A new member of the discoidin family: in silico analysis of Paracentrotus lividus nectin based on its cDNA sequence

The Paracentrotus lividus nectin (Pl-nectin) is an extracellular matrix protein of the sea urchin embryo, composed of two 105-kDa equivalent subunits and shown to be involved in cell adhesion and embryonic morphogenesis (1, 2). We isolated the full length 3593bp cDNA coding for the 984aa precursor containing a 23aa signal peptide and six 151-156aa long, tandemly-repeated Discoidin (DS) domains, also known as F5/8 Type C domains of the Discoidin family (3, 4). Phylogenetic analysis with DS domains from other known proteins confirmed their biological role in cell adhesion and signaling mediated by protein-protein, protein-carbohydrate, or protein-lipid interactions. We identified a LDT motif, also found in the mammalian mucosal addressin molecule and known to bind the integrin ?4?7 receptor (5). We obtained three-dimensional models of the six Pl-nectin domains by homology modelling based on known crystal structures of the C2 domains of the human coagulation factor V and VIII, and the bovine factor Va. Intra-domain S-S bridges were predicted by comparison and superimposition of the Pl-nectin domain models with the galactose oxidase crystal structure. One 105-kDa subunit model was obtained by the association of three dimers models, each consisting of two Pl-nectin domains. In conclusion, the whole quaternary structure proposed here, consists of two 105-kDa C-shaped subunits linked by a S-S bridge; the model is consistent with earlier biochemical reports and extends previous conclusions concerning its function. This project has been partially funded by the Biomintec Project of the EU 7th FP Marie Curie ITN References 1. Matranga V, Di Ferro D, Zito F, Cervello M, Nakano E (1992) A new extracellular matrix protein of the sea urchin embryo with properties of a substrate adhesion molecule. Dev Genes Evol 201:173-178. doi:10.1007/BF00188716 2. Zito F, Costa C, Sciarrino S, Poma V, Russo R, Angerer LM, Matranga V (2003) Expression of univin, a TGF-? growth factor, requires ectoderm-ECM interaction and promotes skeletal growth in the sea urchin embryo. Dev Biol 264:217-27. doi:10.1016/j.ydbio.2003.07.015 3. Costa C, Cavalcante C, Zito F, Yokota Y and Matranga V (2009) Phylogenetic analysis and homology modelling of Paracentrotus lividus nectin. Mol Divers published online:12 November 2009. doi:10.1007/s11030-009-9203-3 4. Kiedzierska A, Smietana K, Czepczynska H, Otlewski J (2007). Structural similarities and functional diversity of eukaryotic discoidin-like domains. Biochim Biophys Acta 1774:1069-1078. doi:10.1016/j.bbapap.2007.07.007 5. Fong S, Jones S, Renz ME, Chiu HH, Ryan AM, Presta LG, Jackson D (1997) Mucosal Addressin Cell Adhesion Molecule-1 (MAdCAM-1). Immunologic Research 16:299-311.