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Structural changes of regulatory domain heterodimer of N-methyl-D-aspartate receptor subunits GluN1 and GluN2B through the binding of spermine and ifenprodil.

ABSTRACT: Modeling the binding sites for spermine and ifenprodil on the regulatory (R) domains of the N-methyl-D-aspartate receptor GluN1 and GluN2B subunits was carried out after measuring spermine stimulation and ifenprodil inhibition at receptors containing GluN1 and GluN2B R domain mutants. Models were constructed based on the published crystal structure of the GluN1 and GluN2B R domains, which form a heterodimer (Nature 475:249-253, 2011). The experimental results and modeling suggest that a binding site for spermine was formed by the residues near the cleft between the R1 and R2 lobes of the GluN1 R domain (GluN1R) together with residues on the surface of the R2 (C-terminal side) lobe of the GluN2B R domain (GluN2BR). The ifenprodil binding site included residues on the surface of the R1 lobe (N-terminal side) of GluN1R together with residues near the cleft between the R1 and R2 lobes of GluN2BR. It was confirmed using a Western blot analysis that GluN1R and GluN2BR formed a heterodimer. Models of spermine and ifenprodil binding to the heterodimer were constructed. The modeling suggests that an open space between the two R1 lobes of GluN1R and GluN2BR is promoted through spermine binding and that the R1 lobes of GluN1R and GluN2BR approach each other through ifenprodil binding--an effect opposite to that seen with the binding of spermine.

SUBMITTER: Tomitori H

PROVIDER: S-EPMC3464035 | biostudies-literature | 2012 Oct

REPOSITORIES: biostudies-literature

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Structural changes of regulatory domain heterodimer of N-methyl-D-aspartate receptor subunits GluN1 and GluN2B through the binding of spermine and ifenprodil.

Tomitori Hideyuki H Suganami Akiko A Saiki Ryotaro R Mizuno Satomi S Yoshizawa Yuki Y Masuko Takashi T Tamura Yutaka Y Nishimura Kazuhiro K Toida Toshihiko T Williams Keith K Kashiwagi Keiko K Igarashi Kazuei K

The Journal of pharmacology and experimental therapeutics 20120628 1

Modeling the binding sites for spermine and ifenprodil on the regulatory (R) domains of the N-methyl-D-aspartate receptor GluN1 and GluN2B subunits was carried out after measuring spermine stimulation and ifenprodil inhibition at receptors containing GluN1 and GluN2B R domain mutants. Models were constructed based on the published crystal structure of the GluN1 and GluN2B R domains, which form a heterodimer (Nature 475:249-253, 2011). The experimental results and modeling suggest that a binding ...[more]

PMID: 22743575

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Project description:Here we report the isolation, kinetic characterization, and X-ray structure determination of a cooperative Escherichia coli aspartate transcarbamoylase (ATCase) without regulatory subunits. The native ATCase holoenzyme consists of six catalytic chains organized as two trimers bridged noncovalently by six regulatory chains organized as three dimers, c(6)r(6). Dissociation of the native holoenzyme produces catalytically active trimers, c(3), and nucleotide-binding regulatory dimers, r(2). By introducing specific disulfide bonds linking the catalytic chains from the upper trimer site specifically to their corresponding chains in the lower trimer prior to dissociation, a new catalytic unit, c(6), was isolated consisting of two catalytic trimers linked by disulfide bonds. Not only does the c(6) species display enhanced enzymatic activity compared to the wild-type enzyme, but the disulfide bonds also impart homotropic cooperativity, never observed in the wild-type c(3). The c(6) ATCase was crystallized in the presence of phosphate and its X-ray structure determined to 2.10 A resolution. The structure of c(6) ATCase liganded with phosphate exists in a nearly identical conformation as other R-state structures with similar values calculated for the vertical separation and planar angles. The disulfide bonds linking upper and lower catalytic trimers predispose the active site into a more active conformation by locking the 240s loop into the position characteristic of the high-affinity R state. Furthermore, the elimination of the structural constraints imposed by the regulatory subunits within the holoenzyme provides increased flexibility to the c(6) enzyme, enhancing its activity over the wild-type holoenzyme (c(6)r(6)) and c(3). The covalent linkage between upper and lower catalytic trimers restores homotropic cooperativity so that a binding event at one or so active sites stimulates binding at the other sites. Reduction of the disulfide bonds in the c(6) ATCase results in c(3) catalytic subunits that display kinetic parameters similar to those of wild-type c(3). This is the first report of an active c(6) catalytic unit that displays enhanced activity and homotropic cooperativity.

Dataset Information

Structural changes of regulatory domain heterodimer of N-methyl-D-aspartate receptor subunits GluN1 and GluN2B through the binding of spermine and ifenprodil.

Publications

Structural changes of regulatory domain heterodimer of N-methyl-D-aspartate receptor subunits GluN1 and GluN2B through the binding of spermine and ifenprodil.

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