PDBsum entry 1p1n

Membrane protein

PDB id: 1p1n

Contents

Protein chain

258 a.a. *

Ligands

KAI

Waters ×123

* Residue conservation analysis

PDB id:

1p1n

Name:

Membrane protein

Title:

Glur2 ligand binding core (s1s2j) mutant l650t in complex with kainate

Structure:

Glutamate receptor 2. Chain: a. Fragment: ligand binding core (s1s2j). 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 or glur2. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Dimer (from PDB file)

Resolution:

1.60Å R-factor: 0.235 R-free: 0.252

Authors:

N.Armstrong,M.L.Mayer,E.Gouaux

Key ref:

N.Armstrong et al. (2003). Tuning activation of the AMPA-sensitive GluR2 ion channel by genetic adjustment of agonist-induced conformational changes. Proc Natl Acad Sci U S A, 100, 5736-5741. PubMed id: 12730367 DOI: 10.1073/pnas.1037393100

Date:

13-Apr-03 Release date: 10-Jun-03

Protein chain

P19491  (GRIA2_RAT) -  Glutamate receptor 2 from Rattus norvegicus

Seq: 883 a.a.

Struc: 258 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DOI no: 10.1073/pnas.1037393100

Proc Natl Acad Sci U S A 100:5736-5741 (2003)

PubMed id: 12730367

Tuning activation of the AMPA-sensitive GluR2 ion channel by genetic adjustment of agonist-induced conformational changes.

N.Armstrong, M.Mayer, E.Gouaux.

ABSTRACT

The (S)-2-amino-3-(3-hydroxy-5-methyl-4-isoxazole) propionic acid (AMPA) receptor discriminates between agonists in terms of binding and channel gating; AMPA is a high-affinity full agonist, whereas kainate is a low-affinity partial agonist. Although there is extensive literature on the functional characterization of partial agonist activity in ion channels, structure-based mechanisms are scarce. Here we investigate the role of Leu-650, a binding cleft residue conserved among AMPA receptors, in maintaining agonist specificity and regulating agonist binding and channel gating by using physiological, x-ray crystallographic, and biochemical techniques. Changing Leu-650 to Thr yields a receptor that responds more potently and efficaciously to kainate and less potently and efficaciously to AMPA relative to the WT receptor. Crystal structures of the Leu-650 to Thr mutant reveal an increase in domain closure in the kainate-bound state and a partially closed and a fully closed conformation in the AMPA-bound form. Our results indicate that agonists can induce a range of conformations in the GluR2 ligand-binding core and that domain closure is directly correlated to channel activation. The partially closed, AMPA-bound conformation of the L650T mutant likely captures the structure of an agonist-bound, inactive state of the receptor. Together with previously solved structures, we have determined a mechanism of agonist binding and subsequent conformational rearrangements.

Selected figure(s)

Figure 4.
Fig. 4. Comparison of WT and S1S2J L650T/AMPA(AS) conformations. (A) Superposition of WT S1S2J/AMPA (gray) with S1S2J L650T/AMPA (AS form) protomer A (blue). (B) Superposition of WT S1S2J/AMPA (gray) with S1S2J L650T/AMPA(AS) protomer B (green). The black arrows in A and B indicate the axis of rotation relating the conformational difference between the WT and L650T structures. (C) Superimposed WT and mutant AMPA dimers.

Figure 6.
Fig. 6. Mechanism of agonist binding and domain closure. (A) The binding site of the open-cleft, closed-channel state (Apo S1S2J, protomer A). (B) The possible first step in agonist binding as observed in molecule B of the L650T/AMPA(AS) structure. We suggest that this semiclosed cleft conformation represents the agonist-bound, closed-channel state. (C) The closed-cleft, open-channel conformation as observed in the WT S1S2J/AMPA binding cleft (protomer A). In B and C, water molecules are shown as green spheres, AMPA is drawn in magenta, and hydrogen bonds are depicted by black dashed lines. The degrees of domain closure relative to the Apo conformation are indicated below each structure.

Figures were selected by an automated process.