Amino Acid Synthesis and Metabolism


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Introduction

All tissues have some capability for synthesis of the non-essential amino acids, amino acid remodeling, and conversion of non-amino acid carbon skeletons into amino acids and other derivatives that contain nitrogen. However, the liver is the major site of nitrogen metabolism in the body. In times of dietary surplus, the potentially toxic nitrogen of amino acids is eliminated via transaminations, deamination, and urea formation; the carbon skeletons are generally conserved as carbohydrate, via gluconeogenesis, or as fatty acid via fatty acid synthesis pathways. In this respect amino acids fall into three categories: glucogenic, ketogenic, or glucogenic and ketogenic. Glucogenic amino acids are those that give rise to a net production of pyruvate or TCA cycle intermediates, such as α-ketoglutarate or oxaloacetate, all of which are precursors to glucose via gluconeogenesis. All amino acids except lysine and leucine are at least partly glucogenic. Lysine and leucine are the only amino acids that are solely ketogenic, giving rise only to acetylCoA or acetoacetylCoA, neither of which can bring about net glucose production.

 

 

 

 

 

 

 

 

 

 

A small group of amino acids comprised of isoleucine, phenylalanine, threonine, tryptophan, and tyrosine give rise to both glucose and fatty acid precursors and are thus characterized as being glucogenic and ketogenic. Finally, it should be recognized that amino acids have a third possible fate. During times of starvation the reduced carbon skeleton is used for energy production, with the result that it is oxidized to CO2 and H2O.

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Intestinal Amino Acid Uptake

Dietary amino acids can be consumed as free amino acids or, more often, they are acquired from digested dietary proteins that are hydrolyzed through the concerted actions of gastric and pancreatic peptidases. Dietary protein digestion begins in the stomach and continues within the lumen of the duodenum. Within the small intestines there are three principal pancreatic enzymes involved in protein digestion; these are pepsin, trypsin, and chymotrypsin. Several additional pancreatic peptidases play a lesser role in peptide digestion and include elastase and the carboxypeptidases.

The initial enzyme involved in protein digestion is gastric pepsins. Pepsins hydrolyze peptide bonds on the C-terminal side of aromatic and hydrophobic amino acids. Approximately 20% of overall protein digestion is accomplished via the actions of pepsins. Due to the acidic pH optimum for the action of pepsins, these enzymes are inhibited when the gastric juices (chyme) passes from the stomach and is mixed with alkaline pancreatic juices in the duodenum.

The remainder of protein digestion occurs within the duodenum and jejunum of the small intestine. Digestion here is primarily the result of the actions of trypsin and chymotrypsin, and to a lesser extent by elastase, and carboxypeptidases A and B, all of which are secreted by the pancreas. Active trypsin is generated via the action of enteropeptidase on pancreatic trypsinogen. Enteropeptidase is an enzyme secreted by cells of the crypts of Lieberkühn and resides in the brush-border membranes of duodenal mucosal cells. Trypsin then cleaves more trypsinogen to trypsin, as well as chymotrypsinogen, proelastase, and procarboxypeptidases to their active forms.

Following digestion, free amino acids, as well as peptides (2-6 amino acids in length) are absorbed by enterocytes of the proximal jejunum. Some absorption also occurs in the duodenum and a minor amount in the ileum. Although there is little nutritional significance to whole protein absorption, some undigested dietary protein does get absorbed by intestinal enterocytes. Of significance is the fact that endogenous proteins, such as intestinal hormones and peptides, are absorbed intact. This uptake occurs primarily within the large intestines.

The absorption of amino acids requires an active transport process that is dependent upon either Na+ or H+ co-transport. There are several amino acid transporters encompassing seven distinct transport systems which are further grouped into three broad categories. There are the neutral amino acid (monoamino monocarboxylic) transporters, the dibasic (and cysteine) amino acid transporters, and the acidic (dicarboxylic) amino acid transporters. All of these transporters are members of the solute carrier (SLC) family of transporters.

Intestinal uptake of peptides involves H+ co-transporters which are also members of the SLC family. The most abundant peptide transporter is PepT1 (SLC15A1) but there are three additional peptide transporters within the SLC15 subfamily. Within intestinal enterocytes the absorbed peptides are hydrolyzed to free amino acids via enterocyte cytoplasmic peptidases. The free amino acids are then transported across the apical membranes of enterocytes and enter the portal circulation.

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Hartnup Disorder

Hartnup disorder was first described in 1956 in the Hartnup family in London as a renal aminoaciduria of neutral amino acids associated with a pellagra-like skin rash and episodes of cerebellar ataxia. The disorder is caused by a defect in neutral amino acid transport in the apical brush border membranes of the small intestine and in kidney proximal tubules. The transporter is a member of the solute carrier family, specifically the SLC6A19 transporter. SLC6A19 is also known as the system B(0) neutral amino acid transporter 1 [B(0)AT1]. SLC6A19 is responsible for the transport of neutral amino acids in a Na+-dependent transport reaction. The lack of intestinal tryptophan transport is responsible for most, if not all, clinical phenotypes of Hartnup disorder. The pellagra-like skin rash seen on sun-exposed areas of skin in Hartnup disorder patients is most likely the result of nicotinamide deficiency due to a lack of tryptophan which is a precursor for its synthesis. Symptoms of Hartnup disorder may begin in infancy or early childhood, but sometimes they begin as late as early adulthood. Symptoms may be triggered by sunlight, fever, drugs, or emotional or physical stress. Most symptoms occur sporadically and are caused by a deficiency of niacin. When Hartnup disorder manifests during infancy the symptoms can be variable in clinical presentation. These symptoms include failure to thrive, photosensitivity, intermittent ataxia, nystagmus and tremor. Patients with Hartnup disorder can remain asymptomatic on a high protein diet due to intestinal peptide absorption via the actions of the transporter, PepT1.

