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PDBsum entry 1pb8
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Ligand binding protein
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PDB id
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1pb8
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Contents |
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* Residue conservation analysis
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Embo J
22:2873-2885
(2003)
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PubMed id:
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Mechanisms of activation, inhibition and specificity: crystal structures of the NMDA receptor NR1 ligand-binding core.
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H.Furukawa,
E.Gouaux.
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ABSTRACT
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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.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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D.Stroebel,
S.Carvalho,
and
P.Paoletti
(2011).
Functional evidence for a twisted conformation of the NMDA receptor GluN2A subunit N-terminal domain.
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Neuropharmacology,
60,
151-158.
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G.Armagan,
L.Kanit,
and
A.Yalcin
(2011).
D-serine treatment induces oxidative stress in rat brain.
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| |
Drug Chem Toxicol,
34,
129-138.
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G.M.Alushin,
D.Jane,
and
M.L.Mayer
(2011).
Binding site and ligand flexibility revealed by high resolution crystal structures of GluK1 competitive antagonists.
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Neuropharmacology,
60,
126-134.
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PDB codes:
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K.M.Vance,
N.Simorowski,
S.F.Traynelis,
and
H.Furukawa
(2011).
Ligand-specific deactivation time course of GluN1/GluN2D NMDA receptors.
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Nat Commun,
2,
294.
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PDB codes:
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M.Koller,
K.Lingenhoehl,
M.Schmutz,
I.T.Vranesic,
J.Kallen,
Y.P.Auberson,
D.A.Carcache,
H.Mattes,
S.Ofner,
D.Orain,
and
S.Urwyler
(2011).
Quinazolinedione sulfonamides: A novel class of competitive AMPA receptor antagonists with oral activity.
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Bioorg Med Chem Lett,
21,
3358-3361.
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PDB code:
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P.Paoletti
(2011).
Molecular basis of NMDA receptor functional diversity.
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Eur J Neurosci,
33,
1351-1365.
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A.H.Ahmed,
C.P.Ptak,
and
R.E.Oswald
(2010).
Molecular mechanism of flop selectivity and subsite recognition for an AMPA receptor allosteric modulator: structures of GluA2 and GluA3 in complexes with PEPA.
|
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Biochemistry,
49,
2843-2850.
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PDB codes:
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A.H.Ahmed,
and
R.E.Oswald
(2010).
Piracetam defines a new binding site for allosteric modulators of alpha-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid (AMPA) receptors.
|
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J Med Chem,
53,
2197-2203.
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PDB codes:
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A.S.Maltsev,
and
R.E.Oswald
(2010).
Hydrophobic side chain dynamics of a glutamate receptor ligand binding domain.
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J Biol Chem,
285,
10154-10162.
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J.Sasabe,
and
S.Aiso
(2010).
Aberrant control of motoneuronal excitability in amyotrophic lateral sclerosis: excitatory glutamate/D-serine vs. inhibitory glycine/gamma-aminobutanoic acid (GABA).
|
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Chem Biodivers,
7,
1479-1490.
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K.Igarashi,
and
K.Kashiwagi
(2010).
Modulation of cellular function by polyamines.
|
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Int J Biochem Cell Biol,
42,
39-51.
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R.Risgaard,
K.B.Hansen,
and
R.P.Clausen
(2010).
Partial agonists and subunit selectivity at NMDA receptors.
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Chemistry,
16,
13910-13918.
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R.Vijayan,
M.A.Sahai,
T.Czajkowski,
and
P.C.Biggin
(2010).
A comparative analysis of the role of water in the binding pockets of ionotropic glutamate receptors.
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Phys Chem Chem Phys,
12,
14057-14066.
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S.M.Dravid,
P.B.Burger,
A.Prakash,
M.T.Geballe,
R.Yadav,
P.Le,
K.Vellano,
J.P.Snyder,
and
S.F.Traynelis
(2010).
Structural determinants of D-cycloserine efficacy at the NR1/NR2C NMDA receptors.
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J Neurosci,
30,
2741-2754.
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T.Nakagawa
(2010).
The biochemistry, ultrastructure, and subunit assembly mechanism of AMPA receptors.
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Mol Neurobiol,
42,
161-184.
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V.Labrie,
and
J.C.Roder
(2010).
The involvement of the NMDA receptor D-serine/glycine site in the pathophysiology and treatment of schizophrenia.
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Neurosci Biobehav Rev,
34,
351-372.
