Solution Structure of Synbindin Atypical PDZ Domain and Interaction with Syndecan-2

Synbindin is one component of Transport protein particle (TRAPP) complexes. In the hippocampal neurons, synbindin binds syndecan-2 by its atypical PDZ domain (APD) and may regulate the formation of dendritic spines. To investigate the interaction of synbindin and syndecan-2, we determined the solution structure of the synbindin APD by NMR. The structure of APD is different from the classical canonical PDZ domains by lacking the typical A helix and the signature sequence Gly-psi-Gly-psi. These differences indicate that APD may not bind syndecan-2 with the typical binding mode of other PDZ domain proteins. In NMR titration experiments, APD do not bind with the C-terminal TKEFYA peptide of syndecan-2, but can interact with the 32-residue cytoplasmic domain of syndecan-2 very weakly.