title: Phylogenetic analysis and homology modelling of Paracentrotus lividus nectin.
abstract: The extracellular matrix protein Pl-nectin, a 210-kDa homodimer originally purified from sea urchin eggs, plays a crucial role in cell adhesion and embryonic morphogenesis. The compiled cDNA sequence, obtained by RT-PCR primer walking and 3' RACE, identified a 984aa product containing a 23aa signal peptide and including all six internal peptides identified by protein microsequencing. The protein is a new member of the galactose-binding protein superfamily as it consists of six 151-156aa-long tandemly repeated domains (D1-D6), homologous to the discoidin-like domains, also known as F5/8-type C domains. Based on homology modelling, we present a three-dimensional structure (3D) for D5, identified as the prototype domain. The molecular modelling of the assembled Pl-nectin homodimer accounts for a Pl-nectin quaternary structure composed of two 105-kDa C-shaped monomers linked by a S-S bridge. The presence of an LDT motif between the first and the second exposed loops of the D2 domain suggests the binding of Pl-nectin to an integrin receptor. Altogether, the in silico analysis described here is consistent with previous biochemical reports and offers a basis for predictions to be experimentally tested.
authors.affiliation: Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare A. Monroy, Via Ugo La Malfa 153, 90146, Palermo, Italy.
authors.forename: Caterina
authors.initials: C
authors.lastname: Costa
authors.forename: Carmela
authors.initials: C
authors.lastname: Cavalcante
authors.forename: Francesca
authors.initials: F
authors.lastname: Zito
authors.forename: Yukio
authors.initials: Y
authors.lastname: Yokota
authors.forename: Valeria
authors.initials: V
authors.lastname: Matranga
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D015815:Cell Adhesion Molecules / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D003198:Computer Simulation; D004625:Embryo, Nonmammalian; D008958:Models, Molecular; D008969:Molecular Sequence Data; D000075983:Nectins; D047328:Paracentrotus / Q000196:embryology / Q000235:genetics*; D010802:Phylogeny; D017385:Sequence Homology
chemical_list: D015815:Cell Adhesion Molecules; D000075983:Nectins