHOG PROTEINS; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; WNT SIGNALING PATHWAY;

CHROMALVEOLATA; DICTYOSTELIUM; ERINACEIDAE; EUKARYOTA; FUNGI; METAZOA;

EID: 84863793247     PISSN: 09618368     EISSN: 1469896X     Source Type: Journal    
DOI: 10.1002/pro.2105     Document Type: Article

References (70)

1. Logan CY, Nusse R (2004) The Wnt signaling pathway in development and disease. Annu Rev Cell Dev Biol 20:781-810. (Pubitemid 39488658)
2. Jiang J, Hui CC (2008) Hedgehog signaling in development and cancer. Dev Cell 15:801-812.
3. Mikels AJ, Nusse R (2006) Wnts as ligands: processing, secretion and reception. Oncogene 25:7461-7468. (Pubitemid 44885745)
4. Fredriksson R, Lagerstrom MC, Lundin LG, Schioth HB (2003) The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol Pharmacol 63:1256-1272. (Pubitemid 36627220)
5. Adamska M, Larroux C, Adamski M, Green K, Lovas E, Koop D, Richards GS, Zwafink C, Degnan BM (2010) Structure and expression of conserved Wnt pathway components in the demosponge Amphimedon queenslandica. Evol Dev 12:494-518.
6. Adamska M, Matus DQ, Adamski M, Green K, Rokhsar DS, Martindale MQ, Degnan BM (2007) The evolutionary origin of Hedgehog proteins. Curr Biol 17:R836-R837. (Pubitemid 47503799)
7. Ingham PW, Nakano Y, Seger C (2011) Mechanisms and functions of Hedgehog signalling across the metazoa. Nat Rev Genet 12:393-406.
8. Dann CE, Hsieh JC, Rattner A, Sharma D, Nathans J, Leahy DJ (2001) Insights into Wnt binding and signalling from the structures of two Frizzled cysteine-rich domains. Nature 412:86-90. (Pubitemid 32851515)
9. Stiegler AL, Burden SJ, Hubbard SR (2009) Crystal structure of the Frizzled-like cysteine-rich domain of the receptor tyrosine kinase MuSK. J Mol Biol 393:1-9.
10. Bazan JF, de Sauvage FJ (2009) Structural ties between cholesterol transport and morphogen signaling. Cell 138:1055-1056.
11. Huang HC, Klein PS (2004) The Frizzled family: receptors for multiple signal transduction pathways. Genome Biol 5:234.
12. Prabhu Y, Eichinger L (2006) The Dictyostelium repertoire of seven transmembrane domain receptors. Eur J Cell Biol 85:937-946. (Pubitemid 44317594)
13. Kawano Y, Kypta R (2003) Secreted antagonists of the Wnt signalling pathway. J Cell Sci 116:2627-2634. (Pubitemid 36857216)
14. Green JL, Kuntz SG, Sternberg PW (2008) Ror receptor tyrosine kinases: orphans no more. Trends Cell Biol 18:536-544.
15. Ghazanfari N, Fernandez KJ, Murata Y, Morsch M, Ngo ST, Reddel SW, Noakes PG, Phillips WD (2011) Muscle specific kinase: organiser of synaptic membrane domains. Int J Biochem Cell Biol 43:295-298.
16. Song L, Fricker LD (1997) Cloning and expression of human carboxypeptidase Z, a novel metallocarboxypeptidase. J Biol Chem 272:10543-10550. (Pubitemid 27181060)
17. Yan W, Sheng N, Seto M, Morser J, Wu Q (1999) Corin, a mosaic transmembrane serine protease encoded by a novel cDNA from human heart. J Biol Chem 274:14926-14935.
18. Seppinen L, Pihlajaniemi T (2011) The multiple functions of collagen XVIII in development and disease. Matrix Biol 30:83-92.
19. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389-3402. (Pubitemid 27359211)
20. Bosanac I, Maun HR, Scales SJ, Wen X, Lingel A, Bazan JF, de Sauvage FJ, Hymowitz SG, Lazarus RA (2009) The structure of SHH in complex with HHIP reveals a recognition role for the Shh pseudo active site in signaling. Nat Struct Mol Biol 16:691-697.
21. Kwon HJ, Abi-Mosleh L, Wang ML, Deisenhofer J, Goldstein JL, Brown MS, Infante RE (2009) Structure of N-terminal domain of NPC1 reveals distinct subdomains for binding and transfer of cholesterol. Cell 137:1213-1224.
22. Monaco HL (1997) Crystal structure of chicken riboflavin- binding protein. EMBO J 16:1475-1483.
23. Soding J (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951-960.
24. Santos AL, Branquinha MH, D'Avila-Levy CM (2006) The ubiquitous gp63-like metalloprotease from lower trypanosomatids: in the search for a function. An Acad Bras Cienc 78:687-714. (Pubitemid 44905151)
25. Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G, Forslund K, Holm L, Sonnhammer EL, Eddy SR, Bateman A (2010) The Pfam protein families database. Nucleic Acids Res 38:D211-D222.