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A.H.Ahmed,
Q.Wang,
H.Sondermann,
and
R.E.Oswald
(2009).
Structure of the S1S2 glutamate binding domain of GLuR3.
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Proteins,
75,
628-637.
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PDB codes:
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A.V.Apkarian,
M.N.Baliki,
and
P.Y.Geha
(2009).
Towards a theory of chronic pain.
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Prog Neurobiol,
87,
81-97.
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A.V.Kenny,
S.L.Cousins,
L.Pinho,
and
F.A.Stephenson
(2009).
The Integrity of the Glycine Co-agonist Binding Site of N-Methyl-D-aspartate Receptors Is a Functional Quality Control Checkpoint for Cell Surface Delivery.
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J Biol Chem,
284,
324-333.
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C.L.Kussius,
and
G.K.Popescu
(2009).
Kinetic basis of partial agonism at NMDA receptors.
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Nat Neurosci,
12,
1114-1120.
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C.T.Smothers,
and
J.J.Woodward
(2009).
Expression of glycine-activated diheteromeric NR1/NR3 receptors in human embryonic kidney 293 cells Is NR1 splice variant-dependent.
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J Pharmacol Exp Ther,
331,
975-984.
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E.Karakas,
N.Simorowski,
and
H.Furukawa
(2009).
Structure of the zinc-bound amino-terminal domain of the NMDA receptor NR2B subunit.
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EMBO J,
28,
3910-3920.
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PDB codes:
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L.Kelamangalath,
C.M.Seymour,
and
J.J.Wagner
(2009).
D-serine facilitates the effects of extinction to reduce cocaine-primed reinstatement of drug-seeking behavior.
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Neurobiol Learn Mem,
92,
544-551.
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M.V.Centeno,
A.Mutso,
M.Millecamps,
and
A.V.Apkarian
(2009).
Prefrontal cortex and spinal cord mediated anti-neuropathy and analgesia induced by sarcosine, a glycine-T1 transporter inhibitor.
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Pain,
145,
176-183.
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Z.Sheng,
Z.Liang,
J.H.Geiger,
M.Prorok,
and
F.J.Castellino
(2009).
The selectivity of conantokin-G for ion channel inhibition of NR2B subunit-containing NMDA receptors is regulated by amino acid residues in the S2 region of NR2B.
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Neuropharmacology,
57,
127-136.
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A.S.Maltsev,
A.H.Ahmed,
M.K.Fenwick,
D.E.Jane,
and
R.E.Oswald
(2008).
Mechanism of partial agonism at the GluR2 AMPA receptor: Measurements of lobe orientation in solution.
|
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Biochemistry,
47,
10600-10610.
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A.Szklarczyk,
O.Ewaleifoh,
J.C.Beique,
Y.Wang,
D.Knorr,
N.Haughey,
T.Malpica,
M.P.Mattson,
R.Huganir,
and
K.Conant
(2008).
MMP-7 cleaves the NR1 NMDA receptor subunit and modifies NMDA receptor function.
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| |
FASEB J,
22,
3757-3767.
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C.Villmann,
J.Hoffmann,
M.Werner,
S.Kott,
N.Strutz-Seebohm,
T.Nilsson,
and
M.Hollmann
(2008).
Different structural requirements for functional ion pore transplantation suggest different gating mechanisms of NMDA and kainate receptors.
|
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J Neurochem,
107,
453-465.
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E.J.Bjerrum,
and
P.C.Biggin
(2008).
Rigid body essential X-ray crystallography: distinguishing the bend and twist of glutamate receptor ligand binding domains.
|
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Proteins,
72,
434-446.
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F.M.Ng,
M.T.Geballe,
J.P.Snyder,
S.F.Traynelis,
and
C.M.Low
(2008).
Structural insights into phenylethanolamines high-affinity binding site in NR2B from binding and molecular modeling studies.
|
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Mol Brain,
1,
16.
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G.Kikuchi,
Y.Motokawa,
T.Yoshida,
and
K.Hiraga
(2008).
Glycine cleavage system: reaction mechanism, physiological significance, and hyperglycinemia.
|
| |
Proc Jpn Acad Ser B Phys Biol Sci,
84,
246-263.
|
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|
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H.Wolosker,
E.Dumin,
L.Balan,
and
V.N.Foltyn
(2008).
