Ion binding sites and intermediate domain closure induced by D-serine in the GluD1 ligand-binding domain

The glutamate delta receptors GluD1 and GluD2 are part of the ionotropic glutamate receptor (iGluR) family; however, delta receptors differ from other iGluRs as they do not bind glutamate. These receptors have important and diverse functions in the brain and are known to be involved in various neurological diseases. Here, we report the monomeric X-ray crystal structure of the ligand-binding domain of rat GluD1 (rGluD1-LBD) with D-serine and Zn²⁺ ions, determined at 2.8 Å resolution. By comparing the structures with Zn²⁺ ions (rGluD1-LBD) and Ca²⁺ ions (human, hGluD1-LBD), we show that species and crystallization differences do not affect intermediate domain closure and D-serine interactions with GluD1. Furthermore, examining the effect of replacing the Ca²⁺ ions in the hGluD1-LBD dimer with Mg²⁺, Zn²⁺ or Na⁺ ions did not reveal significant differences in the overall structure of the hGluD1-LBD for the different cations. We show that the cations were coordinated by the same residues, Glu527, Val530 and Asp531, and several water molecules. In the structure of hGluD1-LBD, Cl^- ions are present at the dimer interface and molecular dynamics (MD) simulations showed that removal of the ions leads to opening of the dimer, highlighting the importance of Cl^- ions in stabilizing the dimer. Finally, MD simulations of hGluD1-LBD and the Pro725 to Ser725 mutant, with and without D-serine in the binding site, suggest that Pro725 hinders full domain closure in GluD1, whereas an apparent synergistic effect of D-serine and mutation to Ser725 leads to a significant interlobe closure of the clamshell-like structure.