Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2003 Jun 16;22(12):2873-85.
doi: 10.1093/emboj/cdg303.

Mechanisms of activation, inhibition and specificity: crystal structures of the NMDA receptor NR1 ligand-binding core

Hiroyasu Furukawa  1 , Eric Gouaux
Affiliations

Mechanisms of activation, inhibition and specificity: crystal structures of the NMDA receptor NR1 ligand-binding core

Hiroyasu Furukawa et al. EMBO J. .

Abstract

Excitatory neurotransmission mediated by the N-methyl-D-aspartate subtype of ionotropic glutamate receptors is fundamental to the development and function of the mammalian central nervous system. NMDA receptors require both glycine and glutamate for activation with NR1 and NR2 forming glycine and glutamate sites, respectively. Mechanisms to describe agonist and antagonist binding, and activation and desensitization of NMDA receptors have been hampered by the lack of high-resolution structures. Here, we describe the cocrystal structures of the NR1 S1S2 ligand-binding core with the agonists glycine and D-serine (DS), the partial agonist D-cycloserine (DCS) and the antagonist 5,7-dichlorokynurenic acid (DCKA). The cleft of the S1S2 'clamshell' is open in the presence of the antagonist DCKA and closed in the glycine, DS and DCS complexes. In addition, the NR1 S1S2 structure reveals the fold and interactions of loop 1, a cysteine-rich region implicated in intersubunit allostery.

