• We are sorry, but NCBI web applications do not support your browser and may not function properly. More information
Logo of prosciprotein sciencecshl presssubscriptionsetoc alertsthe protein societyjournal home
Protein Sci. Jul 1998; 7(7): 1626–1631.
PMCID: PMC2144056

The discoidin domain family revisited: new members from prokaryotes and a homology-based fold prediction.

Abstract

Members of the discoidin (DS) domain family, which includes the C1 and C2 repeats of blood coagulation factors V and VIII, occur in a great variety of eukaryotic proteins, most of which have been implicated in cell-adhesion or developmental processes. So far, no three-dimensional structure of a known example of this extracellular module has been determined, limiting the usefulness of identifying a new sequence as member of this family. Here, we present results of a recent search of the protein sequence database for new DS domains using generalized profiles, a sensitive multiple alignment-based search technique. Several previously unrecognized DS domains could be identified by this method, including the first examples from prokaryotic species. More importantly, we present statistical, structural, and functional evidence that the D1 domain of galactose oxidase whose three-dimensional structure has been determined at 1.7 A resolution, is a distant member of this family. Taken together, these findings significantly expand the concept of the DS domain, by extending its taxonomic range and by implying a fold prediction for all its members. The proposed alignment with the galactose oxidase sequence makes it possible to construct homology-based three-dimensional models for the most interesting examples, as illustrated by an accompanying paper on the C1 and C2 domains of factor V.