D-amino acids in the brain: D-serine in neurotransmission and neurodegeneration.
|
| |
FEBS J,
275,
3514-3526.
|
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|
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K.A.Mankiewicz,
A.Rambhadran,
L.Wathen,
and
V.Jayaraman
(2008).
Chemical interplay in the mechanism of partial agonist activation in alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors.
|
| |
Biochemistry,
47,
398-404.
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M.Du,
A.Rambhadran,
and
V.Jayaraman
(2008).
Luminescence resonance energy transfer investigation of conformational changes in the ligand binding domain of a kainate receptor.
|
| |
J Biol Chem,
283,
27074-27078.
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R.Raabe,
and
L.Gentile
(2008).
Antidepressant interactions with the NMDA NR1-1b subunit.
|
| |
J Biophys,
2008,
474205.
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S.M.Schmid,
and
M.Hollmann
(2008).
To gate or not to gate: are the delta subunits in the glutamate receptor family functional ion channels?
|
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Mol Neurobiol,
37,
126-141.
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S.S.Ali,
J.I.Hardt,
and
L.L.Dugan
(2008).
SOD activity of carboxyfullerenes predicts their neuroprotective efficacy: a structure-activity study.
|
| |
Nanomedicine,
4,
283-294.
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T.Pauly,
M.Ratliff,
E.Pietrowski,
R.Neugebauer,
A.Schlicksupp,
J.Kirsch,
and
J.Kuhse
(2008).
Activity-dependent shedding of the NMDA receptor glycine binding site by matrix metalloproteinase 3: a PUTATIVE mechanism of postsynaptic plasticity.
|
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PLoS ONE,
3,
e2681.
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X.Han,
H.Tomitori,
S.Mizuno,
K.Higashi,
C.Füll,
T.Fukiwake,
Y.Terui,
P.Leewanich,
K.Nishimura,
T.Toida,
K.Williams,
K.Kashiwagi,
and
K.Igarashi
(2008).
Binding of spermine and ifenprodil to a purified, soluble regulatory domain of the N-methyl-D-aspartate receptor.
|
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J Neurochem,
107,
1566-1577.
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A.H.Ahmed,
A.P.Loh,
D.E.Jane,
and
R.E.Oswald
(2007).
Dynamics of the S1S2 glutamate binding domain of GluR2 measured using 19F NMR spectroscopy.
|
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J Biol Chem,
282,
12773-12784.
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B.J.Gaffney
(2007).
Anesthesia, analgesia, and euphoria.
|
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Biophys J,
92,
1-2.
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B.S.Chen,
and
K.W.Roche
(2007).
Regulation of NMDA receptors by phosphorylation.
|
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Neuropharmacology,
53,
362-368.
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H.C.Hemmings
(2007).
Noble meets nouveau: a shared anesthetic binding site for xenon and isoflurane on a glutamate receptor.
|
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Anesthesiology,
107,
694-696.
|
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H.Hald,
P.Naur,
D.S.Pickering,
D.Sprogøe,
U.Madsen,
D.B.Timmermann,
P.K.Ahring,
T.Liljefors,
A.Schousboe,
J.Egebjerg,
M.Gajhede,
and
J.S.Kastrup
(2007).
Partial agonism and antagonism of the ionotropic glutamate receptor iGLuR5: structures of the ligand-binding core in complex with domoic acid and 2-amino-3-[5-tert-butyl-3-(phosphonomethoxy)-4-isoxazolyl]propionic acid.
|
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J Biol Chem,
282,
25726-25736.
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PDB codes:
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H.Takahashi,
Y.Shin,
S.J.Cho,
W.M.Zago,
T.Nakamura,
Z.Gu,
Y.Ma,
H.Furukawa,
R.Liddington,
D.Zhang,
G.Tong,
H.S.Chen,
and
S.A.Lipton
(2007).
Hypoxia enhances S-nitrosylation-mediated NMDA receptor inhibition via a thiol oxygen sensor motif.
|
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Neuron,
53,
53-64.
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H.Wolosker
(2007).
NMDA receptor regulation by D-serine: new findings and perspectives.
|
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Mol Neurobiol,
36,
152-164.
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I.H.Greger,
E.B.Ziff,
and
A.C.Penn
(2007).
Molecular determinants of AMPA receptor subunit assembly.
|
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Trends Neurosci,
30,
407-416.
|
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K.A.Mankiewicz,
and
V.Jayaraman
(2007).
Glutamate receptors as seen by light: spectroscopic studies of structure-function relationships.
|
| |
Braz J Med Biol Res,
40,
1419-1427.