PubMed Disclaimer

Figures

None
Fig. 1. (A) Chemical structures of NMDA NR1 ligands. (B) Domain organization of a NR1 subunit showing the S1 and S2 segments in light blue and pink, respectively. The N-terminal domain (ATD), transmembrane segments and C-terminal domain (CTD) are not included within the S1S2 construct. (C) Multiple sequence alignment of S1 and S2 segments from rat NMDA, AMPA and kainate receptors. DDBJ/EMBL/GenBank accession Nos: X63255 (NR1), M91561 (NR2A), M91562 (NR2B), M91563 (NR2C), L31611 (NR2D), AF073379 (NR3A), AF440691 (NR3B), M85035 (GluR2), M85037 (GluR4) and Z11548 (GluR6). Drawn above the aligned sequences is the secondary structure determined from the NR1 S1S2 glycine structure where α-helices and β-strands are represented as rectangles and arrows, respectively. The color of the S1 and S2 segments is the same as that used in (B). Dots indicate the region where no electron density for the main chain is available. Cysteine residues participating in disulfide bond formation (green circles) are connected to their partners by green lines. Residues directly involved in agonist binding are marked with orange stars, whereas those specifically involved in antagonist binding are marked with blue + symbols. The sequences are numbered according to the predicted mature and immature polypeptides for non-NMDA and NMDA receptors, respectively.
None
Fig. 2. Ligand-binding properties of NR1 S1S2 as assessed by (A) saturation and (B) displacement experiments using the competitive antagonist of [3H]MDL105,519. The measured Kd value for [3H]MDL105,519 is 5.86 nM and the Ki values are 26.4 µM (glycine), 7.02 µM (DS), 241 µM (DCS), 0.54 µM (DCKA) and 2.30 mM (l-serine).
None
Fig. 3. Structure of glycine-bound NR1 S1S2. (A) Ribbon representation of the glycine-bound state with S1 and S2 colored as in Figure 1B and viewed from the side. Glycine binds in the crevice between domains 1 and 2, and is surrounded by Pro516, Thr518, the N-terminal regions of helices D, F and H, and β-strand 14; residues from both domain 1 and domain 2 make contacts with the α substituents of glycine. The three disulfide bonds in NR1 S1S2 (Cys420–Cys454, Cys436–Cys455 and Cys744–Cys798) are drawn as green lines. The first two are in loop 1 and the last one is near the C-terminus (CT). (B) Ribbon representation of domain 1 viewed from the top of the N-terminus (NT). Protruding as far as 15 Å from domain 1 are loops 1 and 2. The disulfide bonds (Cys420–Cys454 and Cys436–Cys455) drawn as green lines are helping to knit together the β-strands and loop regions of loop 1. (C) Schematic representation of the loop 1 region. The dashed line indicates the region (Pro441–Arg448) where no electron density for the main chain is available.
None
Fig. 4. The mechanism of glycine binding. (A) An Fo – Fc ‘omit’ electron density map using data to 1.35 Å resolution where the atoms corresponding to glycine, selected ligand-binding residues and waters W1, W2 and W3 were omitted from the Fc calculation. The contour level is 4.2 σ. (B) Stereo view of glycine (black bonds) and the interacting residues (yellow bonds). Dashed lines indicate hydrogen bonds and ionic interactions (interatom distance <3.2 Å). Water molecules (cyan) make important contributions to the hydrogen bond network and stabilize the binding of glycine.
None
Fig. 5. Superposition of the glycine-bound NR1 S1S2 (light cyan) and the l-glutamate-bound GluR2 S1S2 (light coral) structures using only Cα atoms viewed from (A) the side and (B) the top of the N-terminus. (C) Stereo view of the same superposition structures at the ligand-binding pocket with glycine (black) and l-glutamate (gray) interacting with the residues from NR1 S1S2 (cyan) and GluR2 S1S2 (crimson), respectively. The specificity of NR1 for glycine can be explained by (i) the hydrophobic environment created by Val689 and Trp731 and (ii) a steric constraint caused by the positioning of Trp731, which in GluR2 is Leu704 pointing away from the binding pocket, which disallow the γ-carboxyl group of l-glutamate to reside.
None
Fig. 6. The binding mechanisms of DS and DCS. Stereo view of (A) DS and (B) DCS and interacting residues. In both cases, dashed lines indicate the potential hydrogen bonds and ionic interactions (interatom distance <3.2 Å). Water molecules (cyan), located in the binding pocket, are also forming a critical hydrogen-bond network to stabilize the binding of both DS and DCS.
None
Fig. 7. The binding mechanisms of DCKA. (A) Ribbon representation of the DKCA-bound NR1 S1S2 structure (DCKA molecule A) with S1 and S2 colored as in Figure 1B. (B) Superposition of the two DCKA-bound NR1 S1S2 molecules in an asymmetric unit (DCKA molecules A and B in blue and light blue, respectively) and the glycine-bound molecule (red). The superposition was calculated using Cα atoms. The r.m.s. deviation for DCKA molecules A and B is 0.74 Å. The glycine-bound form has a bilobed structure closed by 23.8° and 18.2° compared with the DCKA molecules A and B, respectively. (C) Stereo view of DCKA and interacting residues.
None
Fig. 8. Solvent-accessible surface of the glycine-bound NR1 S1S2 protein facing (A) helices J and K or (B) loop 1. Hydrophobic residues (Ala, Val, Leu, Ile, Met, Pro, Phe, Tyr and Trp) are in red, whereas the exposed hydrophobic residues in helices J and K and loop 1 are in green.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Aizenman E., Lipton,S.A. and Loring,R.H. (1989) Selective modulation of NMDA responses by reduction and oxidation. Neuron, 2, 1257–1263. - PubMed
    1. Armstrong N. and Gouaux,E. (2000) Mechanisms for activation and antagonism of an AMPA-sensitive glutamate receptor: crystal structures of the GluR2 ligand binding core. Neuron, 28, 165–181. - PubMed
    1. Armstrong N., Sun,Y., Chen,G.-Q. and Gouaux,E. (1998) Structure of a glutamate receptor ligand binding core in complex with kainate. Nature, 395, 913–917. - PubMed
    1. Brunger A.T. et al. (1998) Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D, 54, 905–921. - PubMed
    1. CCP4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr.D, 50, 760–763. - PubMed

Publication types

MeSH terms