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Essential vs. Nonessential Amino Acids

Nonessential Essential
Alanine Arginine*
Asparagine Histidine
Aspartate Isoleucine
Cysteine Leucine
Glutamate Lysine
Glutamine Methionine*
Glycine Phenylalanine*
Proline Threonine
Serine Tyrptophan
Tyrosine Valine

*The amino acids arginine, methionine and phenylalanine are considered essential for reasons not directly related to lack of synthesis. Arginine is synthesized by mammalian cells but at a rate that is insufficient to meet the growth needs of the body and the majority that is synthesized is cleaved to form urea. Methionine is required in large amounts to produce cysteine if the latter amino acid is not adequately supplied in the diet. Similarly, phenylalanine is needed in large amounts to form tyrosine if the latter is not adequately supplied in the diet.

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Non-Essential Amino Acid Biosynthesis

Glutamate and Aspartate

Glutamate is synthesized from its' widely distributed α-keto acid precursor by a simple 1-step transamination reaction catalyzed by glutamate dehydrogenase. As discussed in the Nitrogen Metabolism page, the glutamate dehydrogenase reaction plays a central role in overall nitrogen homeostasis.

Reaction catalyzed by glutamate dehydrogenase

Reactions of glutamate dehydrogenase

Like glutamate, aspartate is synthesized by a simple 1-step transamination reaction catalyzed by aspartate aminotransferase, AST (formerly referred to as serum glutamate-oxalate transaminase, SGOT).

Reaction catalyzed by aspartate aminotransferase (AST)

Aspartate can also be derived from asparagine (whose synthesis is outlined below) through the action of asparaginase. The importance of aspartate as a precursor of ornithine for the urea cycle is described in the Nitrogen Metabolism page.

Reaction catalyzed by asparaginase


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Alanine and the Glucose-Alanine Cycle

Aside from its role in protein synthesis, alanine is second only to glutamine in prominence as a circulating amino acid. In this capacity it serves a unique role in the transfer of nitrogen from peripheral tissue to the liver. Alanine is transferred to the circulation by many tissues, but mainly by muscle, in which alanine is formed from pyruvate at a rate proportional to intracellular pyruvate levels. Liver accumulates plasma alanine, reverses the transamination that occurs in muscle, and proportionately increases urea production. The pyruvate is either oxidized or converted to glucose via gluconeogenesis. When alanine transfer from muscle to liver is coupled with glucose transport from liver back to muscle, the process is known as the glucose-alanine cycle. The key feature of the cycle is that in 1 molecule, alanine, peripheral tissue exports pyruvate and ammonia (which are potentially rate-limiting for metabolism) to the liver, where the carbon skeleton is recycled and most nitrogen eliminated.

There are 2 main pathways to production of muscle alanine: directly from protein degradation, and via the transamination of pyruvate by alanine transaminase, ALT (also referred to as serum glutamate-pyruvate transaminase, SGPT).

Reaction catalyzed by alanine transaminase (ALT)

The glucose-alanine cycle

The glucose-alanine cycle is used primarily as a mechanism for skeletal muscle to eliminate nitrogen while replenishing its energy supply. Glucose oxidation produces pyruvate which can undergo transamination to alanine. This reaction is catalyzed by alanine transaminase, ALT (ALT used to be called serum glutamate-pyruvate transaminase, SGPT). Additionally, during periods of fasting, skeletal muscle protein is degraded for the energy value of the amino acid carbons and alanine is a major amino acid in protein. The alanine then enters the blood stream and is transported to the liver. Within the liver alanine is converted back to pyruvate which is then a source of carbon atoms for gluconeogenesis. The newly formed glucose can then enter the blood for delivery back to the muscle. The amino group transported from the muscle to the liver in the form of alanine is converted to urea in the urea cycle and excreted.


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Cysteine Biosynthesis: Role of Methionine

The sulfur for cysteine synthesis comes from the essential amino acid methionine. A condensation of ATP and methionine catalyzed by methionine adenosyltransferase yields S-adenosylmethionine (SAM or AdoMet).

Synthesis of S-adenosylmethionine (SAM)

Biosynthesis of S-adenosylmethionine, SAM

SAM serves as a precurosor for numerous methyl transfer reactions (e.g. the conversion of norepinephrine to epinenephrine, see Specialized Products of Amino Acids). The result of methyl transfer is the conversion of SAM to S-adenosylhomocysteine. S-adenosylhomocysteine is then cleaved by adenosylhomocyteinase to yield homocysteine and adenosine. Homocysteine can be converted back to methionine by methionine synthase, a reaction that occurs under methionine-sparing conditions and requires N5-methyl-tetrahydrofolate as methyl donor. This reaction was discussed in the context of vitamin B12-requiring enzymes in the Vitamins page.

Transmethylation reactions employing SAM are extremely important, but in this case the role of S-adenosylmethionine in transmethylation is secondary to the production of homocysteine (essentially a by-product of transmethylase activity). In the production of SAM all phosphates of an ATP are lost: one as Pi and two as PPi. It is adenosine which is transferred to methionine and not AMP.

