Virtually all organisms share a few common routes for the utilization of inorganic nitrogen in the form of ammonia. At low levels, ammonia is a central metabolite, but at high levels it is quite toxic. Ammonia is a substrate for five enzymes that convert it to various organic nitrogen compounds.

All organisms assimilate ammonia via reactions leading to glutamate, glutamine, asparagine, and carbamoyl phosphate (Figure 20.7, see below). Most of the nitrogen that finds its way from ammonia to amino acids and other nitrogenous compounds does so via glutamate and glutamine. Thus, the amino nitrogen of glutamate and the amide nitrogen of glutamine are extremely active in biosynthesis.

Glutamate formation - Glutamate dehydrogenase catalyzes the reductive amination of -ketoglutarate:

-Ketoglutarate + NH3 + NAD(P)H + 2H⁺ <=> Glutamate + H2O + NAD(P)

Bacteria growing with ammonia as their sole nitrogen source use this reaction as the primary route for nitrogen assimilation. In animal cells, the reversible reaction can function in either direction. The enzyme is allosterically regulated. ATP or GTP inhibits its action. Glutamate synthase catalyzes a similar reaction:

-Ketoglutarate + Glutamine + NADPH + H⁺ -> 2 Glutamate +  NADP⁺

Glutamate synthase probably plays a larger role in glutamate synthesis in most cells than glutamate dehydrogenase, due to the high KM of the glutamate dehydrogenase for NH3.

Glutamine formation - Glutamine synthetase catalyzes the following reaction:

Glutamate + NH3 + ATP -> Glutamine + ADP + Pi

The E. coli glutamine synthetase is a dodecamer, with 12 identical subunits and the complex has a molecular weight of about 600,000 Daltons. The amide nitrogen of glutamate is used for the synthesis of several amino acids, purine and pyrimidine nucleotides, and amino sugars, so glutamine synthetase plays a central role in nitrogen metabolism. In animals, the enzyme is a key participant in detoxifying ammonia, particularly in the brain, and in ammonia excretion in the kidney. Accumulation of glutamate and glutamine depletes -ketoglutarate, which would interfere with the citric acid cycle. As a result, glutamine synthetase tightly regulated. Mechanisms include the following:

Cumulative feedback Inhibition - Eight specific feedback inhibitors, which are either metabolic end products of glutamine (tryptophan, histidine, glucosamine-6-phosphate, carbamoyl phosphate, CTP, or AMP) or indicators of the general status of amino acid metabolism (alanine or glycine), can bind to any of the subunits of the enzyme and at least partially inhibit it. The more inhibitors that bind, the greater the inhibition.

Covalent modification (adenylylation) - A specific tyrosine residue in glutamine synthetase can react with ATP to form a phosphate ester with AMP (see here). Adenylylation renders the catalytic site of the enzyme inactive. Adenylylation and deadenylylation involve a complex series of regulatory cascades. Figure 20.9 shows regulatory mechanisms of the E. coli enzyme. Both processes are catalyzed by the same enzyme-a complex of adenylyl transferase (AT) and a regulatory protein, PII. The form of PII determines whether the AT-PII complex catalyzes adenylylation or deadenylylation. If PII is uridylyated, the AT-PII complex catalyzes deadenylylation. Deuridylylation of PII causes the AT-PII complex to catalyze adenylylation. The enzyme uridylyl transferase catalyzes uridylylation of PII, whereas deuridylylation is catalyzed by a different enzyme. Uridylyl transferase is allosterically regulated, with ATP and -ketoglutarate activating it and glutamine inhibits it.

Asparagine formation - Asparagine synthetase catalyzes the conversion of aspartate to asparagine as follows:

Aspartate + ATP + NH3 (Gln) -> Asparagine + AMP + PPi + (Glu)

Note that asparagine synthetase cleaves ATP to yield AMP + PPi, whereas glutamine synthetase yields ADP + Pi. Glutamine (Gln) is a preferred substrate over ammonia.

Carbamoyl phosphate formation - Carbamoyl Phosphate Synthetase catalyzes the formation of carbamoyl phosphate in the following two reactions (glutamine is the preferred substrate):

NH3 + HCO3^- + 2ATP -> Carbamoyl Phosphate + 2ADP + Pi

Glutamine + HCO3^- + 2ATP + H2O -> Carbamoyl Phosphate + 2 ADP + Pi + Glutamate

A bacterial reaction catalyzes both reactions. In eukaryotes, two forms of the enzyme (one in mitochondria and one in cytoplasm) are found. The enzyme is inhibited by UTP, consistent with the involvement of carbamoyl phosphate in pyrimidine nucleotide synthesis.