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

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Biochemistry. 5th edition.

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Section 24.2Amino Acids Are Made from Intermediates of the Citric Acid Cycle and Other Major Pathways

Thus far, we have considered the conversion of N2 into NH4+ and the assimilation of NH4+ into glutamate and glutamine. We turn now to the biosynthesis of the other amino acids. The pathways for the biosynthesis of amino acids are diverse. However, they have an important common feature: their carbon skeletons come from intermediates of glycolysis, the pentose phosphate pathway, or the citric acid cycle. On the basis of these starting materials, amino acids can be grouped into six biosynthetic families (Figure 24.7).

Figure 24.7. Biosynthetic Families of Amino Acids in Bacteria and Plants.

Figure 24.7

Biosynthetic Families of Amino Acids in Bacteria and Plants. Major metabolic precursors are shaded blue. Amino acids that give rise to other amino acids are shaded yellow. Essential amino acids are in boldface type.

24.2.1 Human Beings Can Synthesize Some Amino Acids but Must Obtain Others from the Diet

Most microorganisms such as E. coli can synthesize the entire basic set of 20 amino acids, whereas human beings cannot make 9 of them. The amino acids that must be supplied in the diet are called essential amino acids, whereas the others are termed nonessential amino acids (Table 24.1). These designations refer to the needs of an organism under a particular set of conditions. For example, enough arginine is synthesized by the urea cycle to meet the needs of an adult but perhaps not those of a growing child. A deficiency of even one amino acid results in a negative nitrogen balance. In this state, more protein is degraded than is synthesized, and so more nitrogen is excreted than is ingested.

Table 24.1. Basic set of 20 amino acids.

Table 24.1

Basic set of 20 amino acids.

The nonessential amino acids are synthesized by quite simple reactions, whereas the pathways for the formation of the essential amino acids are quite complex. For example, the nonessential amino acids alanine and aspartate are synthesized in a single step from pyruvate and oxaloacetate, respectively. In contrast, the pathways for the essential amino acids require from 5 to 16 steps (Figure 24.8). The sole exception to this pattern is arginine, inasmuch as the synthesis of this nonessential amino acid de novo requires 10 steps. Typically, though, it is made in only 3 steps from ornithine as part of the urea cycle. Tyrosine, classified as a nonessential amino acid because it can be synthesized in 1 step from phenylalanine, requires 10 steps to be synthesized from scratch and is essential if phenylalanine is not abundant. We begin with the biosynthesis of nonessential amino acids.

Figure 24.8. Essential and Nonessential Amino Acids.

Figure 24.8

Essential and Nonessential Amino Acids. Some amino acids are nonessential to human beings because they can be biosynthesized in a small number of steps. Those amino acids requiring a large number of steps for their synthesis are essential in the diet (more...)

24.2.2 A Common Step Determines the Chirality of All Amino Acids

Three α-ketoacids—α-ketoglutarate, oxaloacetate, and pyruvate—can be converted into amino acids in one step through the addition of an amino group. We have seen that α-ketoglutarate can be converted into glutamate by reductive amination (Section 24.1.2). The amino group from glutamate can be transferred to other α-ketoacids by transamination reactions. Thus, aspartate and alanine can be made from the addition of an amino group to oxaloacetate and pyruvate, respectively.

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These reactions are carried out by pyridoxal phosphate-dependent transaminases. Transamination reactions participate in the synthesis of most amino acids. We shall review the transaminase mechanism (Section 23.3.1) as it applies to amino acid biosynthesis (see Figure 23.10).

The reaction pathway begins with pyridoxal phosphate in a Schiff-base linkage with lysine at the transaminase active site, forming an internal aldimine (Figure 24.9). An external aldimine forms between PLP and the amino-group donor, glutamate, which displaces the lysine residue. The transfer of the amino group from glutamate to pyridoxal phosphate forms pyridoxamine phosphate, the actual amino donor. When the amino group has been incorporated into pyridoxamine, the reaction pathway proceeds in reverse, and the amino group is transferred to an α-ketoacid to form an amino acid.

Figure 24.9. Amino Acid Biosynthesis by Transamination.

Figure 24.9

Amino Acid Biosynthesis by Transamination. Within a transaminase, the internal aldimine is converted into pyridoxamine phosphate (PMP) by reaction with glutamate. PMP then reacts with an α-ketoacid to generate a ketimine. This intermediate is (more...)

