title: Crystal structure of afadin PDZ domain-nectin-3 complex shows the structural plasticity of the ligand-binding site.
abstract: Afadin, a scaffold protein localized in adherens junctions (AJs), links nectins to the actin cytoskeleton. Nectins are the major cell adhesion molecules of AJs. At the initial stage of cell-cell junction formation, the nectin-afadin interaction plays an indispensable role in AJ biogenesis via recruiting and tethering other components. The afadin PDZ domain (AFPDZ) is responsible for binding the cytoplasmic C-terminus of nectins. AFPDZ is a class II PDZ domain member, which prefers ligands containing a class II PDZ-binding motif, X-Φ-X-Φ (Φ, hydrophobic residues); both nectins and other physiological AFPDZ targets contain this class II motif. Here, we report the first crystal structure of the AFPDZ in complex with the nectin-3 C-terminal peptide containing the class II motif. We engineered the nectin-3 C-terminal peptide and AFPDZ to produce an AFPDZ-nectin-3 fusion protein and succeeded in obtaining crystals of this complex as a dimer. This novel dimer interface was created by forming an antiparallel β sheet between β2 strands. A major structural change compared with the known AFPDZ structures was observed in the α2 helix. We found an approximately 2.5 Å-wider ligand-binding groove, which allows the PDZ to accept bulky class II ligands. Apparently, the last three amino acids of the nectin-3 C-terminus were sufficient to bind AFPDZ, in which the two hydrophobic residues are important.
authors.affiliation: Division of Structural Biology, Graduate School of Medicine, Kobe University, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe, Hyogo, 650-0017, Japan; Research Center for Structural and Functional Proteomics, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, 565-0871, Japan; Global-COE (Center of Excellence) Program for Integrative Membrane Biology, Kobe University, 7-5-1 Kusunoki-cho, Chuo, Kobe, Hyogo, 650-0017, Japan.
authors.forename: Yoshie
authors.initials: Y
authors.lastname: Fujiwara
authors.forename: Natsuko
authors.initials: N
authors.lastname: Goda
authors.forename: Tomonari
authors.initials: T
authors.lastname: Tamashiro
authors.forename: Hirotaka
authors.initials: H
authors.lastname: Narita
authors.forename: Kaori
authors.initials: K
authors.lastname: Satomura
authors.forename: Takeshi
authors.initials: T
authors.lastname: Tenno
authors.forename: Atsushi
authors.initials: A
authors.lastname: Nakagawa
authors.forename: Masayuki
authors.initials: M
authors.lastname: Oda
authors.forename: Mamoru
authors.initials: M
authors.lastname: Suzuki
authors.forename: Toshiaki
authors.initials: T
authors.lastname: Sakisaka
authors.forename: Yoshimi
authors.initials: Y
authors.lastname: Takai
authors.forename: Hidekazu
authors.initials: H
authors.lastname: Hiroaki
mesh_terms: D000818:Animals; D001665:Binding Sites; D015815:Cell Adhesion Molecules / Q000737:chemistry* / Q000378:metabolism*; D018360:Crystallography, X-Ray; D008024:Ligands; D051379:Mice; D008840:Microfilament Proteins / Q000737:chemistry* / Q000378:metabolism; D008958:Models, Molecular; D000075983:Nectins; D054731:PDZ Domains; D011485:Protein Binding; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism
chemical_list: D015815:Cell Adhesion Molecules; D008024:Ligands; D008840:Microfilament Proteins; C000619017:Nectin3 protein, mouse; D000075983:Nectins; D011994:Recombinant Proteins; C108835:afadin
keywords: PDZ domain; adherens junction; afadin-nectin complex; crystallography; sequence specific recognition