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PDBsum entry 1ii5
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Membrane protein
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PDB id
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1ii5
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Mechanisms for ligand binding to glur0 ion channels: crystal structures of the glutamate and serine complexes and a closed apo state.
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Authors
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M.L.Mayer,
R.Olson,
E.Gouaux.
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Ref.
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J Mol Biol, 2001,
311,
815-836.
[DOI no: ]
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PubMed id
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Abstract
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High-resolution structures of the ligand binding core of GluR0, a glutamate
receptor ion channel from Synechocystis PCC 6803, have been solved by X-ray
diffraction. The GluR0 structures reveal homology with bacterial periplasmic
binding proteins and the rat GluR2 AMPA subtype neurotransmitter receptor. The
ligand binding site is formed by a cleft between two globular alpha/beta
domains. L-Glutamate binds in an extended conformation, similar to that observed
for glutamine binding protein (GlnBP). However, the L-glutamate gamma-carboxyl
group interacts exclusively with Asn51 in domain 1, different from the
interactions of ligand with domain 2 residues observed for GluR2 and GlnBP. To
address how neutral amino acids activate GluR0 gating we solved the structure of
the binding site complex with L-serine. This revealed solvent molecules acting
as surrogate ligand atoms, such that the serine OH group makes solvent-mediated
hydrogen bonds with Asn51. The structure of a ligand-free, closed-cleft
conformation revealed an extensive hydrogen bond network mediated by solvent
molecules. Equilibrium centrifugation analysis revealed dimerization of the
GluR0 ligand binding core with a dissociation constant of 0.8 microM. In the
crystal, a symmetrical dimer involving residues in domain 1 occurs along a
crystallographic 2-fold axis and suggests that tetrameric glutamate receptor ion
channels are assembled from dimers of dimers. We propose that ligand-induced
conformational changes cause the ion channel to open as a result of an increase
in domain 2 separation relative to the dimer interface.
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Figure 9.
Figure 9. Molecular surface properties of GluR dimer
interfaces. (a) Dimer surface of a GluR0 subunit (left) showing
in yellow atoms making van der Waals contacts with the partner
subunit; main-chain carbonyl and side-chain oxygen atoms making
hydrogen-bond contacts are red; the side-chain amide groups of
Gln127, Asn349 and Gln353 are colored cyan; the NZ atom of
Lys345 is blue; (right) surface view colored by electrostatic
surface potential which changes smoothly from red ( -10 kT)
through white (neutral) to blue (+10 kT). The calculation was
performed in the absence of the dimer partner assuming an ionic
strength equivalent to 150 mM NaCl, and dielectric constants of
2 and 80 for protein and solvent. (b) Surface properties of the
GluR2 dimer interface colored using the same scheme as for
GluR0. (c) Structure-based alignments of the dimer interface
contact regions for GluR0 and GluR2 plus the corresponding
sequence for GlnBP, LAOBP and HisBP; residues boxed in purple
make van der Waals contacts in the dimer interface; cyan
indicates residues making hydrogen-bond contacts; asterisks
denote hydrophobic side-chains in GluR0 and GluR2, which are
replaced by Gly or by polar residues in GlnBP.
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Figure 10.
Figure 10. Gating models for GluR activation and
desensitization. Cyan and bronze rods indicate domains 1 and 2
of the ligand binding core; green rods indicate membrane
spanning helices. At rest the ligand binding domains are relaxed
and the ion channel is closed. Binding of agonists promotes
domain closure; due to the dimer interface contacts made by
domain 1, agonists produce an increase in separation of the
domain 2 protomers; this scissors-like movement opens the ion
channel by causing rotation and translation of the transmembrane
helices. During desensitization the ligand binding domains
remain closed; we speculate that movement of the dimer interface
reduces the separation between domain 2 protomers and allows the
channel to enter a non-conducting state.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2001,
311,
815-836)
copyright 2001.
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Secondary reference #1
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Title
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Functional characterization of a potassium-Selective prokaryotic glutamate receptor.
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Authors
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G.Q.Chen,
C.Cui,
M.L.Mayer,
E.Gouaux.
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Ref.
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Nature, 1999,
402,
817-821.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1 GluR0 is related to eukaryotic GluRs (eGluRs) and to
potassium channels. Domain structures for prokaryotic GluRs
(pGluRs) such as GluR0 and eukaryotic GluRs and for the
transmembrane segments of the KcsA potassium channel are shown
in the centre of the Figure. Extracellular portions of GluRs
that comprise the ligand-binding core (S1 and S2) are shown in
purple and the membrane-associated regions are turquoise. Top,
alignments of the sequences of selected GluRs in structurally or
functionally important areas. Conserved or conservatively
substituted residues are highlighted: residues in or near the
ligand-binding site are green; residues in key structural areas
are violet; and Leu 361, which is predicted to form an exposed
hydrophobic patch on helix J, is pink. Bottom left, alignments
of the P and M2 regions of GluR0, KcsA and eukaryotic GluRs,
with conserved or conservatively substituted residues
highlighted in blue. A blue bar is drawn over the residues
comprising the selectivity filter in GluR0 and KcsA. Shown above
S1 and S2 and below P and M2 are elements of secondary structure
derived from the GluR2 S1S2 and KcsA structures, respectively13,
17. Bottom right, the predicted membrane topology of pGluRs
(GluR0) and the membrane topologies of eukaryotic GluRs and
KcsA; glutamate is shown as a pink circle. Sequences are defined
as follows: GluR0, NCBI Entrez accession number 1652933; Ara (a
putative eukaryotic GluR from Arabidopsis thaliana); NR2B (rat);
 1
(rat); GluR6 (rat); GluR2 (rat, flop)2; KcsA (Streptomyces
lividans)3.
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Figure 2.
Figure 2 GluR0 binds L-glutamate, L-glutamine and other amino
acids. a, Different parts of the glutamate structure were varied
to probe ligand structure-activity relationships: D-glutamate,
 -carbon
stereochemistry;  -Ala,
location of amino group; L-aspartate, L- -amino
adipic acid (L-AA), and D,L- -aminopimelic
acid (APA), chain length; L-glutamine, L-AP[4] and L-homocysteic
acid (HCA), carboxylic acid group; the 20 amino acids,
side-chain composition. b, Ligands competing for the binding of
3H-L-Glu to GluR0 S1S2 using a 1:10^5 molar ratio of 3H-L-Glu to
cold ligand. The measurement using L-Glu was taken as 100%
inhibition, and other values were normalized accordingly.
Compounds were examined at 1 mM to detect low-affinity ligands.
At 1 mM, L-glutamate, L-glutamine and HCA most effectively
compete for 3H-L-glutamate binding to GluR0 S1S2; L-serine,
L-alanine, L-threonine, glycine, L-AA, APA and DNQX (DX) are
significantly less potent. In contrast to eukaryotic GluRs, 1 mM
AMPA, kainate (KAI) and NMDA (NM) do not block binding of
3H-L-glutamate to GluR0 S1S2. Each measurement was carried out
in triplicate. c, The K[d] of 3H-L-glutamate binding to GluR0
S1S2 is  215
nM. Measurements were performed in triplicate and by
filter-binding and resin-binding methods. d, Pharmacological
profile of GluR0. IC[50] values for selected ligands are:
L-glutamate, 0.116 然; HCA, 1.62 然; L-glutamine, 16.3 然;
L-serine, 30.0 然; glycine, 303 然. IC[50] data were from
duplicate measurements. All points are given as mean  s.e.m.
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The above figures are
reproduced from the cited reference
with permission from Macmillan Publishers Ltd
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