In cysteine synthesis, homocysteine condenses with serine to produce cystathionine, which is subsequently cleaved by cystathionine lyase (also called cystathionase) to produce cysteine and α-ketobutyrate. The sum of the latter two reactions is known as trans-sulfuration.

Cysteine is used for protein synthesis and other body needs, while the α-ketobutyrate is first converted to propionyl-CoA and then via a 3-step process to the TCA cycle intermediate succinyl-CoA. While cysteine readily oxidizes to form the disulfide cystine, cells contain little if any free cystine because the ubiquitous reducing agent, glutathione, effectively reverses the formation of cystine by a non-enzymatic reduction reaction.

Reactions of methionine conversion to cysteine

Utilization of Methionine in the Synthesis of Cysteine

The 2 key enzymes of this pathway, cystathionine β-synthase (cystathionine beta synthase: CBS) and cystathionine lyase, both use pyridoxal phosphate as a cofactor, and both are under regulatory control. Cystathionine lyase is also negatively regulated by cysteine-mediated allosteric control. In addition, cysteine inhibits the expression of the cystathionine β-synthase gene. Genetic defects are known for both the CBS and the cystathionine lyase genes.

Homocystinuria/Homocystinemia

Homocystinurias represent a family of inherited disorders resulting from defects in several of the genes involved in the conversion of methionine to cysteine. As the name implies, these disorders result in elevated levels of homocysteine in the urine. In addition, patients excrete elevated levels of methionine and metabolites of homocysteine. The most common causes of homocystinuria are defects in the cystathionine β-synthase (CBS) gene. Homocystinuria is often associated with mental retardation, although the complete syndrome is multifaceted and many individuals with this disease are mentally normal, while others experience variable levels of developmental delay along with learning problems. Common symptoms of homocystinuria are dislocated optic lenses, osteoporosis, lengthening and thinning of the long bones, and an increased risk of abnormal blood clotting (thromboembolism). Some instances of genetic homocystinuria respond favorably to pyridoxine therapy, suggesting that in these cases the defect in CBS is a decreased affinity for the cofactor, pyridoxal phosphate. Homocystinuria can also result from vitamin deficiencies due to the role of the co-factor forms of B6, B12, and folate in the overall metabolism of methionine. Vitamin B6 (as pyridoxal phosphate) is required for the activity of CBS and the homocystinuria that results with B6 deficiency is also associated with elevated methionine levels in the blood. Vitamin B12 and folate (as N5-methyl-THF) are required for the methionine synthase reaction so a deficiency of either vitamin can result in homocystinuria presenting with reduced levels of plasma methionine. The enzyme methylmalonyl-CoA mutase also requires B12 and so a homocystinuria resulting from a deficiency in this vitamin is also associated with methylmalonic academia. Indeed, the measurement of serum methionine and methylmalonic acid in cases of homocystinuria allows for a differential diagnosis of the nutritional (non-genetic) cause.

Elevated levels of homocysteine in the blood have been shown to correlate with cardiovascular dysfunction. The role of homocysteine in cardiovascular disease is related to its ability to induce a state of inflammation. Homocysteine serves as a negatively charged surface that attracts the contact phase of the intrinsic pathway of blood coagulation. Activation of the intrinsic coagulation cascade leads to inappropriate thrombolytic events as well as resulting in increases in inflammatory cytokine release from leukocytes that are activated as a result of the pro-coagulant state. Therefore, it is important to ensure that proper function of the methionine synthase reaction is maintained. Although it would be assumed that increased intake of vitamin B12 should lead to increased conversion of homocysteine to methionine, and thus reduced levels of circulating homocysteine, controlled studies have shown that this does not occur.

Missing or impaired cystathionase leads to excretion of cystathionine in the urine but does not have any other untoward effects. Rare cases are known in which cystathionase is defective and operates at a low level. This genetic disease leads to methioninuria with no other consequences.

Cystinuria

As the name implies, cystinuria is a disorder associated with excess cystine in the urine. Cystine is the oxidized disulfide homodimer of two cysteines. Cystinuria is an autosomal recessive disorder that results from a failure of the renal proximal tubules to reabsorb cystine that was filtered by the glomerulus. The disorder results from defects in either of the two protein subunits of the cystine transporter which is distinct from the renal cysteine transporter. In addition to excess cystine in the urine, the disorder is also associated with increased urinary excretion of dibasic amino acids arginine, lysine, and ornithine. However, clinical consequences are only associated with the increased urinary cystine and is due to the poor solubility of this homodimeric compound. Cystine will precipitate in the urine resulting in the formation of renal calculi (stones) that can lead to renal failure. The two subunits of the cystine transporter are encoded by the SLC3A1 and SLC7A9 genes that encode the basic amino acid transport protein (rBAT) and the functional subunit that transports neutral and basic amino acids (b(0,+)AT; where the AT stands for amino acid transporter), respectively. Common treatments for patients with cystinuria are to decrease protein and salt intake as well as to ensure increased hydration as this will dilute the cystine in the urine reducing the potential for crystal formation. In addition, patients are given drugs, such as acetazolamide (a carbonic anhydrase inhibitor principally utilized in the treatment of hypertension), which alkalizes the urine thereby reducing the potential for urinary precipitation of cystine. In addition, thiol drugs can be used to compete for the formation of cystine. These drugs include captopril [an angiotensin converting enzyme (ACE) inhibitor also used principally in the treatment of hypertension], D-penicillamine, and alpha-MPG (alpha-mercaptopropionylglycine).

