Crystal structure of the second PDZ domain of SAP97 in complex with a GluR‐A C‐terminal peptide

• Published in: The FEBS journal 2006-11, Vol.273 (22), p.5219-5229
• Main Authors: von Ossowski, Ingemar, Oksanen, Esko, von Ossowski, Lotta, Cai, Chunlin, Sundberg, Maria, Goldman, Adrian, Keinänen, Kari
• Format: Article
• Language: English
• Subjects: Adaptor Proteins, Signal Transducing - chemistry; Adaptor Proteins, Signal Transducing - metabolism; Amino Acid Sequence; Binding sites; Biochemistry; Cells, Cultured; Crystal structure; Crystallography, X-Ray - methods; Dimerization; GluR1; GluR‐A; Humans; Ligands; Membrane Proteins - chemistry; Membrane Proteins - metabolism; Models, Molecular; Molecular Sequence Data; Mutation; PDZ domain; Peptides; Protein Binding; Protein Conformation; Protein Structure, Secondary; Protein Structure, Tertiary; Receptors, Glutamate - metabolism; SAP97; Sequence Homology, Amino Acid
• ISSN: 1742-464X; 1742-4658
• DOI: 10.1111/j.1742-4658.2006.05521.x

Synaptic targeting of GluR‐A subunit‐containing glutamate receptors involves an interaction with synapse‐associated protein 97 (SAP97). The C‐terminus of GluR‐A, which contains a class I PDZ ligand motif (‐x‐Ser/Thr‐x‐φ‐COOH where φ is an aliphatic amino acid) associates preferentially with the second PDZ domain of SAP97 (SAP97PDZ2). To understand the structural basis of this interaction, we have determined the crystal structures of wild‐type and a SAP97PDZ2 variant in complex with an 18‐mer C‐terminal peptide (residues 890–907) of GluR‐A and of two variant PDZ2 domains in unliganded state at 1.8–2.44 Å resolutions. SAP97PDZ2 folds to a compact globular domain comprising six β‐strands and two α‐helices, a typical architecture for PDZ domains. In the structure of the peptide complex, only the last four C‐terminal residues of the GluR‐A are visible, and align as an antiparallel β‐strand in the binding groove of SAP97PDZ2. The free carboxylate group and the aliphatic side chain of the C‐terminal leucine (Leu907), and the hydroxyl group of Thr905 of the GluR‐A peptide are engaged in essential class I PDZ interactions. Comparison between the free and complexed structures reveals conformational changes which take place upon peptide binding. The βΑ−βΒ loop moves away from the C‐terminal end of αB leading to a slight opening of the binding groove, which may better accommodate the peptide ligand. The two conformational states are stabilized by alternative hydrogen bond and coulombic interactions of Lys324 in βΑ−βΒ loop with Asp396 or Thr394 in βΒ. Results of in vitro binding and immunoprecipitation experiments using a PDZ motif‐destroying L907A mutation as well as the insertion of an extra alanine residue between the C‐terminal Leu907 and the stop codon are also consistent with a ‘classical’ type I PDZ interaction between SAP97 and GluR‐A C‐terminus.