NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.

Berg JM, Tymoczko JL, Stryer L. Biochemistry. 5th edition. New York: W H Freeman; 2002.

  • By agreement with the publisher, this book is accessible by the search feature, but cannot be browsed.
Cover of Biochemistry

Biochemistry. 5th edition.

Show details

Section 23.3The First Step in Amino Acid Degradation Is the Removal of Nitrogen

What is the fate of amino acids released on protein digestion or turnover? Any not needed as building blocks are degraded to specific compounds. The major site of amino acid degradation in mammals is the liver. The amino group must be removed, inasmuch as there are no nitrogenous compounds in energy-transduction pathways. The α-ketoacids that result from the deamination of amino acids are metabolized so that the carbon skeletons can enter the metabolic mainstream as precursors to glucose or citric acid cycle intermediates. The fate of the α-amino group will be considered first, followed by that of the carbon skeleton (Section 23.5).

23.3.1. Alpha-Amino Groups Are Converted into Ammonium Ions by the Oxidative Deamination of Glutamate

The α-amino group of many amino acids is transferred to α-ketoglutarate to form glutamate, which is then oxidatively deaminated to yield ammonium ion (NH4+).

Image ch23fu3.jpg

Aminotransferases catalyze the transfer of an α-amino group from an α-amino acid to an α-ketoacid. These enzymes, also called transaminases, generally funnel α-amino groups from a variety of amino acids to α-keto-glutarate for conversion into NH4+.

Image ch23fu4.jpg

Aspartate aminotransferase, one of the most important of these enzymes, catalyzes the transfer of the amino group of aspartate to α-ketoglutarate.

Image ch23e1.jpg

Alanine aminotransferase catalyzes the transfer of the amino group of alanine to α-ketoglutarate.

Image ch23e2.jpg

These transamination reactions are reversible and can thus be used to synthesize amino acids from α-ketoacids, as we shall see in Chapter 24.

The nitrogen atom that is transferred to α-ketoglutarate in the transamination reaction is converted into free ammonium ion by oxidative deamination. This reaction is catalyzed by glutamate dehydrogenase. This enzyme is unusual in being able to utilize either NAD+ or NADP+, at least in some species. The reaction proceeds by dehydrogenation of the C-N bond, followed by hydrolysis of the resulting Schiff base.

Image ch23fu5.jpg

The equilibrium for this reaction favors glutamate; the reaction is driven by the consumption of ammonia. Glutamate dehydrogenase is located in mitochondria, as are some of the other enzymes required for the production of urea. This compartmentalization sequesters free ammonia, which is toxic.

In vertebrates, the activity of glutamate dehydrogenase is allosterically regulated. The enzyme consists of six identical subunits. Guanosine triphosphate and adenosine triphosphate are allosteric inhibitors, whereas guanosine diphosphate and adenosine diphosphate are allosteric activators. Hence, a lowering of the energy charge accelerates the oxidation of amino acids.

The sum of the reactions catalyzed by aminotransferases and glutamate dehydrogenase is

Image ch23e3.jpg

In most terrestrial vertebrates, NH4+ is converted into urea, which is excreted.

Image ch23fu6.jpg

23.3.2. Pyridoxal Phosphate Forms Schiff-Base Intermediates in Aminotransferases

All aminotransferases contain the prosthetic group pyridoxal phosphate (PLP), which is derived from pyridoxine (vitamin B6). Pyridoxal phosphate includes a pyridine ring that is slightly basic as well as a phenolic hydroxyl group that is slightly acidic. Thus, pyridoxal phosphate derivatives can form stable tautomeric forms in which the pyridine nitrogen atom is protonated and, hence, positively charged while the hydroxyl group is deprotonated, forming a phenolate.

Image ch23fu7.jpg
Image ch23fu8.jpg

The most important functional group on PLP is the aldehyde. This group allows PLP to form covalent Schiff-base intermediates with amino acid substrates. Indeed, even in the absence of substrate, the aldehyde group of PLP usually forms a Schiff-base linkage with the ϵ-amino group of a specific lysine residue of the enzyme. A new Schiff-base linkage is formed on addition of an amino acid substrate. These Schiff-base linkages are often protonated, with the positive charge stabilized by interaction with the negatively charged phenolate group of PLP.

