Glutamate dehydrogenase of lupin nodules: kinetics of the deamination reaction

Structural Studies of Glutamate Dehydrogenase (Isoform 1) From Arabidopsis thaliana, an Important Enzyme at the Branch-Point Between Carbon and Nitrogen Metabolism

Glutamate dehydrogenase (GDH) releases ammonia in a reversible NAD(P)⁺-dependent oxidative deamination of glutamate that yields 2-oxoglutarate (2OG). In current perception, GDH contributes to Glu homeostasis and plays a significant role at the junction of carbon and nitrogen assimilation pathways. GDHs are members of a superfamily of ELFV (Glu/Leu/Phe/Val) amino acid dehydrogenases and are subdivided into three subclasses, based on coenzyme specificity: NAD⁺-specific, NAD⁺/NADP⁺ dual-specific, and NADP⁺-specific. We determined in this work that the mitochondrial AtGDH1 isozyme from A. thaliana is NAD⁺-specific. Altogether, A. thaliana expresses three GDH isozymes (AtGDH1-3) targeted to mitochondria, of which AtGDH2 has an extra EF-hand motif and is stimulated by calcium. Our enzymatic assays of AtGDH1 established that its sensitivity to calcium is negligible. In vivo the AtGDH1-3 enzymes form homo- and heterohexamers of varied composition. We solved the crystal structure of recombinant AtGDH1 in the apo-form and in complex with NAD⁺ at 2.59 and 2.03 Å resolution, respectively. We demonstrate also that both in the apo form and in 1:1 complex with NAD⁺, it forms D ₃-symmetric homohexamers. A subunit of AtGDH1 consists of domain I, which is involved in hexamer formation and substrate binding, and of domain II which binds coenzyme. Most of the subunits in our crystal structures, including those in NAD⁺ complex, are in open conformation, with domain II forming a large (albeit variable) angle with domain I. One of the subunits of the AtGDH1-NAD⁺ hexamer contains a serendipitous 2OG molecule in the active site, causing a dramatic (∼25°) closure of the domains. We provide convincing evidence that the N-terminal peptide preceding domain I is a mitochondrial targeting signal, with a predicted cleavage site for mitochondrial processing peptidase (MPP) at Leu17-Leu18 that is followed by an unexpected potassium coordination site (Ser27, Ile30). We also identified several MPD [(+/-)-2-methyl-2,4-pentanediol] binding sites with conserved sequence. Although AtGDH1 is insensitive to MPD in our assays, the observation of druggable sites opens a potential for non-competitive herbicide design.

Multiple Forms of Glutamate Dehydrogenase in Animals: Structural Determinants and Physiological Implications

Glutamate dehydrogenase (GDH) of animal cells is usually considered to be a mitochondrial enzyme. However, this enzyme has recently been reported to be also present in nucleus, endoplasmic reticulum and lysosomes. These extramitochondrial localizations are associated with moonlighting functions of GDH, which include acting as a serine protease or an ATP-dependent tubulin-binding protein. Here, we review the published data on kinetics and localization of multiple forms of animal GDH taking into account the splice variants, post-translational modifications and GDH isoenzymes, found in humans and apes. The kinetic properties of human GLUD1 and GLUD2 isoenzymes are shown to be similar to those published for GDH1 and GDH2 from bovine brain. Increased functional diversity and specific regulation of GDH isoforms due to alternative splicing and post-translational modifications are also considered. In particular, these structural differences may affect the well-known regulation of GDH by nucleotides which is related to recent identification of thiamine derivatives as novel GDH modulators. The thiamine-dependent regulation of GDH is in good agreement with the fact that the non-coenzyme forms of thiamine, i.e., thiamine triphosphate and its adenylated form are generated in response to amino acid and carbon starvation.

Regulation of peanut glutamate dehydrogenase by methionine sulphoximine

Peanut glutamate dehydrogenase (GDH) was electrophoretically purified to homogeneity. Rotofor IEF fractionated the peanut GDH to 7 isoelectric (charge) isomers, which focused in the pH 5-8 range. Western blot analysis of the charge isomers using anti-GDH serum showed that methionine sulphoximine (MSX) treatment suppressed the b-subunit (69 KDa), but enhanced the a-subunit (45 KDa), and alpha-subunit (46 KDa) of the enzyme. The MSX-mediated suppression of the b-subunit increased the NH4+ Km value of the acidic charge isomers from 7.7 mM in the control to 50 mM in the MSX-treated peanut, and also increased the 2-ketoglutarate Km value of the basic charge isomers from 0.4 mM in the control to 7.0 mM in the MSX treatment. Therefore, the control peanut could salvage NH4+ with its GDH activity. But by increasing the NH4+ Km value, the MSX rendered the enzyme ineffective in NH4+ salvage. In the deamination direction, despite the enhancement of the a-, and alpha-subunits by MSX, the basic charge isomers of GDH had very high Km value for L-glu (50 mM), similar to that (25 mM) of the control. Thus, the GDHs of the control, and MSX treatment could not function in the deamination reaction in vivo. These results show that the treatment of peanut with MSX impaired the amination function of GDH.

