PDBsum entry 1ii5

Membrane protein

PDB id: 1ii5

Contents

Protein chain

221 a.a. *

Ligands

GLU

Waters ×134

* Residue conservation analysis

PDB id:

1ii5

Name:

Membrane protein

Title:

Crystal structure of the glur0 ligand binding core complex with l- glutamate

Structure:

Slr1257 protein. Chain: a. Fragment: glur0 ligand binding core, residues 44-140, 256-385. Engineered: yes

Source:

Synechocystis sp. Pcc 6803 substr. Kazusa. Organism_taxid: 1111708. Strain: pcc 6803 / kazusa. Gene: glur0 slr1257, slr1257. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.60Å R-factor: 0.216 R-free: 0.263

Authors:

M.L.Mayer,R.Olson,E.Gouaux

Key ref:

M.L.Mayer et al. (2001). Mechanisms for ligand binding to GluR0 ion channels: crystal structures of the glutamate and serine complexes and a closed apo state. J Mol Biol, 311, 815-836. PubMed id: 11518533 DOI: 10.1006/jmbi.2001.4884

Date:

20-Apr-01 Release date: 19-Sep-01

Protein chain

P73797  (P73797_SYNY3) -  Slr1257 protein from Synechocystis sp. (strain PCC 6803 / Kazusa)

Seq: 397 a.a.

Struc: 221 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

DOI no: 10.1006/jmbi.2001.4884

J Mol Biol 311:815-836 (2001)

PubMed id: 11518533

Mechanisms for ligand binding to GluR0 ion channels: crystal structures of the glutamate and serine complexes and a closed apo state.

M.L.Mayer, R.Olson, E.Gouaux.

ABSTRACT

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.

Selected figure(s)

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.

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.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 311, 815-836) copyright 2001.

Figures were selected by an automated process.