26. Etges R, Bouvier J, Bordier C (1986) The major surface protein of Leishmania promastigotes is a protease. J Biol Chem 261:9098-9101. (Pubitemid 17218176)
27. Cobbe N, Marshall KM, Gururaja Rao S, Chang CW, Di Cara F, Duca E, Vass S, Kassan A, Heck MM (2009) The conserved metalloprotease invadolysin localizes to the surface of lipid droplets. J Cell Sci 122:3414-3423.
28. Fankhauser N, Maser P (2005) Identification of GPI anchor attachment signals by a Kohonen self-organizing map. Bioinformatics 21:1846-1852. (Pubitemid 40668020)
29. Poisson G, Chauve C, Chen X, Bergeron A (2007) FragAnchor: a large-scale predictor of glycosylphosphatidylinositol anchors in eukaryote protein sequences by qualitative scoring. Genomics Proteomics Bioinformatics 5:121-130. (Pubitemid 47430313)
30. Cavalier-Smith T (2009) Megaphylogeny, cell body plans, adaptive zones: causes and timing of eukaryote basal radiations. J Eukaryot Microbiol 56:26-33.
31. Shashoua VE (1991) Ependymin, a brain extracellular glycoprotein, and CNS plasticity. Ann NY Acad Sci 627:94-114.
32. Suarez-Castillo EC, Garcia-Arraras JE (2007) Molecular evolution of the ependymin protein family: a necessary update. BMC Evol Biol 7:23.
33. Moy GW, Mendoza LM, Schulz JR, Swanson WJ, Glabe CG, Vacquier VD (1996) The sea urchin sperm receptor for egg jelly is a modular protein with extensive homology to the human polycystic kidney disease protein, PKD1. J Cell Biol 133:809-817. (Pubitemid 26160983)
34. Schroder S, Fraternali F, Quan X, Scott D, Qian F, Pfuhl M (2011) When a module is not a domain: the case of the REJ module and the redefinition of the architecture of polycystin-1. Biochem J 435:651-660.
35. Frickey T, Lupas A (2004) CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics 20:3702-3704. (Pubitemid 40136822)
36. Fischer M, Schnell N, Chattaway J, Davies P, Dixon G, Sanders D (1997) The Saccharomyces cerevisiae CCH1 gene is involved in calcium influx and mating. FEBS Lett 419:259-262. (Pubitemid 28010822)
37. Iida H, Nakamura H, Ono T, Okumura MS, Anraku Y (1994) MID1, a novel Saccharomyces cerevisiae gene encoding a plasma membrane protein, is required for Ca2+ influx and mating. Mol Cell Biol 14:8259-8271.
38. Kanzaki M, Nagasawa M, Kojima I, Sato C, Naruse K, Sokabe M, Iida H (1999) Molecular identification of a eukaryotic, stretch-activated nonselective cation channel. Science 285:882-886. (Pubitemid 29381987)
39. Maruoka T, Nagasoe Y, Inoue S, Mori Y, Goto J, Ikeda M, Iida H (2002) Essential hydrophilic carboxyl-terminal regions including cysteine residues of the yeast stretch-activated calcium-permeable channel Mid1. J Biol Chem 277:11645-11652. (Pubitemid 34952715)
40. Takahashi C, Sheng Z, Horan TP, Kitayama H, Maki M, Hitomi K, Kitaura Y, Takai S, Sasahara RM, Horimoto A, Ikawa Y, Ratzkin BJ, Arakawa T, Noda M (1998) Regulation of matrix metalloproteinase-9 and inhibition of tumor invasion by the membrane-anchored glycoprotein RECK. Proc Natl Acad Sci USA 95:13221-13226. (Pubitemid 28509552)
41. Oh J, Takahashi R, Kondo S, Mizoguchi A, Adachi E, Sasahara RM, Nishimura S, Imamura Y, Kitayama H, Alexander DB, Ide C, Horan TP, Arakawa T, Yoshida H, Nishikawa S, Itoh Y, Seiki M, Itohara S, Takahashi C, Noda M (2001) The membrane-anchored MMP inhibitor RECK is a key regulator of extracellular matrix integrity and angiogenesis. Cell 107:789-800. (Pubitemid 34033671)
42. Clark JC, Thomas DM, Choong PF, Dass CR (2007) RECK - a newly discovered inhibitor of metastasis with prognostic significance in multiple forms of cancer. Cancer Metastasis Rev 26:675-683. (Pubitemid 350115122)
43. Chang CK, Hung WC, Chang HC (2008) The Kazal motifs of RECK protein inhibit MMP-9 secretion and activity and reduce metastasis of lung cancer cells in vitro and in vivo. J Cell Mol Med 12:2781-2789.
44. Harrington AE, Morris-Triggs SA, Ruotolo BT, Robinson CV, Ohnuma S, Hyvonen M (2006) Structural basis for the inhibition of activin signalling by follistatin. EMBO J 25:1035-1045. (Pubitemid 43372117)
45. Phelan MM, Thai CT, Soares DC, Ogata RT, Barlow PN, Bramham J (2009) Solution structure of factor I-like modules from complement C7 reveals a pair of follistatin domains in compact pseudosymmetric arrangement. J Biol Chem 284:19637-19649.