Image ch23fu9.jpg

The α -amino group of the amino acid substrate displaces the ε-amino group of the active-site lysine residue. In other words, an internal aldimine becomes an external aldimine. The amino acid-PLP Schiff base that is formed remains tightly bound to the enzyme by multiple noncovalent interactions.

The Schiff base between the amino acid substrate and PLP, the external aldimine, loses a proton from the α-carbon atom of the amino acid to form a quinonoid intermediate (Figure 23.10).

Figure 23.10. Transamination Mechanism.

Figure 23.10

Transamination Mechanism. The external aldimine loses a proton to form a quinonoid intermediate. Reprotonation of this intermediate at the aldehyde carbon atom yields a ketimine. This intermediate is hydrolyzed to generate the α-ketoacid product (more...)

The negative charge that is left on the amino acid is stabilized by delocalization into the pyridinium ring. Reprotonation of this intermediate at the aldehyde carbon atom yields a ketimine. The ketimine is then hydrolyzed to an α-ketoacid and pyridoxamine phosphate (PMP). These steps constitute half of the transamination reaction.

Image ch23e4.jpg

The second half takes place by the reverse of the preceding pathway. A second α-ketoacid reacts with the enzyme-pyridoxamine phosphate complex (E-PMP) to yield a second amino acid and regenerate the enzyme-pyridoxal phosphate complex (E-PLP).

Image ch23e5.jpg
Image ch23fu10.jpg

The sum of these partial reactions is

Image ch23e6.jpg

23.3.3. Aspartate Aminotransferase Is a Member of a Large and Versatile Family of Pyridoxal-Dependent Enzymes

The mitochondrial enzyme aspartate aminotransferase provides an especially well studied example of PLP as a coenzyme for transamination reactions (Figure 23.11). The results of X-ray crystallographic studies provided detailed views of how PLP and substrates are bound and confirmed much of the proposed catalytic mechanism. Each of the identical 45-kd subunits of this dimer consists of a large domain and a small one. PLP is bound to the large domain, in a pocket near the subunit interface. In the absence of substrate, the aldehyde group of PLP is in a Schiff-base linkage with lysine 258, as anticipated. Adjacent to the coenzyme's binding site is a conserved arginine residue that interacts with the α-carboxylate group of the substrate, helping to orient the substrate appropriately in the active site. The transamination reaction (see Figure 23.10) requires a base to remove a proton from the α-carbon group of the amino acid and to transfer it to the aldehyde carbon atom of PLP. The lysine amino group that was initially in Schiff-base linkage with PLP appears to serve this role.

Figure 23.11. Aspartate Aminotransferase.

Figure 23.11

Aspartate Aminotransferase. Image mouse.jpg The active site of this prototypical PLP-dependent enzyme includes pyridoxal phosphate attached to the enzyme by a Schiff-base linkage with lysine 258. An arginine residue in the active site helps orient substrates by binding (more...)

Transamination is just one of a wide range of amino acid transformations that are catalyzed by PLP enzymes. The other reactions catalyzed by PLP enzymes at the α-carbon atom of amino acids are decarboxylations, deam-inations, racemizations, and aldol cleavages (Figure 23.12). In addition, PLP enzymes catalyze elimination and replacement reactions at the β-carbon atom (e.g., tryptophan synthetase; Section 24.2.11) and the γ-carbon atom (e.g., cytathionine β-synthase, Section 24.2.9) of amino acid substrates. Three common features of PLP catalysis underlie these diverse reactions.

Figure 23.12. Bond Cleavage by PLP Enzymes.

Figure 23.12

Bond Cleavage by PLP Enzymes. Pyridoxal phosphate enzymes labilize one of three bonds at the α-carbon atom of an amino acid substrate. For example, bond a is labilized by aminotransferases, bond b by decarboxylases, and bond c by aldolases (such (more...)


A Schiff base is formed by the amino acid substrate (the amine component) and PLP (the carbonyl component).


The protonated form of PLP acts as an electron sink to stabilize catalytic intermediates that are negatively charged. Electrons from these intermediates can be transferred into the pyridine ring to neutralize the positive charge on the pyridinium nitrogen. In other words, PLP is an electrophilic catalyst.


