PDBsum entry 3gbb

Membrane protein

PDB id: 3gbb

Contents

Protein chains

255 a.a. *

Ligands

MS8 ×2

Waters ×346

* Residue conservation analysis

PDB id:

3gbb

Name:

Membrane protein

Title:

X-ray structure of iglur5 ligand-binding core (s1s2) in complex with msviii-19 at 2.10a resolution

Structure:

Glutamate receptor, ionotropic kainate 1. Chain: a, b. Fragment: iglur5 ligand-binding core (s1s2). Synonym: glutamate receptor 5, glur-5, glur5. Engineered: yes

Source:

Rattus norvegicus. Rat. Organism_taxid: 10116. Gene: glur5, grik1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.201 R-free: 0.251

Authors:

K.Frydenvang,P.Naur,M.Gajhede,J.S.Kastrup

Key ref:

K.Frydenvang et al. (2009). Full domain closure of the ligand-binding core of the ionotropic glutamate receptor iGluR5 induced by the high-affinity agonist dysiherbaine and the functional antagonist MSVIII-19. J Biol Chem, 284, 14219-14229. PubMed id: 19297335 DOI: 10.1074/jbc.M808547200

Date:

19-Feb-09 Release date: 17-Mar-09

Protein chains

P22756  (GRIK1_RAT) -  Glutamate receptor ionotropic, kainate 1 from Rattus norvegicus

Seq: 949 a.a.

Struc: 255 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1074/jbc.M808547200

J Biol Chem 284:14219-14229 (2009)

PubMed id: 19297335

Full domain closure of the ligand-binding core of the ionotropic glutamate receptor iGluR5 induced by the high-affinity agonist dysiherbaine and the functional antagonist MSVIII-19.

K.Frydenvang, L.L.Lash, P.Naur, P.A.Postila, D.S.Pickering, C.M.Smith, M.Gajhede, M.Sasaki, R.Sakai, O.T.Pentikäinen, G.T.Swanson, J.S.Kastrup.

ABSTRACT

The prevailing structural model for ligand activation of ionotropic glutamate receptors posits that agonist efficacy arises from the stability and magnitude of induced domain closure in the ligand-binding core structure. Here we describe an exception to the correlation between ligand efficacy and domain closure. A weakly efficacious partial agonist of very low potency for homomeric iGluR5 kainate receptors, 8,9-dideoxy-neodysiherbaine (MSVIII-19), induced a fully closed iGluR5 ligand-binding core. The degree of relative domain closure, ~30 degrees , was similar to that we resolved with the structurally related high-affinity agonist dysiherbaine (DH), and to that of L-glutamate. The pharmacological activity of MSVIII-19 was confirmed in patch-clamp recordings from transfected HEK293 cells, where MSVIII-19 predominantly inhibits iGluR5-2a, with little activation apparent at a high concentration (1 mM) of MSVIII-19 (<1% of mean glutamate-evoked currents). To determine the efficacy of the ligand quantitatively, we constructed concentration-response relationships for MSVIII-19 following potentiation of steady-state currents with concanavalin A (EC50 3.6 muM) and on the non-desensitizing receptor mutant iGluR5-2b(Y506C/L768C) (EC50 8.1 muM). MSVIII-19 exhibited a maximum of 16% of full agonist efficacy as measured in parallel recordings with glutamate. Molecular dynamics simulations and electrophysiological recordings confirm that the specificity of MSVIII-19 for iGluR5 is partly attributable to inter-domain hydrogen bonds residues Glu441 and Ser721 in the iGluR5-S1S2 structure. The weaker interactions of MSVIII-19 with iGluR5 compared to DH, together with altered stability of the inter-domain interaction, may be responsible for the apparent uncoupling of domain closure and channel opening in this kainate receptor subunit.

Selected figure(s)

Figure 1.
Chemical structures of dysiherbaine and MSVIII-19. The two compounds differ in positions C8 (NH-Me substituent in DH versus H in MSVIII-19) and C9 (OH versus H).

Figure 3.
MSVIII-19 induces full domain closure in the ligand-binding core of iGluR5. A, superimposition of the MSVIII-19 (cyan), DH (yellow), and l-glutamate (Protein Data Bank code 1YCJ, molecule A; salmon) complexes with iGluR5-S1S2 on D1 residues. B, superimposition of the MSVIII-19 (cyan) and UBP302 (Protein Data Bank code 2F35, molecule A; blue) complexes with iGluR5-S1S2 on D1 residues. The high degree of domain closure introduced by MSVIII-19 compared with UBP302 is evident from the change of the D2 domain position.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 14219-14229) copyright 2009.

Figures were selected by an automated process.