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Tyrosine Biosynthesis

Tyrosine is produced in cells by hydroxylating the essential amino acid phenylalanine. This relationship is much like that between cysteine and methionine. Half of the phenylalanine required goes into the production of tyrosine; if the diet is rich in tyrosine itself, the requirements for phenylalanine are reduced by about 50%.

Phenylalanine hydroxylase is a mixed-function oxygenase: one atom of oxygen is incorporated into water and the other into the hydroxyl of tyrosine. The reductant is the tetrahydrofolate-related cofactor tetrahydrobiopterin, which is maintained in the reduced state by the NADH-dependent enzyme dihydropteridine reductase (DHPR).

Reaction catalyzed by phenylalanine hydroxylase in the synthesis of tyrosine

Biosynthesis of Tyrosine from Phenylalanine

Missing or deficient phenylalanine hydroxylase results in hyperphenylalaninemia. Hyperphenylalaninemia is defined as a plasma phenylalanine concentration greater than 2mg/dL (120μM). The most widely recognized hyperphenylalaninemia (and most severe) is the genetic disease known as phenlyketonuria (PKU). Patients suffering from PKU have plasma phenylalanine levels >1000μM, whereas the non-PKU hyperphenylalaninemias exhibit levels of plasma phenylalanine <1000μM. Untreated PKU leads to severe mental retardation. The mental retardation is caused by the accumulation of phenylalanine, which becomes a major donor of amino groups in aminotransferase activity and depletes neural tissue of α-ketoglutarate. This absence of α-ketoglutarate in the brain shuts down the TCA cycle and the associated production of aerobic energy, which is essential to normal brain development.

The product of phenylalanine transamination, phenylpyruvic acid, is reduced to phenylacetate and phenyllactate, and all 3 compounds appear in the urine. The presence of phenylacetate in the urine imparts a "mousy" odor. If the problem is diagnosed early, the addition of tyrosine and restriction of phenylalanine from the diet can minimize the extent of mental retardation.

Because of the requirement for tetrahydrobiopterin in the function of phenylalanine hydroxylase, deficiencies in DHPR can manifest with hyperphenylalaninemia. However, since tetrahydrobiopterin is a cofactor in several other enzyme catalyzed reactions (e.g. see the synthesis of the tyrosine- and tryptophan-derived neurotransmitters as well as nitric oxide in Specialized Products of Amino Acids), the effects of missing or defective DHPR cause even more severe neurological difficulties than those usually associated with PKU caused by deficient phenylalanine hydroxylase activity.

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Ornithine and Proline Biosynthesis

Glutamate is the precursor of both proline and ornithine, with glutamate semialdehyde being a branch point intermediate leading to one or the other of these 2 products. While ornithine is not one of the 20 amino acids used in protein synthesis, it plays a significant role as the acceptor of carbamoyl phosphate in the urea cycle. Ornithine serves an additional important role as the precursor for the synthesis of the polyamines. The production of ornithine from glutamate is important when dietary arginine, the other principal source of ornithine, is limited.

Ornithine and proline synthesis

Synthesis of Ornithine and Proline from Glutamic Semialdehyde

The fate of glutamate semialdehyde depends on prevailing cellular conditions. Ornithine production occurs from the semialdehyde via a simple glutamate-dependent transamination, producing ornithine. When arginine concentrations become elevated, the ornithine contributed from the urea cycle plus that from glutamate semialdehyde inhibit the aminotransferase reaction, with accumulation of the semialdehyde as a result. The semialdehyde cyclizes spontaneously to Δ1-pyrroline-5-carboxylate which is then reduced to proline by an NADPH-dependent reductase.

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Serine Biosynthesis

The main pathway to de novo biosynthesis of serine starts with the glycolytic intermediate 3-phosphoglycerate. An NADH-linked dehydrogenase converts 3-phosphoglycerate into a keto acid, 3-phosphopyruvate, suitable for subsequent transamination. Aminotransferase activity with glutamate as a donor produces 3-phosphoserine, which is converted to serine by phosphoserine phosphatase.

As indicated below, serine can be derived from glycine (and visa versa) by a single step reaction that involves serine hydroxymethyltransferase and tetrahydrofolate (THF).

Synthesis of serine

Serine Biosynthesis


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Glycine Biosynthesis

The main pathway to glycine is a 1-step reversible reaction catalyzed by serine hydroxymethyltransferase (SHMT). This enzyme is a member of the family of one-carbon transferases and is also known as glycine hydroxymethyltransferase. This reaction involves the transfer of the hydroxymethyl group from serine to the cofactor tetrahydrofolate (THF), producing glycine and N5,N10-methylene-THF. There are mitochondrial and cytosolic versions of serine hydroxymethyltransferase. The cytosolic enzyme is referred to as SHMT1 and the mitochondrial enzyme is SHMT2.

Reaction catalyzed by serine hydroxymethyltransferase

Glycine produced from serine or from the diet can also be oxidized by glycine decarboxylase (also referred to as the glycine cleavage complex, GCC) to yield a second equivalent of N5,N10-methylene-tetrahydrofolate as well as ammonia and CO2.