Aspartate aminotransferase is the prototype of a large family of PLP-dependent enzymes. Comparisons of amino acid sequences as well as several three-dimensional structures reveal that almost all transaminases having roles in amino acid biosynthesis are related to aspartate aminotransferase by divergent evolution. An examination of the aligned amino acid sequences reveals that two residues are completely conserved. These residues are the lysine residue that forms the Schiff base with the pyridoxal phosphate cofactor (lysine 258 in aspartate aminotransferase) and an arginine residue that interacts with the α-carboxylate group of the ketoacid (see Figure 23.11).

An essential step in the transamination reaction is the protonation of the quinonoid intermediate to form the external aldimine. The chirality of the amino acid formed is determined by the direction from which this proton is added to the quinonoid form. (Figure 24.10). This protonation step determines the l configuration of the amino acids produced. The interaction between the conserved arginine residue and the α-carboxylate group helps orient the substrate so that, when the lysine residue transfers a proton to the face of the quinonoid intermediate, it generates an aldimine with an l configuration at the Cα center.

Figure 24.10. Stereochemistry of Proton Addition.

Figure 24.10

Stereochemistry of Proton Addition. In a transaminase active site, the addition of a proton from the lysine residue to the bottom face of the quinonoid intermediate determines the l configuration of the amino acid product. The conserved arginine residue (more...)

24.2.3 An Adenylated Intermediate Is Required to Form Asparagine from Aspartate

The formation of asparagine from aspartate is chemically analogous to the formation of glutamine from glutamate. Both transformations are amidation reactions and both are driven by the hydrolysis of ATP. The actual reactions are different, however. In bacteria, the reaction for the asparagine synthesis is

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Thus, the products of ATP hydrolysis are AMP and PPi rather than ADP and Pi. Aspartate is activated by adenylation rather than by phosphorylation.

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We have encountered this mode of activation in fatty acid degradation and will see it again in lipid and protein synthesis.

In mammals, the nitrogen donor for asparagine is glutamine rather than ammonia as in bacteria. Ammonia is generated by hydrolysis of the side chain of glutamine and directly transferred to activated aspartate, bound in the active site. An advantage is that the cell is not directly exposed to NH4+, which is toxic at high levels to human beings and other mammals. The use of glutamine hydrolysis as a mechanism for generating ammonia for use within the same enzyme is a motif common throughout biosynthetic pathways.

24.2.4 Glutamate Is the Precursor of Glutamine, Proline, and Arginine

The synthesis of glutamate by the reductive amination of α-ketoglutarate has already been discussed, as has the conversion of glutamate into glutamine (Section 24.1.2). Glutamate is the precursor of two other nonessential amino acids: proline and arginine. First, the γ-carboxyl group of glutamate reacts with ATP to form an acyl phosphate. This mixed anhydride is then reduced by NADPH to an aldehyde.

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Glutamic γ-semialdehyde cyclizes with a loss of H2O in a nonenzymatic process to give Δ1-pyrroline-5-carboxylate, which is reduced by NADPH to proline. Alternatively, the semialdehyde can be transaminated to ornithine, which is converted in several steps into arginine (Section 23.4.1).

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24.2.5 Serine, Cysteine, and Glycine Are Formed from 3-Phosphoglycerate

Serine is synthesized from 3-phosphoglycerate, an intermediate in glycolysis. The first step is an oxidation to 3-phosphohydroxypyruvate. This α-ketoacid is transaminated to 3-phosphoserine, which is then hydrolyzed to serine.

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Serine is the precursor of glycine and cysteine. In the formation of glycine, the side-chain methylene group of serine is transferred to tetrahydrofolate, a carrier of one-carbon units that will be discussed shortly.

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This interconversion is catalyzed by serine transhydroxymethylase, another PLP enzyme that is homologous to aspartate aminotransferase (Figure 24.11). The bond between the α- and β-carbon atoms of serine is labilized by the formation of a Schiff base between serine and PLP (Section 23.3.3). The side-chain methylene group of serine is then transferred to tetrahydrofolate. The conversion of serine into cysteine requires the substitution of a sulfur atom derived from methionine for the side-chain oxygen atom (Section 24.2.8).

Figure 24.11. Structure of Serine Hydroxymethyltransferase.

Figure 24.11

Structure of Serine Hydroxymethyltransferase. Image mouse.jpg This enzyme transfers a one-carbon unit from the side chain of serine to tetrahydrofolate. One subunit of the dimeric enzyme is shown.

24.2.6 Tetrahydrofolate Carries Activated One-Carbon Units at Several Oxidation Levels

Tetrahydrofolate (also called tetrahydropteroylglutamate), a highly versatile carrier of activated one-carbon units, consists of three groups: a substituted pteridine, p-aminobenzoate, and a chain of one or more glutamate residues (Figure 24.12). Mammals can synthesize the pteridine ring, but they are unable to conjugate it to the other two units. They obtain tetrahydrofolate from their diets or from microorganisms in their intestinal tracts.

