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

We obtained the cDNA sequence coding for Pl-nectin, an extracellular matrix protein purified from the sea urchin, composed of two 105 kDa equivalent subunits. The protein, synthesized as a 984aa precursor containing a 23aa signal peptide, is a new member of the galactose-binding protein superfamily. In fact, it consists of six 151-156aa-long tandemly-repeated domains, which are homologous to the discoidin-like domains, also known as F5/8 Type C domains. Phylogenetic analysis with discoidin domains from other known proteins confirmed the importance of their biological role during evolution. In addition, we describe the three-dimensional structure for each Pl-nectin domain, obtained on the basis of the homology modelling with crystal structures of the human coagulation factor V and VIII C2 domains and neuropilin-1 b1 domain. A further two-domains modelling and the subsequent association of the three two-domains modelled dimers produced the assembled Pl-nectin subunit. The in silico quaternary structure of the two subunits, composed of two 105kDa C-shaped monomers linked by a disulfide bridge accounts for the whole 210 kDa Pl-nectin molecule. The model presented is consistent with earlier biochemical reports on the molecule and extends previous conclusions concerning its function. In addition, the in silico analysis offers a basis for predictions to be experimentally tested.