Reaction catalyzed by glycine decarboxylase

Glycine is involved in many anabolic reactions other than protein synthesis including the synthesis of purine nucleotides, heme, glutathione, creatine and serine. In addition, glycine functions in the central nervous system as an inhibitory neurotransmitter where it participates in regulating signals that process motor and sensory information that permit movement, vision and audition. Glycine is co-released with GABA which is the primary inhibitory neurotransmitter. Glycine action as a neurotransmitter is a function of the amino acid binding to a specific receptor,  GlyR. GlyR is a member of the nicitinicoid receptor superfamily that includes the GABAA receptor (GABAAR), the excitatory nicotinic acetylcholine receptors (nAChR) and the serotonin type 3 receptor (5HT3). GlyR is a heteromeric complex consisting of a complex of either three or four α-subunits and one β-subunit. There are four different α-subunit genes (α1-4) and a single β-subunit gene in the human genome. GlyR is a ligand-gated ionotropic receptor that is a chloride channel. In addition to glycine, GlyR can be activated by several other small amino acids such as alanine and taurine. Glycine is also involved in the modulation of excitatory neurotransmission exerted via glutamate binding to N-methyl-D-aspartate (NMDA) receptors.

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Aspartate/Asparagine and Glutamate/Glutamine Biosynthesis

Glutamate is synthesized by the reductive amination of α-ketoglutarate catalyzed by glutamate dehydrogenase; it is thus a nitrogen-fixing reaction. In addition, glutamate arises by aminotransferase reactions, with the amino nitrogen being donated by a number of different amino acids. Thus, glutamate is a general collector of amino nitrogen.

Reactions catalyzed by glutamate dehydrogenase

Aspartate is formed in a transamination reaction catalyzed by aspartate transaminase, AST. This reaction uses the aspartate α-keto acid analog, oxaloacetate, and glutamate as the amino donor. Aspartate can also be formed by deamination of asparagine catalyzed by asparaginase.

Reaction catalyzed by aspartate transaminase (AST)

Reaction catalyzed by asparaginase

Asparagine synthetase and glutamine synthetase, catalyze the production of asparagine and glutamine from their respective α-amino acids. Glutamine is produced from glutamate by the direct incorporation of ammonia; and this can be considered another nitrogen fixing reaction. Asparagine, however, is formed by an amidotransferase reaction.

Reaction catalyzed by asparagine synthetase

Reaction catalyzed by glutamine synthetase

Aminotransferase reactions are readily reversible. The direction of any individual transamination depends principally on the concentration ratio of reactants and products. By contrast, transamidation reactions, which are dependent on ATP, are considered irreversible. As a consequence, the degradation of asparagine and glutamine take place by a hydrolytic pathway rather than by a reversal of the pathway by which they were formed. As indicated above, asparagine can be degraded to aspartate.

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Amino Acid Catabolism

Glutamine/Glutamate and Asparagine/Aspartate Catabolism

Glutaminase is an important kidney tubule enzyme involved in converting glutamine (from liver and from other tissue) to glutamate and NH4+, with the NH4+ being excreted in the urine. Glutaminase activity is present in many other tissues as well, although its activity is not nearly as prominent as in the kidney. The glutamate produced from glutamine is converted to α-ketoglutarate, making glutamine a glucogenic amino acid.

Reaction catalyzed by glutaminase

Asparaginase (see above) is also widely distributed within the body, where it converts asparagine into ammonia and aspartate. Aspartate transaminates to oxaloacetate, which follows the gluconeogenic pathway to glucose.

Glutamate and aspartate are important in collecting and eliminating amino nitrogen via glutamine synthetase and the urea cycle, respectively. The catabolic path of the carbon skeletons involves simple 1-step aminotransferase reactions that directly produce net quantities of a TCA cycle intermediate. The glutamate dehydrogenase reaction operating in the direction of α-ketoglutarate production provides a second avenue leading from glutamate to gluconeogenesis.

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Alanine Catabolism

Alanine is also important in intertissue nitrogen transport as part of the glucose-alanine cycle (see above). Alanine's catabolic pathway involves a simple aminotransferase reaction that directly produces pyruvate. Generally pyruvate produced by this pathway will result in the formation of oxaloacetate, although when the energy charge of a cell is low the pyruvate will be oxidized to CO2 and H2O via the PDH complex and the TCA cycle. This makes alanine a glucogenic amino acid.

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Arginine, Ornithine and Proline Catabolism

The catabolism of arginine begins within the context of the urea cycle. It is hydrolyzed to urea and ornithine by arginase.

Ornithine, in excess of urea cycle needs, is transaminated to form glutamate semialdehyde. Glutamate semialdehyde can serve as the precursor for proline biosynthesis as described above or it can be converted to glutamate.

Proline catabolism is a reversal of its synthesis process.

The glutamate semialdehyde generated from ornithine and proline catabolism is oxidized to glutamate by an ATP-independent glutamate semialdehyde dehydrogenase. The glutamate can then be converted to α-ketoglutarate in a transamination reaction. Thus arginine, ornithine and proline, are glucogenic.

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Serine Catabolism

The conversion of serine to glycine and then glycine oxidation to CO2 and NH3, with the production of two equivalents of N5,N10-methyleneTHF, was described above in the section on glycine biosynthesis. Serine can be catabolized back to the glycolytic intermediate, 3-phosphoglycerate, by a pathway that is essentially a reversal of serine biosynthesis. However, the enzymes are different. Although it has been demonstrated in mammals such as rodents and dogs that serine can be converted to pyruvate through a deamination reaction catalyzed by serine/threonine dehydratase, this activity of the enzyme appears to be lacking in humans.

