The structure and allosteric regulation of glutamate dehydrogenase

Glutamate dehydrogenase (GDH) has been extensively studied for more than 50 years. Of particular interest is the fact that, while considered by most to be a ‘housekeeping’ enzyme, the animal form of GDH is heavily regulated by a wide array of allosteric effectors and exhibits extensive inter-subunit communication. While the chemical mechanism for GDH has remained unchanged through epochs of evolution, it was not clear how or why animals needed to evolve such a finely tuned form of this enzyme. As reviewed here, recent studies have begun to elucidate these issues. Allosteric regulation first appears in the Ciliates and may have arisen to accommodate evolutionary changes in organelle function. The occurrence of allosteric regulation appears to be coincident with the formation of an ‘antenna’ like feature rising off the tops of the subunits that may be necessary to facilitate regulation. In animals, this regulation further evolved as GDH became integrated into a number of other regulatory pathways. In particular, mutations in GDH that abrogate GTP inhibition result in dangerously high serum levels of insulin and ammonium. Therefore, allosteric regulation of GDH plays an important role in insulin homeostasis. Finally, several compounds have been identified that block GDH-mediated insulin secretion that may be to not only find use in treating these insulin disorders but to kill tumors that require glutamine metabolism for cellular energy.     

The structure and allosteric regulation of mammalian glutamate dehydrogenase

Glutamate dehydrogenase (GDH) is a homohexameric enzyme that catalyzes the reversible oxidative deamination of l-glutamate to 2-oxoglutarate. Only in the animal kingdom is this enzyme heavily allosterically regulated by a wide array of metabolites. The major activators are ADP and leucine, while the most important inhibitors include GTP, palmitoyl CoA, and ATP. Recently, spontaneous mutations in the GTP inhibitory site that lead to the hyperinsulinism/hyperammonemia (HHS) syndrome have shed light as to why mammalian GDH is so tightly regulated. Patients with HHS exhibit hypersecretion of insulin upon consumption of protein and concomitantly extremely high levels of ammonium in the serum. The atomic structures of four new inhibitors complexed with GDH complexes have identified three different allosteric binding sites. Using a transgenic mouse model expressing the human HHS form of GDH, at least three of these compounds were found to block the dysregulated form of GDH in pancreatic tissue. EGCG from green tea prevented the hyper-response to amino acids in whole animals and improved basal serum glucose levels. The atomic structure of the ECG-GDH complex and mutagenesis studies is directing structure-based drug design using these polyphenols as a base scaffold. In addition, all of these allosteric inhibitors are elucidating the atomic mechanisms of allostery in this complex enzyme.     

Structural basis for leucine-induced allosteric activation of glutamate dehydrogenase

Glutamate dehydrogenase (GDH) catalyzes reversible conversion between glutamate and 2-oxoglutarate using NAD(P)(H) as a coenzyme. Although mammalian GDH is regulated by GTP through the antenna domain, little is known about the mechanism of allosteric activation by leucine. An extremely thermophilic bacterium, Thermus thermophilus, possesses GDH with a unique subunit configuration composed of two different subunits, GdhA (regulatory subunit) and GdhB (catalytic subunit). T. thermophilus GDH is unique in that the enzyme is subject to allosteric activation by leucine. To elucidate the structural basis for leucine-induced allosteric activation of GDH, we determined the crystal structures of the GdhB-Glu and GdhA-GdhB-Leu complexes at 2.1 and 2.6 Å resolution, respectively. The GdhB-Glu complex is a hexamer that binds 12 glutamate molecules: six molecules are bound at the substrate-binding sites, and the remaining six are bound at subunit interfaces, each composed of three subunits. The GdhA-GdhB-Leu complex is crystallized as a heterohexamer composed of four GdhA subunits and two GdhB subunits. In this complex, six leucine molecules are bound at subunit interfaces identified as glutamate-binding sites in the GdhB-Glu complex. Consistent with the structure, replacement of the amino acid residues of T. thermophilus GDH responsible for leucine binding made T. thermophilus GDH insensitive to leucine. Equivalent amino acid replacement caused a similar loss of sensitivity to leucine in human GDH2, suggesting that human GDH2 also uses the same allosteric site for regulation by leucine.     

Structural requirements for maximal inhibitory allosteric effect of estrogens and estrogen analogues on glutamate dehydrogenase

The inhibition of glutamate dehydrogenase by estrogens, estrogen analogues or polyphenylethylene derivatives (about one hundred molecules, most of them having estrogenic or antiestrogenic activities) was measured. The efficiency of these compounds in inducing allosteric inhibition of the enzyme was compared and correlated to their chemical structure: an aromatic ring A, a free phenolic group in the region of carbon 3 of the steroid nucleus and a lipophilic substitution in the region of C-12, C-13 or C-17 were found to be the main structural features required for maximal efficiency on glutamate dehydrogenase. A tentative model for the relative orientation of the main inhibitor families is proposed. It accounts for most of the kinetic results and can be used as a tool for the selection of affinity labels directed towards the estrogen binding site of glutamate dehydrogenase.     

