PDBsum entry 2anj

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Membrane protein PDB id
Protein chain
262 a.a. *
Waters ×250
* Residue conservation analysis
PDB id:
Name: Membrane protein
Title: Crystal structure of the glur2 ligand binding core (s1s2j- y450w) mutant in complex with the partial agonist kainic acid at 2.1 a resolution
Structure: Glutamate receptor 2. Chain: a. Fragment: ligand binding core. Synonym: glur-2, glur-b, glur-k2, glutamate receptor ionotropic, ampa 2. Engineered: yes. Mutation: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: gria2, glur2. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
2.10Å     R-factor:   0.187     R-free:   0.248
Authors: M.M.Holm,P.Naur,B.Vestergaard,M.T.Geballe,M.Gajhede, J.S.Kastrup,S.F.Traynelis,J.Egebjerg
Key ref:
M.M.Holm et al. (2005). A binding site tyrosine shapes desensitization kinetics and agonist potency at GluR2. A mutagenic, kinetic, and crystallographic study. J Biol Chem, 280, 35469-35476. PubMed id: 16103115 DOI: 10.1074/jbc.M507800200
11-Aug-05     Release date:   30-Aug-05    
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Protein chain
Pfam   ArchSchema ?
P19491  (GRIA2_RAT) -  Glutamate receptor 2
883 a.a.
262 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   1 term 
  Biological process     transport   1 term 
  Biochemical function     transporter activity     3 terms  


DOI no: 10.1074/jbc.M507800200 J Biol Chem 280:35469-35476 (2005)
PubMed id: 16103115  
A binding site tyrosine shapes desensitization kinetics and agonist potency at GluR2. A mutagenic, kinetic, and crystallographic study.
M.M.Holm, P.Naur, B.Vestergaard, M.T.Geballe, M.Gajhede, J.S.Kastrup, S.F.Traynelis, J.Egebjerg.
Binding of an agonist to the 2-amino-3-(3-hydroxy-5-methyl-4-isoxazolyl)-propionic acid (AMPA) receptor family of the glutamate receptors (GluRs) results in rapid activation of an ion channel. Continuous application results in a non-desensitizing response for agonists like kainate, whereas most other agonists, such as the endogenous agonist (S)-glutamate, induce desensitization. We demonstrate that a highly conserved tyrosine, forming a wedge between the agonist and the N-terminal part of the bi-lobed ligand-binding site, plays a key role in the receptor kinetics as well as agonist potency and selectivity. The AMPA receptor GluR2, with mutations in Tyr-450, were expressed in Xenopus laevis oocytes and characterized in a two-electrode voltage clamp setup. The mutation GluR2(Y450A) renders the receptor highly kainate selective, and rapid application of kainate to outside-out patches induced strongly desensitizing currents. When Tyr-450 was substituted with the larger tryptophan, the (S)-glutamate desensitization is attenuated with a 10-fold increase in steady-state/peak currents (19% compared with 1.9% at the wild type). Furthermore, the tryptophan mutant was introduced into the GluR2-S1S2J ligand binding core construct and co-crystallized with kainate, and the 2.1-A x-ray structure revealed a slightly more closed ligand binding core as compared with the wild-type complex. Through genetic manipulations combined with structural and electrophysiological analysis, we report that mutations in position 450 invert the potency of two central agonists while concurrently strongly shaping the agonist efficacy and the desensitization kinetics of the AMPA receptor GluR2.
  Selected figure(s)  
Figure 1.
FIGURE 1. Structure of ionotropic glutamate receptors and ligands. A, an individual subunit is highlighted on the left and is formed by a single polypeptide chain beginning with the N-terminal LIVBP (leucine-isoleucine-valine-binding protein)-like domain, which is followed by S1 forming the majority of domain 1 (D1) of the ligand binding core (red). The amino acid chain then transverses domain 2 (D2) of the ligand binding core and forms M1, the P-loop, and M2. Subsequently, the rest of domain 2 (D2, blue) is formed by S2, ending up in the last transmembrane -helix (M3) and the intracellular C-terminal domain. The flip/flop region lies on the back, primarily of the D1. Scissors indicate where the corresponding receptor has been cleaved during construction of the GluR2-S1S2J construct. B, structures of selected AMPA receptor agonists.
Figure 7.
FIGURE 7. Details of the structure of GluR2-S1S2J(Y450W) in complex with kainate. A, schematic representation of the overall structure of GluR2-S1S2J(Y450W) with zoom on a F[o] - F[c] omit map contoured at 3.0 for kainate (blue in D1 and green in D2). B, stereo view of the ligand binding pocket of GluR2-S1S2J(Y450W) showing the hydrogen-bonding network to kainate (black). C, comparison of the ligand binding pocket of wild-type GluR2-S1S2J (6) (PDB code 1FT0 [PDB] , black) and GluR2-S1S2J(Y450W) (blue in D1 and green in D2), both in complex with kainate. The side chain of residue 450 is depicted showing the 6° difference of the aromatic wedge. Nitrogen atoms are blue, oxygen atoms are red, and sulfur atoms are yellow. The figure was prepared using Molscript (36) and Raster3d (37).
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 35469-35476) copyright 2005.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20713069 J.Pøhlsgaard, K.Frydenvang, U.Madsen, and J.S.Kastrup (2011).
Lessons from more than 80 structures of the GluA2 ligand-binding domain in complex with agonists, antagonists and allosteric modulators.
  Neuropharmacology, 60, 135-150.  
21280122 V.A.Muñiz, S.Srinivasan, S.A.Boswell, D.W.Meinhold, T.Childs, R.Osuna, and W.Colón (2011).
The role of the local environment of engineered Tyr to Trp substitutions for probing the denaturation mechanism of FIS.
  Protein Sci, 20, 302-312.  
20107073 A.Birdsey-Benson, A.Gill, L.P.Henderson, and D.R.Madden (2010).
Enhanced efficacy without further cleft closure: reevaluating twist as a source of agonist efficacy in AMPA receptors.
  J Neurosci, 30, 1463-1470.
PDB codes: 3kei 3kfm
18387631 M.K.Fenwick, and R.E.Oswald (2008).
NMR spectroscopy of the ligand-binding core of ionotropic glutamate receptor 2 bound to 5-substituted willardiine partial agonists.
  J Mol Biol, 378, 673-685.  
17260963 K.A.Mankiewicz, A.Rambhadran, M.Du, G.Ramanoudjame, and V.Jayaraman (2007).
Role of the chemical interactions of the agonist in controlling alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor activation.
  Biochemistry, 46, 1343-1349.  
17472701 P.Bannerman, M.Horiuchi, D.Feldman, A.Hahn, A.Itoh, J.See, Z.P.Jia, T.Itoh, and D.Pleasure (2007).
GluR2-free alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionate receptors intensify demyelination in experimental autoimmune encephalomyelitis.
  J Neurochem, 102, 1064-1070.  
17178406 A.Priel, S.Selak, J.Lerma, and Y.Stern-Bach (2006).
Block of kainate receptor desensitization uncovers a key trafficking checkpoint.
  Neuron, 52, 1037-1046.  
16554805 M.L.Mayer (2006).
Glutamate receptors at atomic resolution.
  Nature, 440, 456-462.  
16474411 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.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.