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Threonine Catabolism

There are at least 3 pathways for threonine catabolism that have been identified in yeasts, insects, and vertebrates including mammals. The principal threonine catabololizing pathway in humans involves glycine-independent serine/threonine dehydratase yielding α-ketobutyrate which is further catabolized to propionyl-CoA and finally the TCA cycle intermediate, succinyl-CoA. Serine/threonine dehydratase is expressed at high levels only in the liver. It appears that in newborn infants catabolism of threonine occurs exclusively via the action of the serine/threonine dehydratase. Therefore, it is presumed that this is the predominant threonine catabolizing pathway in humans.

The second pathway of threonine catabolism utilizes serine hydroxymethyltransferase. As indicated above this enzyme belongs to a family of one-carbon transferases and is alternatively named glycine hydroxymethyltransferase or threonine aldolase. The products of this reaction are acetyl-CoA and glycine. The glycine can be converted to serine via the same enzyme and the serine is then catabolized as described above yielding pyruvate and NH4+. Thus, via this catabolic pathway threonine yields ketogenic and glucogenic byproducts. In humans it appears that threonine aldolase is actually encoded by a non-functional pseudogene, whereas in other mammals and vertebrates (e.g. mice, zebrafish, and clawed frogs) the threonine aldolase gene encodes a functional threonine catabolizing enzyme.

An additional pathway occurs in the mitochondria and is initiated by threonine dehydrogenase yielding α-amino-β-ketobutyrate (2-amino-3-ketobutyrate). The 2-amino-3-ketobutyrate is either converted to acetyl-CoA and glycine, via the action of 2-amino-3-ketobutyrate coenzyme A ligase (also called glycine C-acetyltransfease), or it can spontaneously degrade to aminoacetone which is converted to pyruvate. The threonine dehydrogenase gene in humans appears to be non-functional due to the incorporation of three inactivating mutations. Thus, whereas, this enzyme is a major threonine catabolizing enzyme in other mammals such as mice, it is the serine/threonine dehydratase gene that is most important in threonine catabolism in humans.

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Glycine Catabolism

Glycine is classified as a glucogenic amino acid, since it can be converted to serine by serine hydroxymethyltransferase (see above), and serine can be converted back to the glycolytic intermediate, 3-phosphoglycerate or to pyruvate by serine/threonine dehydratase, although the latter reaction (serine to pyruvate) appears not be occur in human tissues. Nevertheless, the main glycine catabolic pathway leads to the production of CO2, ammonia, and one equivalent of N5,N10-methyleneTHF by the mitochondrial glycine decarboxylase, also called the glycine cleavage complex, GCC. See above for diagram of the cleavage reaction. Glycine decarboxylase is a mitochondrial enzyme complex composed of four distinct proteins identified as H, L, P, and T. The H protein is a lipoic acid-containing protein. The L protein is a dihydrolipoamide dehydrogenase (DLD) similar to the DLD subunit of the pyruvate dehydrogenase and α-ketoglutarate (2-oxoglutarate) dehydrogenase complexes. The P protein is a pyridoxal phosphate-dependent glycine decarboxylase. The T protein is a tetrahydrofolate-requiring aminotransferase. Deficiencies in the H, P, or T proteins results in glycine encephalopathy which is characterized by nonketotic hyperglycinemia. These gene defects result in severe mental retardation that is due to highly elevated levels of glycine in the CNS.

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Cysteine Catabolism

There are several pathways for cysteine catabolism. The simplest, but least important pathway is catalyzed by a liver desulfurase and produces hydrogen sulfide, (H2S) and pyruvate. The major catabolic pathway in animals is via cysteine dioxygenase that oxidizes the cysteine sulfhydryl to sulfinate, producing the intermediate cysteinesulfinate. Cysteinesulfinate can serve as a biosynthetic intermediate undergoing decarboxylation and oxidation to produce taurine. Catabolism of cysteinesulfinate proceeds through transamination to β-sulfinylpyruvate which then undergoes desulfuration yielding bisulfite, (HSO3) and the glucogenic product, pyruvate. The enzyme sulfite oxidase uses O2 and H2O to convert HSO3 to sulfate, (SO4) and H2O2. The resultant sulfate is used as a precursor for the formation of 3'-phosphoadenosine-5'-phosphosulfate, (PAPS). PAPS is used for the transfer of sulfate to biological molecules such as the sugars of the glycosphingolipids.

Synthesis of 3'-phosphoadenosine-5'-phosphosulfate, PAPS

Other than protein, the most important product of cysteine metabolism is the bile salt precursor taurine, which is used to form the bile acid conjugates taurocholate and taurochenodeoxycholate.

The enzyme cystathionase can also transfer the sulfur from one cysteine to another generating thiocysteine and pyruvate. Transamination of cysteine yields β-mercaptopyruvate which then reacts with sulfite, (SO32–), to produce thiosulfate, (S2O32–) and pyruvate. Both thiocysteine and thiosulfate can be used by the enzyme rhodanese to incorporate sulfur into cyanide, (CN), thereby detoxifying the cyanide to thiocyanate.

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Methionine Catabolism

The principal fates of the essential amino acid methionine are incorporation into polypeptide chains, and use in the production of α-ketobutyrate and cysteine via SAM as described above. The transulfuration reactions that produce cysteine from homocysteine and serine also produce α-ketobutyrate, the latter being converted first to propionyl-CoA and then via a 3-step process to succinyl-CoA.