Kinetic studies of glutamate dehydrogenase with glutamate and norvaline as substrates. Coenzyme activation and negative homotropic interactions in allosteric enzymes

1. Kinetic studies of glutamate dehydrogenase were made with wide concentration ranges of the coenzymes NAD(+) and NADP(+) and the substrates glutamate and norvaline. Initial-rate parameters were evaluated. 2. Deviations from Michaelis-Menten behaviour towards higher activity were observed with increasing concentrations of either coenzyme with glutamate as substrate, but not with norvaline as substrate. 3. In phosphate buffer, pH7.0, Lineweaver-Burk plots with either coenzyme as variable and a constant, large glutamate concentration showed three or four linear regions of different slope with relatively sharp discontinuities. Maximum rates obtained by extrapolation and Michaelis constants for the coenzymes increased in steps with increase of coenzyme concentration. 4. In the absence of evidence of heterogeneity of the enzyme and coenzyme preparations, the results are interpreted in terms of negative homotropic interactions between the enzyme subunits. It is suggested that sharp discontinuities in Lineweaver-Burk plots or reciprocal binding plots may be characteristic of this new type of interaction, which can be explained in terms of an Adair-Koshland model, but not by the model of Monod, Wyman & Changeux.     

Kinetic studies of ox-liver glutamate dehydrogenase oxidative deamination of two glutamate analogues, L-threo-gamma-methylglutamate and L-alpha-amino-gamma-nitraminobutyrate, in the presence of the allosteric effector ADP

Ox-liver glutamate dehydrogenase is known to utilise a wide range of amino acid substrates. Kinetic studies are presented here for L-threo-gamma-methylglutamate and L-alpha-amino-gamma-nitraminobutyrate in the presence of the allosteric effector ADP. The results presented are considered in the light of similar studies presented elsewhere in which the cofactor was systematically replaced by a variety of analogues. These amino acid analogues share the same pH optimum as glutamate, unlike the monocarboxylic amino acids including alanine and norvaline, and give linear double-reciprocal plots under the conditions used here. Studies with the alternative coenzymes have suggested an ordered addition of glutamate before coenzyme in the presence of ADP. The present results obtained under identical conditions support this conclusion.     

Novel missense mutations outside the allosteric domain of glutamate dehydrogenase are prevalent in European patients with the congenital hyperinsulinism-hyperammonemia syndrome

The hyperinsulinism-hyperammonemia syndrome (HHS) has been shown to result from 'gain-of-function' mutations of the glutamate dehydrogenase (GlDH) gene, GLUD1. In the original report, all mutations were found in a narrow range of 27 base pairs within exons 11 and 12 which predicted an effect on the presumed allosteric domain of the enzyme and all these mutations were associated by a diminished inhibitory effect of guanosine triphosphate (GTP) on GlDH activity. We have investigated 14 patients from seven European families with mild hyperinsulinism. In four families, more than one member was affected. In eight cases hyperammonemia was documented, and eight cases had signs of significant leucine sensitivity. In one of the families, a novel heterozygous missense mutation in exon 6 [c.833C>T (R221C)] was detected, and in all other cases from six unrelated families the novel heterozygous missense mutation c.978G>A (R269H) was found in exon 7. When GIDH activity was measured in lymphocytes isolated from affected patients, both mutations were shown to result in a normal basal activity but a diminished sensitivity to GTP. It is the first time that this effect is reported for mutations located in the presumed catalytic site and outside the GTP allosteric domain of the enzyme. The observation of the high prevalence of the exon 7 mutation both in familial and sporadic cases of HHS suggests a mutation hot spot and justifies a mutation screening for this novel mutation by mismatch PCR-based restriction enzyme digestion in patients with hyperinsulinism.     

Mechanism of the glutamate dehydrogenase reaction

The data concerning the chemical and kinetic mechanisms of the glutamate dehydrogenase reaction have been reviewed. Based on the differences between two catalytically active glutamate dehydrogenase conformations induced by the substrates as well as on some other evidence, it has been proposed that the amino groups of lysine residues 27 and 126 in the beef liver enzyme are interchangeable depending on the direction of the glutamate dehydrogenase reaction.     

Dynamical structure of glutamate dehydrogenase as monitored by tryptophan phosphorescence. Signal transmission following binding of allosteric effectors

Changes in conformation of glutamate dehydrogenase from beef liver as a result of interactions with allosteric effectors have been demonstrated from the phosphorescence emission of tryptophan. The triplet state lifetime shows that whereas activators ADP and L-leucine enhance considerably the rigidity of the protein structure surrounding the chromophore, inhibitors GTP, Zn2+ and Ag+ act in an opposite manner increasing the flexibility of this region of the macromolecule. Such changes in dynamical structure of the protein are confirmed independently for the ADP and GTP complexes by oxygen diffusion studies. Phosphorescence lifetime measurements at various protein concentrations and with the enzyme crosslinked by glutaraldehyde demonstrate that ADP and GTP exert the same effect on the structure of the protein regardless of its degree of polymerization. The connection between changes in protein structure and regulatory function is strengthened by the finding that (1) ligands with no regulatory function (Eu3+) do not affect protein structure; (2) pairs of opposite effectors which neutralize each other's influence on catalytic activity do restore an apparent native-like structure in the enzyme. Mutual neutralization and the observation that ADP and GTP display maximum activity at partial saturation of the binding sites has been interpreted in terms of a model which assumes asymmetry in the hexameric enzyme at the trimer level. Evidence for the existence of conformational heterogeneity among the subunits of the enzyme has been provided.