Figure 24.12. Tetrahydrofolate.

Figure 24.12

Tetrahydrofolate. This cofactor includes three components: a pteridine ring, p-aminobenzoate, and one or more glutamate residues.

The one-carbon group carried by tetrahydrofolate is bonded to its N-5 or N-10 nitrogen atom (denoted as N5 and N10) or to both. This unit can exist in three oxidation states (Table 24.2). The most-reduced form carries a methyl group, whereas the intermediate form carries a methylene group. More-oxidized forms carry a formyl, formimino, or methenyl group. The fully oxidized one-carbon unit, CO2, is carried by biotin rather than by tetrahydrofolate.

Table 24.2. One-carbon groups carried by tetrahydrofolate.

Table 24.2

One-carbon groups carried by tetrahydrofolate.

The one-carbon units carried by tetrahydrofolate are interconvertible (Figure 24.13). N5,N10-Methylenetetrahydrofolate can be reduced to N5-methyltetrahydrofolate or oxidized to N5,N10-methenyltetrahydrofolate. N5, N10-Methenyltetrahydrofolate can be converted into N5-formiminotetrahydrofolate or N10-formyltetrahydrofolate, both of which are at the same oxidation level. N10-Formyltetrahydrofolate can also be synthesized from tetrahydrofolate, formate, and ATP.

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N5-Formyltetrahydrofolate can be reversibly isomerized to N10-formyltetrahydrofolate or it can be converted into N5,N10-methenyltetrahydrofolate.

Figure 24.13. Conversions of One-Carbon Units Attached to Tetrahydrofolate.

Figure 24.13

Conversions of One-Carbon Units Attached to Tetrahydrofolate.

These tetrahydrofolate derivatives serve as donors of one-carbon units in a variety of biosyntheses. Methionine is regenerated from homocysteine by transfer of the methyl group of N5-methyltetrahydrofolate, as will be discussed shortly. We shall see in Chapter 25 that some of the carbon atoms of purines are acquired from derivatives of N10-formyltetrahydrofolate. The methyl group of thymine, a pyrimidine, comes from N5,N10-methylenetetrahydrofolate. This tetrahydrofolate derivative can also donate a one-carbon unit in an alternative synthesis of glycine that starts with CO2 and NH4+, a reaction catalyzed by glycine synthase (called the glycine cleavage enzyme when it operates in the reverse direction).

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Thus, one-carbon units at each of the three oxidation levels are utilized in biosyntheses. Furthermore, tetrahydrofolate serves as an acceptor of one-carbon units in degradative reactions. The major source of one-carbon units is the facile conversion of serine into glycine, which yields N5,N10-methylenetetrahydrofolate. Serine can be derived from 3-phosphoglycerate, and so this pathway enables one-carbon units to be formed de novo from carbohydrates.

24.2.7 S-Adenosylmethionine Is the Major Donor of Methyl Groups

Tetrahydrofolate can carry a methyl group on its N-5 atom, but its transfer potential is not sufficiently high for most biosynthetic methylations. Rather, the activated methyl donor is usually S-adenosylmethionine (SAM), which is synthesized by the transfer of an adenosyl group from ATP to the sulfur atom of methionine.

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The methyl group of the methionine unit is activated by the positive charge on the adjacent sulfur atom, which makes the molecule much more reactive than N5-methyltetrahydrofolate. The synthesis of S-adenosylmethionine is unusual in that the triphosphate group of ATP is split into pyrophosphate and orthophosphate; the pyrophosphate is subsequently hydrolyzed to two molecules of Pi. S-Adenosylhomocysteine is formed when the methyl group of S-adenosylmethionine is transferred to an acceptor. S-Adenosylhomocysteine is then hydrolyzed to homocysteine and adenosine.

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Methionine can be regenerated by the transfer of a methyl group to homocysteine from N5-methyltetrahydrofolate, a reaction catalyzed by methionine synthase (also known as homocysteine methyltransferase).

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The coenzyme that mediates this transfer of a methyl group is methylcobalamin, derived from vitamin B12. In fact, this reaction and the rearrangement of l-methylmalonyl CoA to succinyl CoA (Section 23.5.4), catalyzed by a homologous enzyme, are the only two B12-dependent reactions known to take place in mammals. Another enzyme that converts homocysteine into methionine without vitamin B12 also is present in many organisms.

These reactions constitute the activated methyl cycle (Figure 24.14). Methyl groups enter the cycle in the conversion of homocysteine into methionine and are then made highly reactive by the addition of adenosyl groups, which make the sulfur atoms positively charged and the methyl groups much more electrophilic. The high transfer potential of the S-methyl group enables it to be transferred to a wide variety of acceptors.