Synthesis of S-adenosylmethionine (SAM)

Biosynthesis of S-adenosylmethionine, SAM

Regulation of the methionine metabolic pathway is based on the availability of methionine and cysteine. If both amino acids are present in adequate quantities, SAM accumulates and is a positive effector on cystathionine synthase, encouraging the production of cysteine and α-ketobutyrate (both of which are glucogenic). However, if methionine is scarce, SAM will form only in small quantities, thus limiting cystathionine synthase activity. Under these conditions accumulated homocysteine is remethylated to methionine, using N5-methylTHF and other compounds as methyl donors.

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Leucine, Isoleucine, and Valine Catabolism: Branched-chain Amino Acids (BCAA)

This group of essential amino acids are identified as the branched-chain amino acids, BCAAs. Because this arrangement of carbon atoms cannot be made by humans, these amino acids are an essential element in the diet. The catabolism of all three compounds initiates in muscle and yields NADH and FADH2 which can be utilized for ATP generation. The catabolism of all three of these amino acids uses the same enzymes in the first two steps. The first step in each case is a transamination using a BCAA aminotransferase (termed a branched-chain aminotransferase, BCAT), with α-ketoglutarate as amine acceptor. As a result, three different α-keto acids are produced and are oxidized using a common branched-chain α-keto acid dehydrogenase (BCKD), yielding the three different CoA derivatives. Subsequently the metabolic pathways diverge, producing many intermediates.

There are two genes encoding BCAT identified as BCAT1 and BCAT2. BCAT1 (located on chromosome 12p12.1) encodes a cytosolic version of the enzyme and the protein is identified as BCATc. BCAT2 (located on chromosome 19q13.33) encodes a mitochondrial version of the enzyme and this protein is designated BCATm. Expression of BCAT1 is seen in the CNS as well as several peripheral tissues. BCAT2 expression is observed in most non-neuronal tissues except the liver.

The principal product from valine is propionylCoA, the glucogenic precursor of succinyl-CoA. Isoleucine catabolism terminates with production of acetylCoA and propionylCoA; thus isoleucine is both glucogenic and ketogenic. Leucine gives rise to acetylCoA and acetoacetylCoA, and is thus classified as strictly ketogenic.

There are a number of genetic diseases associated with faulty catabolism of the BCAAs. The most common defect is in the branched-chain α-keto acid dehydrogenase, BCKD. Since there is only one dehydrogenase enzyme for all three amino acids, all three α-keto acids accumulate and are excreted in the urine. The disease is known as Maple syrup urine disease because of the characteristic odor of the urine in afflicted individuals. Mental retardation in these cases is extensive. Unfortunately, since these are essential amino acids, they cannot be heavily restricted in the diet. The main neurological problems are due to poor formation of myelin in the CNS. Although the outcomes for afflicted individuals used to quite severe with abnormal development and a short life-span, many advances in the treatment of MSUD in recent years have improved the clinical picture. Liver transplantation can result in a relatively normal life for MSUD patients.

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Leucine Signaling and Metabolic Regulation

Numerous studies have shown that diets high in protein increase fatty acid oxidation and overall energy expenditure and thus, promote weight loss. In addition, high protein diets are known to improve glucose homeostasis and therefore, can have a positive impact on insulin sensitivity and diabetes. In animal models of obesity and diabetes, increasing the protein to carbohydrate ratio in a high-fat diet results in a delay in the development of obesity while simultaneously improving glucose tolerance. In studies on obese humans, subjects that consumed a milk whey-protein-enriched diet exhibited demonstrable improvement in fatty liver symptoms (hepatic steatosis) and reduced plasma lipid profiles. The composition of whey protein is approximately 65% β-lactoglobulin, 25% α-lactalbumin, and 8% serum albumin. In studies examining the effects of dietary protein on energy expenditure, appetite suppression, and weight loss, whey protein is the more beneficial source when comparing the effects of consumption of whey proteins, soy proteins, or casein.

Whey proteins are enriched in the branched-chain amino acids (BCAA) leucine, isoleucine, and valine and are thus, excellent sources of energy production in skeletal muscle as well as serving as building blocks for muscle protein synthesis. Leucine has been proposed to be the primary mediator of the metabolic changes that occur when consuming a high protein diet. At the molecular level, leucine has been shown to activate the metabolic regulatory kinase known as mammalian target of rapamycin, mTOR. For more information on the activities and regulation of mTOR go to the Insulin Functions page or to the Protein Synthesis page. Activation of skeletal muscle mTOR results in increased protein synthesis and thus, increased energy expenditure. Hypothalamic mTOR activation is also involved in the regulation of feeding behaviors. Of note is the fact that direct injection of leucine into the hypothalamus results in increased mTOR signaling leading to decreased feeding behavior and body weight. This effect is unique to leucine, as direct injection of valine, another BCAA, does not result in hypothalamic mTOR activation nor reductions in food intake or body weight.

The effects of leucine supplementation, on the above described parameters, are not as pronounced as the effects observed when consuming a high-protein diet. This suggests that additional factors are likely involved in the effects of high-protein diets. One of these factors may be that consuming a high protein diet is associated with a reduction in total carbohydrate intake. The reduced carbohydrate intake would thus, be associated with a reduction in hepatic lipogenesis and an increase in adipose tissue lipolysis. Although leucine alone is not as effective as high-protein diets at reducing body weight and food intake it cannot be discounted as an important dietary supplement.