46. Zhang JL, Huang Y, Qiu LY, Nickel J, Sebald W (2007) von Willebrand factor type C domain-containing proteins regulate bone morphogenetic protein signaling through different recognition mechanisms. J Biol Chem 282:20002-20014. (Pubitemid 47100074)
47. Bishop B, Aricescu AR, Harlos K, O'Callaghan CA, Jones EY, Siebold C (2009) Structural insights into Hedgehog ligand sequestration by the human Hedgehog-interacting protein HHIP. Nat Struct Mol Biol 16:698-703.
48. Adachi J, Hasegawa M (1996) MOLPHY version 2.3, programs for molecular phylogenetics based on maximum likelihood. Comput Sci Monogr 28:1-150.
49. White HB, 3rd, Merrill AH, Jr (1988) Riboflavin-binding proteins. Annu Rev Nutr 8:279-299.
50. Wistow G, Bernstein SL, Wyatt MK, Ray S, Behal A, Touchman JW, Bouffard G, Smith D, Peterson K (2002) Expressed sequence tag analysis of human retina for the NEIBank Project: retbindin, an abundant, novel retinal cDNA and alternative splicing of other retina-preferred gene transcripts. Mol Vis 8:196-204. (Pubitemid 36153609)
51. Altmann SW, Davis HR, Jr, Zhu LJ, Yao X, Hoos LM, Tetzloff G, Iyer SP, Maguire M, Golovko A, Zeng M, Wang L, Murgolo N, Graziano MP (2004) Niemann- Pick C1 Like 1 protein is critical for intestinal cholesterol absorption. Science 303:1201-1204. (Pubitemid 38233587)
52. Kwon HJ, Palnitkar M, Deisenhofer J (2011) The structure of the NPC1L1 N-terminal domain in a closed conformation. PLoS One 6:e18722.
53. Dorrell RG, Smith AG (2011) Do red and green make brown?: perspectives on plastid acquisitions within chromalveolates. Eukaryot Cell 10:856-868.
54. Filmus J, Capurro M, Rast J (2008) Glypicans. Genome Biol 9:224.
55. Lin X (2004) Functions of heparan sulfate proteoglycans in cell signaling during development. Development 131:6009-6021.
56. Capurro MI, Xiang YY, Lobe C, Filmus J (2005) Glypican- 3 promotes the growth of hepatocellular carcinoma by stimulating canonical Wnt signaling. Cancer Res 65:6245-6254. (Pubitemid 40994410)
57. Capurro MI, Xu P, Shi W, Li F, Jia A, Filmus J (2008) Glypican-3 inhibits Hedgehog signaling during development by competing with patched for Hedgehog binding. Dev Cell 14:700-711. (Pubitemid 351622615)
58. Williams EH, Pappano WN, Saunders AM, Kim MS, Leahy DJ, Beachy PA (2010) Dally-like core protein and its mammalian homologues mediate stimulatory and inhibitory effects on Hedgehog signal response. Proc Natl Acad Sci USA 107:5869-5874.
59. Kim MS, Saunders AM, Hamaoka BY, Beachy PA, Leahy DJ (2011) Structure of the protein core of the glypican Dally-like and localization of a region important for Hedgehog signaling. Proc Natl Acad Sci USA 108:13112-13117.
60. Svensson G, Awad W, Hakansson M, Mani K, Logan DT (2012) Crystal structure of N-glycosylated human glypican-1 core protein: structure of two loops evolutionarily conserved in vertebrate glypican-1. J Biol Chem 287:14040-14051
61. Holm L, Kaariainen S, Wilton C, Plewczynski D (2006) Using Dali for structural comparison of proteins. Curr Protoc Bioinformatics Chapter 5:Unit 5.5.
62. Fico A, Maina F, Dono R (2011) Fine-tuning of cell signaling by glypicans. Cell Mol Life Sci 68:923-929.
63. Murzin AG, Brenner SE, Hubbard T, Chothia C (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 247:536-540.
64. Kall L, Krogh A, Sonnhammer EL (2007) Advantages of combined transmembrane topology and signal peptide prediction - the Phobius web server. Nucleic Acids Res 35:W429-W432.
65. Emanuelsson O, Brunak S, von Heijne G, Nielsen H (2007) Locating proteins in the cell using TargetP, SignalP and related tools. Nat Protoc 2:953-971. (Pubitemid 46745592)
66. Pei J, Kim BH, Grishin NV (2008) PROMALS3D: a tool for multiple protein sequence and structure alignments. Nucleic Acids Res 36:2295-2300. (Pubitemid 351567002)
67. Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 30:3059-3066. (Pubitemid 34851225)
68. Li W, Godzik A (2006) Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22:1658-1659. (Pubitemid 43985301)
69. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275-282.
70. Hasegawa M, Kishino H, Saitou N (1991) On the maximum likelihood method in molecular phylogenetics. J Mol Evol 32:443-445.