Figure 24.14. Activated Methyl Cycle.

Figure 24.14

Activated Methyl Cycle. The methyl group of methionine is activated by the formation of S-adenosylmethionine.

Among the acceptors modified by S-adenosylmethionine are specific bases in DNA. The methylation of DNA protects bacterial DNA from cleavage by restriction enzymes (Section 9.3). The base to be methylated is flipped out of the DNA double helix into the active site where it can accept a methyl group from S-adenosylmethionine (Figure 24.15). A recurring S-adenosylmethionine-binding domain is present in many SAM-dependent methylases.

Figure 24.15. DNA Methylation.

Figure 24.15

DNA Methylation. Image mouse.jpg The structure of a DNA methylase bound to an oligonucleotide target shows that the base to be methylated is flipped out of the DNA helix into the active site of a SAM-dependent methylase.

S-Adenosylmethionine is also the precursor of ethylene, a gaseous plant hormone that induces the ripening of fruit. S-Adenosylmethionine is cyclized to a cyclopropane derivative that is then oxidized to form ethylene. The Greek philosopher Theophrastus recognized more than 2000 years ago that sycamore figs do not ripen unless they are scraped with an iron claw. The reason is now known: wounding triggers ethylene production, which in turn induces ripening. Much effort is being made to understand this biosynthetic pathway because ethylene is a culprit in the spoilage of fruit.

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24.2.8 Cysteine Is Synthesized from Serine and Homocysteine

In addition to being a precursor of methionine in the activated methyl cycle, homocysteine is an intermediate in the synthesis of cysteine. Serine and homocysteine condense to form cystathionine. This reaction is catalyzed by cystathionine β-synthase. Cystathionine is then deaminated and cleaved to cysteine and α-ketobutyrate by cystathioninase. Both of these enzymes utilize PLP and are homologous to aspartate aminotransferase. The net reaction is

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Note that the sulfur atom of cysteine is derived from homocysteine, whereas the carbon skeleton comes from serine.

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24.2.9 High Homocysteine Levels Are Associated with Vascular Disease

Image caduceus.jpg People with elevated serum levels of homocysteine or the disulfide-linked dimer homocystine have an unusually high risk for coronary heart disease and arteriosclerosis. The most common genetic cause of high homocysteine levels is a mutation within the gene encoding cystathionine β-synthase. The molecular basis of homocysteine's action has not been clearly identified, although it appears to damage cells lining blood vessels and to increase the growth of vascular smooth muscle. The amino acid raises oxidative stress as well. Vitamin treatments are effective in reducing homocysteine levels in some people. Treatment with vitamins maximizes the activity of the two major metabolic pathways processing homocysteine. Pyridoxal phosphate, a vitamin B6 derivative, is necessary for the activity of cystathionine β-synthase, which converts homocysteine into cystathione; tetrahydrofolate, and vitamin B12, supports the methylation of homocysteine to methionine.

24.2.10 Shikimate and Chorismate Are Intermediates in the Biosynthesis of Aromatic Amino Acids

We turn now to the biosynthesis of essential amino acids. These amino acids are synthesized by plants and microorganisms, and those in the human diet are ultimately derived primarily from plants. The essential amino acids are formed by much more complex routes than are the nonessential amino acids. The pathways for the synthesis of aromatic amino acids in bacteria have been selected for discussion here because they are well understood and exemplify recurring mechanistic motifs.

Phenylalanine, tyrosine, and tryptophan are synthesized by a common pathway in E. coli (Figure 24.16). The initial step is the condensation of phosphoenolpyruvate (a glycolytic intermediate) with erythrose 4-phosphate (a pentose phosphate pathway intermediate). The resulting seven-carbon open-chain sugar is oxidized, loses its phosphoryl group, and cyclizes to 3-dehydroquinate. Dehydration then yields 3-dehydroshikimate, which is reduced by NADPH to shikimate. Phosphorylation of shikimate by ATP gives shikimate 3-phosphate, which condenses with a second molecule of phosphoenolpyruvate. This 5-enolpyruvyl intermediate loses its phosphoryl group, yielding chorismate, the common precursor of all three aromatic amino acids. The importance of this pathway is revealed by the effectiveness of glyphosate (Roundup), a broad-spectrum herbicide. This compound inhibits the enzyme that produces 5-enolpyruvylshikimate 3-phosphate and, hence, blocks aromatic amino acid biosynthesis in plants. Because animals lack this enzyme, the herbicide is fairly nontoxic.