Steady state kinetics of the glutamate dehydrogenase from an archaebacterial extreme thermophile, isolate AN1

A steady state kinetic study was carried out with the glutamate dehydrogenase from the thermophilic, archaebacterial isolate AN1. Initial velocity studies of the oxidative deamination reaction showed the mechanism is sequential and indicated that the order of substrate addition is random, while inhibition studies with products and substrate analogues suggested a strong preference for NADP+ to bind first. Initial velocity studies of the reductive amination reaction showed that the mechanism is sequential and indicated that the order of substrate addition is random, while product inhibition studies and the effect of substrate saturation on the initial velocity suggested that the preferred order of substrate addition is NADPH, 2-ketoglutarate, ammonia.

Functional studies of a glutamate dehydrogenase with known three-dimensional structure: steady-state kinetics of the forward and reverse reactions catalysed by the NAD(+)-dependent glutamate dehydrogenase of Clostridium symbiosum

Steady-state kinetic properties of glutamate dehydrogenase from Clostridium symbiosum are reported. Rates with NADP(H) are over three hundred times lower than with NAD(H) under identical conditions. The 3-acetyl pyridine and 6-deamino adenine analogues of NAD+, on the other hand, are used almost as well as NAD+ itself. Amino acid specificity is very tight at both pH 7 and pH 9. The best alternative substrate of those tested, L-alpha-amino-gamma-nitraminobutyrate, gave only 0.5% of the rate seen with glutamate. With 400 microM NAD+ a 160-fold variation of the glutamate concentration gave a linear Eadie plot apart from slight inhibition at the highest concentrations. With 40 mM L-glutamate and varied [NAD+], the Eadie plot appeared linear between 1.6 microM and 60 microM and again between 60 microM and 2000 microM, but the slopes of the two lines differed by a factor of 8.4. This striking pattern is not attributable to impurities in the coenzyme or to changes in the state of aggregation of the enzyme. For the high concentration range (greater than 60 microM NAD+), the presence of all four linear terms in the reciprocal form of the initial rate equation indicates a sequential mechanism. Similar measurements made for APAD+ and dnNAD+ show no sign of non-linearity in the Eadie plot over the wide concentration ranges explored. In the reductive amination direction, with NADH as coenzyme, linear reciprocal plots were obtained for all three substrates. Systematic variation of concentrations led via primary, secondary and tertiary plots to all eight possible initial-rate parameters in a linear reciprocal initial-rate equation. Compulsory-order and enzyme-substitution mechanisms appear to be excluded, and a random route to the central complex seems the only possibility compatible with the results.

A kinetic study of the oxidative deamination of L-glutamate by Peptostreptococcus asaccharolyticus glutamate dehydrogenase using a variety of coenzymes

The NAD+-specific glutamate dehydrogenase from Peptostreptococcus asaccharolyticus follows Michaelis-Menten kinetics in contrast to the enzyme from several other sources, and thus gives linear double-reciprocal plots of initial-rate data. The initial-rate parameters have been determined for this bacterial dehyrogenase in the direction of oxidative deamination. The use of alternative coenzymes leads to some conclusions about the order of substrate addition. An investigation of the pH dependence of this reaction reveals that the binding of oxidised coenzyme is independent of pH over the range 6-9. The kinetic data are consistent with an ordered addition of coenzyme prior to glutamate, the reverse of the mechanism derived with ox glutamate dehydrogenase in the presence of ADP.

Bicarbonate and the pathway of glutamate oxidation in isolated rat-liver mitochondria

1. The factors affecting the pathway of glutamate oxidation were studied in isolated rat-liver mitochondria in incubations of 2-3 min. 2. It was found that bicarbonate at a physiological concentration has a profound effect on the pathway of glutamate oxidation. Ammonia formation via glutamate dehydrogenase is stimulated by bicarbonate [from 5.48 +/- 0.29 (n = 10) to 9.57 +/- 0.73 (n = 8) nmol X min-1 X mg protein-1], whereas aspartate formation via the transamination pathway is inhibited [from 38.41 +/- 2.24 (n = 9) to 24.56 +/- 3.28 (n = 6) nmol X min-1 X mg protein-1]. 3. Bicarbonate has no effect on the rate of transport of glutamate via the glutamate-hydroxyl translocator. 4. The interaction of bicarbonate with the pathway of glutamate oxidation occurs primarily at the level of succinate dehydrogenase, due to competitive inhibition of the enzyme by bicarbonate. 5. Inhibition by bicarbonate of the transamination pathway leads to a decrease in intramitochondrial 2-oxoglutarate, so that the deamination pathway is stimulated. 6. Using an equation which describes flux through glutamate dehydrogenase kinetically, it could be shown that the bicarbonate-induced decrease in intramitochondrial 2-oxoglutarate quantitatively accounts for the enhanced rate of deamination. 7. It is concluded that in the intact liver flux through glutamate dehydrogenase is sufficient to account for the ammonia formation required for urea synthesis from substrates such as alanine.