The product Schiff base is cleaved at the completion of the reaction.

Image tree.jpg Many of the enzymes that catalyze these reactions, such as serine hy- droxymethyltransferase, which converts serine into glycine, have the same fold as that of aspartate aminotransferase and are clearly related by divergent evolution. Others, such as tryptophan synthetase, have quite different overall structures. Nonetheless, the active sites of these enzymes are remarkably similar to that of aspartate aminotransferase, revealing the effects of convergent evolution.

How does a particular enzyme selectively favor the cleavage of one of three bonds at the α-carbon atom of an amino acid substrate? An important principle is that the bond being broken must be perpendicular to the π orbitals of the electron sink (Figure 23.13). An aminotransferase, for example, achieves this goal by binding the amino acid substrate so that the Cα-H bond is perpendicular to the PLP ring (Figure 23.14). In serine hydroxymethyltransferase, the N-Cα bond is rotated so that the Cα-Cβ bond is most nearly perpendicular to the plane of the PLP ring, favoring its cleavage. This means of choosing one of several possible catalytic outcomes is called stereoelectronic control.

Figure 23.13. Stereoelectronic Effects.

Figure 23.13

Stereoelectronic Effects. The orientation about the NH-Cα bond determines the most favored reaction catalyzed by a pyridoxal phosphate enzyme. The bond that is most nearly perpendicular to the π orbitals of the pyridoxal phosphate electron (more...)

Figure 23.14. Reaction Choice.

Figure 23.14

Reaction Choice. In aspartate aminotransferase, the Cα-H bond is most nearly perpendicular to the π-orbital system and is cleaved. In serine hydroxymethyltransferase, a small rotation about the N-Cα bond places the Cα-Cβ (more...)

23.3.4. Serine and Threonine Can Be Directly Deaminated

Although the nitrogen atoms of most amino acids are transferred to α-ketoglutarate before removal, the α-amino groups of serine and threonine can be directly converted into NH4+. These direct deaminations are catalyzed by serine dehydratase and threonine dehydratase, in which PLP is the prosthetic group.

Image ch23e7.jpg
Image ch23e8.jpg
Image ch23fu11.jpg

These enzymes are called dehydratases because dehydration precedes deamination. Serine loses a hydrogen ion from its α-carbon atom and a hydroxide ion group from its β-carbon atom to yield aminoacrylate. This unstable compound reacts with H2O to give pyruvate and NH4+. Thus, the presence of a hydroxyl group attached to the β-carbon atom in each of these amino acids permits the direct deamination.

23.3.5. Peripheral Tissues Transport Nitrogen to the Liver

Most amino acid degradation takes place in tissues other than the liver. For instance, muscle uses amino acids as a source of fuel during prolonged exercise and fasting. How is the nitrogen processed in these other tissues? As in the liver, the first step is the removal of the nitrogen from the amino acid. However, muscle lacks the enzymes of the urea cycle, so the nitrogen must be released in a form that can be absorbed by the liver and converted into urea.

Nitrogen is transported from muscle to the liver in two principal transport forms. Glutamate is formed by transamination reactions, but the nitrogen is then transferred to pyruvate to form alanine, which is released into the blood (Figure 23.15). The liver takes up the alanine and converts it back into pyruvate by transamination. The pyruvate can be used for gluconeogenesis and the amino group eventually appears as urea. This transport is referred to as the alanine cycle. It is reminiscent of the Cori cycle discussed earlier (Section 16.4.2) and again illustrates the ability of the muscle to shift some of its metabolic burden to the liver.

Figure 23.15. The Alanine Cycle.

Figure 23.15

The Alanine Cycle. Glutamate in muscle is transaminated to alanine, which is released into the bloodstream. In the liver, alanine is taken up and converted into pyruvate for subsequent metabolism.

Nitrogen can also be transported as glutamine. Glutamine synthetase (Section 24.1.2) catalyzes the synthesis of glutamine from glutamate and NH4+ in an ATP-dependent reaction:

Image ch23e9.jpg

The nitrogens of glutamine can be converted into urea in the liver.

By agreement with the publisher, this book is accessible by the search feature, but cannot be browsed.

Copyright © 2002, W. H. Freeman and Company.
Bookshelf ID: NBK22475