Full Text

The Full Text of this article is available as a PDF (4.3M).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Bairoch A, Bucher P, Hofmann K. The PROSITE database, its status in 1995. Nucleic Acids Res. 1996 Jan 1;24(1):189–196. [PMC free article] [PubMed]
  • Baumgartner S, Littleton JT, Broadie K, Bhat MA, Harbecke R, Lengyel JA, Chiquet-Ehrismann R, Prokop A, Bellen HJ. A Drosophila neurexin is required for septate junction and blood-nerve barrier formation and function. Cell. 1996 Dec 13;87(6):1059–1068. [PubMed]
  • Bork P, Doolittle RF. Drosophila kelch motif is derived from a common enzyme fold. J Mol Biol. 1994 Mar 11;236(5):1277–1282. [PubMed]
  • Bucher P, Karplus K, Moeri N, Hofmann K. A flexible motif search technique based on generalized profiles. Comput Chem. 1996 Mar;20(1):3–23. [PubMed]
  • Canard B, Garnier T, Saint-Joanis B, Cole ST. Molecular genetic analysis of the nagH gene encoding a hyaluronidase of Clostridium perfringens. Mol Gen Genet. 1994 Apr;243(2):215–224. [PubMed]
  • Gobron S, Monnerie H, Meiniel R, Creveaux I, Lehmann W, Lamalle D, Dastugue B, Meiniel A. SCO-spondin: a new member of the thrombospondin family secreted by the subcommissural organ is a candidate in the modulation of neuronal aggregation. J Cell Sci. 1996 May;109(Pt 5):1053–1061. [PubMed]
  • He Z, Tessier-Lavigne M. Neuropilin is a receptor for the axonal chemorepellent Semaphorin III. Cell. 1997 Aug 22;90(4):739–751. [PubMed]
  • Hidai C, Zupancic T, Penta K, Mikhail A, Kawana M, Quertermous EE, Aoka Y, Fukagawa M, Matsui Y, Platika D, et al. Cloning and characterization of developmental endothelial locus-1: an embryonic endothelial cell protein that binds the alphavbeta3 integrin receptor. Genes Dev. 1998 Jan 1;12(1):21–33. [PMC free article] [PubMed]
  • Hofmann K, Bucher P. The FHA domain: a putative nuclear signalling domain found in protein kinases and transcription factors. Trends Biochem Sci. 1995 Sep;20(9):347–349. [PubMed]
  • Ito N, Phillips SE, Yadav KD, Knowles PF. Crystal structure of a free radical enzyme, galactose oxidase. J Mol Biol. 1994 May 20;238(5):794–814. [PubMed]
  • Jenny RJ, Pittman DD, Toole JJ, Kriz RW, Aldape RA, Hewick RM, Kaufman RJ, Mann KG. Complete cDNA and derived amino acid sequence of human factor V. Proc Natl Acad Sci U S A. 1987 Jul;84(14):4846–4850. [PMC free article] [PubMed]
  • Johnson JD, Edman JC, Rutter WJ. A receptor tyrosine kinase found in breast carcinoma cells has an extracellular discoidin I-like domain. Proc Natl Acad Sci U S A. 1993 Jun 15;90(12):5677–5681. [PMC free article] [PubMed]
  • Karn T, Holtrich U, Bräuninger A, Böhme B, Wolf G, Rübsamen-Waigmann H, Strebhardt K. Structure, expression and chromosomal mapping of TKT from man and mouse: a new subclass of receptor tyrosine kinases with a factor VIII-like domain. Oncogene. 1993 Dec;8(12):3433–3440. [PubMed]
  • Kotani E, Yamakawa M, Iwamoto S, Tashiro M, Mori H, Sumida M, Matsubara F, Taniai K, Kadono-Okuda K, Kato Y, et al. Cloning and expression of the gene of hemocytin, an insect humoral lectin which is homologous with the mammalian von Willebrand factor. Biochim Biophys Acta. 1995 Feb 21;1260(3):245–258. [PubMed]
  • Ogura K, Nara K, Watanabe Y, Kohno K, Tai T, Sanai Y. Cloning and expression of cDNA for O-acetylation of GD3 ganglioside. Biochem Biophys Res Commun. 1996 Aug 23;225(3):932–938. [PubMed]
  • Ohno I, Hashimoto J, Shimizu K, Takaoka K, Ochi T, Matsubara K, Okubo K. A cDNA cloning of human AEBP1 from primary cultured osteoblasts and its expression in a differentiating osteoblastic cell line. Biochem Biophys Res Commun. 1996 Nov 12;228(2):411–414. [PubMed]
  • Piendl W, Eichenseer C, Viel P, Altenbuchner J, Cullum J. Analysis of putative DNA amplification genes in the element AUD1 of Streptomyces lividans 66. Mol Gen Genet. 1994 Aug 15;244(4):439–443. [PubMed]
  • Poole S, Firtel RA, Lamar E, Rowekamp W. Sequence and expression of the discoidin I gene family in Dictyostelium discoideum. J Mol Biol. 1981 Dec 5;153(2):273–289. [PubMed]
  • Rost B. PHD: predicting one-dimensional protein structure by profile-based neural networks. Methods Enzymol. 1996;266:525–539. [PubMed]
  • Sauer CG, Gehrig A, Warneke-Wittstock R, Marquardt A, Ewing CC, Gibson A, Lorenz B, Jurklies B, Weber BH. Positional cloning of the gene associated with X-linked juvenile retinoschisis. Nat Genet. 1997 Oct;17(2):164–170. [PubMed]
  • Stubbs JD, Lekutis C, Singer KL, Bui A, Yuzuki D, Srinivasan U, Parry G. cDNA cloning of a mouse mammary epithelial cell surface protein reveals the existence of epidermal growth factor-like domains linked to factor VIII-like sequences. Proc Natl Acad Sci U S A. 1990 Nov;87(21):8417–8421. [PMC free article] [PubMed]
  • Takagi S, Hirata T, Agata K, Mochii M, Eguchi G, Fujisawa H. The A5 antigen, a candidate for the neuronal recognition molecule, has homologies to complement components and coagulation factors. Neuron. 1991 Aug;7(2):295–307. [PubMed]

Articles from Protein Science : A Publication of the Protein Society are provided here courtesy of The Protein Society

Formats:

Related citations in PubMed

See reviews...See all...

Cited by other articles in PMC

See all...

Links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...