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L.Stoll,
J.Hall,
N.Van Buren,
A.Hall,
L.Knight,
A.Morgan,
S.Zuger,
H.Van Deusen,
and
L.Gentile
(2007).
Differential regulation of ionotropic glutamate receptors.
|
| |
Biophys J,
92,
1343-1349.
|
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M.J.Scolari,
and
G.B.Acosta
(2007).
D-serine: a new word in the glutamatergic neuro-glial language.
|
| |
Amino Acids,
33,
563-574.
|
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M.Millecamps,
M.V.Centeno,
H.H.Berra,
C.N.Rudick,
S.Lavarello,
T.Tkatch,
and
A.V.Apkarian
(2007).
D-cycloserine reduces neuropathic pain behavior through limbic NMDA-mediated circuitry.
|
| |
Pain,
132,
108-123.
|
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P.Naur,
K.B.Hansen,
A.S.Kristensen,
S.M.Dravid,
D.S.Pickering,
L.Olsen,
B.Vestergaard,
J.Egebjerg,
M.Gajhede,
S.F.Traynelis,
and
J.S.Kastrup
(2007).
Ionotropic glutamate-like receptor delta2 binds D-serine and glycine.
|
| |
Proc Natl Acad Sci U S A,
104,
14116-14121.
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PDB codes:
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P.T.Atlason,
M.L.Garside,
E.Meddows,
P.Whiting,
and
R.A.McIlhinney
(2007).
N-Methyl-D-aspartate (NMDA) receptor subunit NR1 forms the substrate for oligomeric assembly of the NMDA receptor.
|
| |
J Biol Chem,
282,
25299-25307.
|
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R.Dickinson,
B.K.Peterson,
P.Banks,
C.Simillis,
J.C.Martin,
C.A.Valenzuela,
M.Maze,
and
N.P.Franks
(2007).
Competitive inhibition at the glycine site of the N-methyl-D-aspartate receptor by the anesthetics xenon and isoflurane: evidence from molecular modeling and electrophysiology.
|
| |
Anesthesiology,
107,
756-767.
|
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W.Maier,
R.Schemm,
C.Grewer,
and
B.Laube
(2007).
Disruption of interdomain interactions in the glutamate binding pocket affects differentially agonist affinity and efficacy of N-methyl-D-aspartate receptor activation.
|
| |
J Biol Chem,
282,
1863-1872.
|
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A.S.Kristensen,
M.T.Geballe,
J.P.Snyder,
and
S.F.Traynelis
(2006).
Glutamate receptors: variation in structure-function coupling.
|
| |
Trends Pharmacol Sci,
27,
65-69.
|
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D.Colquhoun
(2006).
Agonist-activated ion channels.
|
| |
Br J Pharmacol,
147,
S17-S26.
|
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D.J.Wyllie,
A.R.Johnston,
D.Lipscombe,
and
P.E.Chen
(2006).
Single-channel analysis of a point mutation of a conserved serine residue in the S2 ligand-binding domain of the NR2A NMDA receptor subunit.
|
| |
J Physiol,
574,
477-489.
|
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H.Betz,
and
B.Laube
(2006).
Glycine receptors: recent insights into their structural organization and functional diversity.
|
| |
J Neurochem,
97,
1600-1610.
|
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|
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L.Scott,
S.Zelenin,
S.Malmersjö,
J.M.Kowalewski,
E.Z.Markus,
A.C.Nairn,
P.Greengard,
H.Brismar,
and
A.Aperia
(2006).
Allosteric changes of the NMDA receptor trap diffusible dopamine 1 receptors in spines.
|
| |
Proc Natl Acad Sci U S A,
103,
762-767.
|
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M.Martineau,
G.Baux,
and
J.P.Mothet
(2006).
D-serine signalling in the brain: friend and foe.
|
| |
Trends Neurosci,
29,
481-491.
|
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M.Volgraf,
P.Gorostiza,
R.Numano,
R.H.Kramer,
E.Y.Isacoff,
and
D.Trauner
(2006).
Allosteric control of an ionotropic glutamate receptor with an optical switch.
|
| |
Nat Chem Biol,
2,
47-52.
|
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P.E.Chen,
and
D.J.Wyllie
(2006).
Pharmacological insights obtained from structure-function studies of ionotropic glutamate receptors.
|
| |
Br J Pharmacol,
147,
839-853.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
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so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
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shown on the right.
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