PDBsum entry 1syi

Membrane protein

PDB id: 1syi

Contents

Protein chains

259 a.a.

Ligands

CPW ×2

Waters ×372

References listed in PDB file

Key reference

Title

Tyr702 is an important determinant of agonist binding and domain closure of the ligand-Binding core of glur2.

Authors

A.Frandsen, D.S.Pickering, B.Vestergaard, C.Kasper, B.B.Nielsen, J.R.Greenwood, G.Campiani, C.Fattorusso, M.Gajhede, A.Schousboe, J.S.Kastrup.

Ref.

Mol Pharmacol, 2005, 67, 703-713.

PubMed id

15591246

Abstract

Ionotropic glutamate receptors mediate most rapid excitatory synaptic transmission in the mammalian central nervous system, and their involvement in neurological diseases has stimulated widespread interest in their structure and function. Despite a large number of agonists developed so far, few display selectivity among (S)-2-amino-3-(3-hydroxy-5-methylisoxazol-4-yl) propionic acid (AMPA)-receptor subtypes. The present study provides X-ray structures of the glutamate receptor 2 (GluR2)-selective partial agonist (S)-2-amino-3-(1,3,5,6,7-pentahydro-2,4-dioxocyclopenta[e] pyrimidin-1-yl) propanoic acid [(S)-CPW399] in complex with the ligand-binding core of GluR2 (GluR2-S1S2J) and with a (Y702F)GluR2-S1S2J mutant. In addition, the structure of the nonselective partial agonist kainate in complex with (Y702F)GluR2-S1S2J was determined. The results show that the selectivity of (S)-CPW399 toward full-length GluR2 relative to GluR3 is reflected in the binding data on the two soluble constructs, allowing the use of (Y702F)GluR2-S1S2J as a model system for studying GluR2/GluR3 selectivity. Structural comparisons suggest that selectivity arises from disruption of a water-mediated network between ligand and receptor. A D1-D2 domain closure occurs upon agonist binding. (S)-CPW399 and kainate induce greater domain closure in the Y702F mutant, indicating that these partial agonists here act in a manner more reminiscent of full agonists. Both kainate and (S)-CPW399 exhibited higher efficacy at (Y702F)GluR2(Q)i than at wild-type GluR2(Q)i. Whereas an excellent correlation exists between domain closure and efficacy of a range of agonists at full-length GluR2 determined by electrophysiology in Xenopus laevis oocytes, a direct correlation between agonist induced domain closure of (Y702F)GluR2-S1S2J and efficacy at the GluR3 receptor is not observed. Although it clearly controls selectivity, mutation of this residue alone is insufficient to explain agonist-induced conformational rearrangements occurring in this variant.

Secondary reference #1

Title

Structural basis for ampa receptor activation and ligand selectivity: crystal structures of five agonist complexes with the glur2 ligand-Binding core.

Authors

A.Hogner, J.S.Kastrup, R.Jin, T.Liljefors, M.L.Mayer, J.Egebjerg, I.K.Larsen, E.Gouaux.

Ref.

J Mol Biol, 2002, 322, 93. [DOI no: 10.1016/S0022-2836(02)00650-2]

PubMed id

12215417

Figure 3.
Figure 3. Drawings showing the three agonists and their interactions with the S1S2J protein. (a) 2-Me-Tet-AMPA, (b) ACPA, and (c) Br-HIBO. The bonds of the protein are displayed in yellow and the bound agonists bonds are in blue. Water molecules are shown as red spheres, while remaining atoms are in standard atomic colours (carbon is black, oxygen is red, nitrogen is blue, and bromine is green). Broken lines indicate all potential hydrogen bonds or ionic interactions within 3.3 Å. Radiating spheres indicate hydrophobic contacts within 3.9 Å between carbon atoms in the agonist and neighbouring residues. The only exception is in (c), where hydrophobic contacts between the bromine atom and neighbouring residues are displayed. The binding site of protomer A was employed for (a) and (b), and the binding sites for protomers B and C have similar structures. This Figure was prepared with the program Ligplot.[55.] (d) F[o]−F[c] omit electron density map contoured at 3.0σ for S1S2J:2-Me-Tet-AMPA, S1S2J:ACPA, S1S2J:Br-HIBO, and S1S2J-Y702F:Br-HIBO was prepared by BOBSCRIPT.[56.]

Figure 4.
Figure 4. Surface electrostatic potential of part of the binding site of 2-Me-Tet-AMPA in complex with S1S2J. Positive potential is coloured in blue and negative potential in red, as indicated by the coloured bar to the left. The labelled residues form a well-defined partly hydrophobic and partly polar cavity within the binding site of S1S2J. These residues are within 3.9 Å from the 2-methyltetrazole ring, except from residues Thr686 and Leu704, which are at a distance of 4.2 Å and 4.7 Å, respectively. The ligand 2-Me-Tet-AMPA is shown in ball-and-stick representation, coloured as follows: carbon is white, oxygen is red, and nitrogen is blue. The Figure was prepared with the program Sybyl (Tripos Assoc. Inc.).

The above figures are reproduced from the cited reference with permission from Elsevier

Secondary reference #2

Title

Mechanisms for activation and antagonism of an ampa-Sensitive glutamate receptor: crystal structures of the glur2 ligand binding core.

Authors

N.Armstrong, E.Gouaux.

Ref.

Neuron, 2000, 28, 165-181. [DOI no: 10.1016/S0896-6273(00)00094-5]

PubMed id

11086992

Figure 1.
Figure 1. Ligand Binding Constants for S1S2J(A) Domain structure of iGluRs showing the S1 and S2 segments in turquoise and pink, respectively. “Cut” and “link” denote the edges of the S1S2 construct.(B) K[D] for ^3H-AMPA binding was 24.8 ± 1.8 nM.(C) IC[50] for displacement of ^3H-AMPA by glutamate, kainate, and DNQX were 821 nM, 14.5 μM, and 998 nM, respectively.

Figure 2.
Figure 2. Superposition of the Expanded Cleft Structures and Stereo View of the DNQX Binding Site(A) The two apo molecules (ApoA and ApoB) and two DNQX molecules (DNQXA and DNQXB) in each asymmetric unit were superimposed using only Cα atoms from domain 1. Apo protomers are shaded red and pink while DNQX protomers are colored light green and dark green. DNQX is depicted in black, and selected side chains from DNQXB are shown in dark green. The conformational change undergone by Glu-705 is illustrated by comparing its orientation in ApoB and DNQXB. In the apo state, Glu-705 accepts hydrogen bonds from the side chains of Lys-730 and Thr-655.(B) The chemical structure of DNQX and F[o]-F[c] omit electron density for DNQX and sulfate contoured at 2.5 σ.(C) Stereo image of the interactions between DNQX, sulfate, and S1S2J. DNQXB side chains are colored gray. Water molecules are shown as green balls. DNQX is colored black. Hydrogen bonds between DNQX, sulfate, and S1S2J are indicated by black dashed lines.

The above figures are reproduced from the cited reference with permission from Cell Press

Secondary reference #3

Title

Probing the ligand binding domain of the glur2 receptor by proteolysis and deletion mutagenesis defines domain boundaries and yields a crystallizable construct.

Authors

G.Q.Chen, Y.Sun, R.Jin, E.Gouaux.

Ref.

Protein Sci, 1998, 7, 2623-2630. [DOI no: 10.1002/pro.5560071216]

PubMed id

9865957