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Figure 24.16. Pathway to Chorismate.

Figure 24.16

Pathway to Chorismate. Chorismate is an intermediate in the biosynthesis of phenylalanine, tyrosine, and tryptophan.

The pathway bifurcates at chorismate. Let us first follow the prephenate branch (Figure 24.17). A mutase converts chorismate into prephenate, the immediate precursor of the aromatic ring of phenylalanine and tyrosine. This fascinating conversion is a rare example of an electrocyclic reaction in biochemistry, mechanistically similar to the well-known Diels-Alder reaction from organic chemistry. Dehydration and decarboxylation yield phenylpyruvate. Alternatively, prephenate can be oxidatively decarboxylated to p-hydroxyphenylpyruvate. These α-ketoacids are then transaminated to form phenylalanine and tyrosine.

Figure 24.17. Synthesis of Phenylalanine and Tyrosine.

Figure 24.17

Synthesis of Phenylalanine and Tyrosine. Chorismate can be converted into prephenate, which is subsequently converted into phenylalanine and tyrosine.

The branch starting with anthranilate leads to the synthesis of tryptophan (Figure 24.18). Chorismate acquires an amino group derived from the hydrolysis of the side chain of glutamine and releases pyruvate to form anthranilate. Then anthranilate condenses with 5-phosphoribosyl-1-pyrophosphate (PRPP), an activated form of ribose phosphate. PRPP is also an important intermediate in the synthesis of histidine, purine nucleotides, and pyrimidine nucleotides (Sections 25.1.4 and 25.2.2). The C-1 atom of ribose 5-phosphate becomes bonded to the nitrogen atom of anthranilate in a reaction that is driven by the release and hydrolysis of pyrophosphate. The ribose moiety of phosphoribosylanthranilate undergoes rearrangement to yield 1-(o-carboxyphenylamino)-1-deoxyribulose 5-phosphate. This intermediate is dehydrated and then decarboxylated to indole-3-glycerol phosphate, which is cleaved to indole. Then indole reacts with serine to form tryptophan. In these final steps, which are catalyzed by tryptophan synthetase, the side chain of indole-3-glycerol phosphate is removed as glyceraldehyde 3-phosphate and replaced by the carbon skeleton of serine.

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Figure 24.18. Synthesis of Tryptophan.

Figure 24.18

Synthesis of Tryptophan. Chorismate can be converted into anthranilate, which is subsequently converted into tryptophan.

24.2.11 Tryptophan Synthetase Illustrates Substrate Channeling in Enzymatic Catalysis

Tryptophan synthetase of E. coli, an α2β2 tetramer, can be dissociated into two α subunits and a β2 subunit (Figure 24.19). The α subunit catalyzes the formation of indole from indole-3-glycerol phosphate, whereas each β subunit has a PLP-containing active site that catalyzes the condensation of indole and serine to form tryptophan. The overall three-dimensional structure of this enzyme is distinct from that of aspartate aminotransferase and the other PLP enzymes already discussed. Serine forms a Schiff base with this PLP, which is then dehydrated to give the Schiff base of aminoacrylate. This reactive intermediate is attacked by indole to give tryptophan.

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Figure 24.19. Structure of Tryptophan Synthetase.

Figure 24.19

Structure of Tryptophan Synthetase. Image mouse.jpg The structure of the complex formed by one α subunit and one β subunit. PLP is bound to the β subunit.

The synthesis of tryptophan poses a challenge. Indole, a hydrophobic molecule, readily traverses membranes and would be lost from the cell if it were allowed to diffuse away from the enzyme. This problem is solved in an ingenious way. A 25-Å-long channel connects the active site of the α subunit with that of the adjacent β subunit in the α2β2 tetramer (Figure 24.20). Thus, indole can diffuse from one active site to the other without being released into bulk solvent. Indeed, the results of isotopic-labeling experiments showed that indole formed by the α subunit does not leave the enzyme when serine is present. Furthermore, the two partial reactions are coordinated. Indole is not formed by the α subunit until the highly reactive aminoacrylate is ready and waiting in the β subunit. We see here a clear-cut example of substrate channeling in catalysis by a multienzyme complex. Channeling substantially increases the catalytic rate. Furthermore, a deleterious side reaction—in this case, the potential loss of an intermediate—is prevented. We shall encounter other examples of substrate channeling in Chapter 25.

Figure 24.20. Substrate Channeling.

Figure 24.20

Substrate Channeling. A 25-Å tunnel runs from the active site of the α subunit of tryptophan synthetase (yellow) to the PLP cofactor (red) in the active site of the β subunit (blue).

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Copyright © 2002, W. H. Freeman and Company.
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