However, it must be pointed out that some controversy surrounds the role of high protein consumption, and in particular leucine intake, in overall metabolic homeostasis. This is due to the fact that some studies in laboratory animals have shown that leucine supplementation results in insulin resistance. This latter effect would certainly lead to an increased likelihood for development of type 2 diabetes. In the typical Western diet consisting of high dairy and meat, the role of leucine in the pathogeneis of type 2 diabetes is suggested by the consequent over activation of mTOR. With respect to diabetes, activation of mTOR results in phosphorylation and activation of the kinase, p70S6K, which in turn phosphorylates the insulin receptor substrate 1 (IRS-1). Phosphorylation of IRS-1 by p70S6K results in reduced insulin-mediated signaling via the insulin receptor, thereby, increasing the metabolic burden on pancreatic β-cells. In addition, increased mTOR activation leads to adipogenesis which can lead to obesity-mediated insulin resistance. Most of the work in laboratory animals demonstrates that the positive effects of increased leucine intake or high-protein diets are most pronounced when the animals are also consuming a high-fat diet. Therefore, it is suggestive that there are definite benefits for overweight and obese individuals to increase their intake of leucine and/or total protein as a means for appetite and weight control. However, although high-protein diets or leucine supplementation are important considerations in a healthy diet, the total amount consumed must be taken into account so as not to lead to excess mTOR activation.

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Phenylalanine and Tyrosine Catabolism

Phenylalanine normally has only two fates: incorporation into polypeptide chains, and production of tyrosine via the tetrahydrobiopterin-requiring phenylalanine hydroxylase. Thus, phenylalanine catabolism always follows the pathway of tyrosine catabolism. The main pathway for tyrosine degradation involves conversion to fumarate and acetoacetate, allowing phenylalanine and tyrosine to be classified as both glucogenic and ketogenic.

Tyrosine is equally important for protein biosynthesis as well as an intermediate in the biosynthesis of several physiologically important metabolites e.g. dopamine, norepinephrine and epinephrine (see Specialized Products of Amino Acids).

As in phenylketonuria (deficiency of phenylalanine hydroxylase, PAH), deficiency of tyrosine aminotransferase (TAT) leads to hypertyrosinemia and the urinary excretion of tyrosine and the catabolic intermediates between phenylalanine and tyrosine. The adverse neurological symptoms are similar for PAH and TAT deficiencies. In addition, hypertyrosinemia leads to painful corneal eruptions and photophobia.

The first inborn error in metabolism ever recognized, alkaptonuria, was demonstrated to be the result of a defect in phenylalanine and tyrosine catabolism. Alkaptonuria is caused by defective homogentisic acid oxidase. Homogentisic acid accumulation is relatively innocuous, causing urine to darken on exposure to air, but no life-threatening effects accompany the disease. The only untoward consequence of alkaptonuria is ochronosis (bluish-black discoloration of the tissues) and arthritis.

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Lysine Catabolism

Like all amino acids, catabolism of lysine can initiate from uptake of dietary lysine or from the breakdown of intracellular protein. Intestinal uptake of lysine involves specific transporter proteins. In most tissues, cationic amino acids are transported principally by a Na+-independent system, specific for L-isomers of lysine, arginine, and ornithine. This transport system is known as the Y(+) system and these transporters are members of the SCL7 family of membrane transporters. There are actually at least three transport mechanisms for lysine transport. One is the aforementioned Y(+) system that can be inhibited by leucine with high affinity when Na+ is present, but this affinity is reduced in the absence of sodium. Another mechanism involves a Na+-independent system that is inhibited by leucine with high affinity only when Na+ is present. An additional transporter is a Na+-dependent transport system that can be inhibited by leucine with high affinity and also by alanine. Once taken up by the intestines, dietary lysine can be incorporated into protein or catabolized.

There are several, at least three, pathways for lysine catabolism but the primary pathway utilized within the liver is one that begins with the formation of an adduct between lysine and 2-oxoglutarate (α-ketoglutarate) called saccharopine. Lysine catabolism is unusual in the way that the ε-amino group is transferred to 2-oxoglutarate and into the general nitrogen pool. The reaction is a transamination in which the ε-amino group is transferred to the α-keto carbon of 2-oxoglutarate forming the metabolite, saccharopine. Unlike the majority of transamination reactions, this one does not employ pyridoxal phosphate as a cofactor. The formation of saccharopine and its hydrolysis to α-aminoadipic-6-semialdehyde is catalyzed by the bifunctional enzyme α-aminoadipic semialdehyde synthase. This reaction results in the amino nitrogen remaining with the α-carbon of 2-oxoglutarate, producing glutamate and α-aminoadipic-6-semialdehyde. Because this transamination reaction is not reversible, lysine is an essential amino acid. In yeast the first two reactions of lysine catabolism are catalyzed by two distinct gene products identified as lysine:2-oxoglutarate reductase (LYS1) and saccharopine dehydrogenase (LYS9). Mammalian α-aminoadipic semialdehyde synthase is encoded by the AASS gene found on chromosome 7q31.32 and is composed of 24 exons spanning 68 kb. The protein contains 927 amino acids with the N-terminal half harboring the lysine:2-oxoglutarate reductase activity and the C-terminal half harboring the saccharopine dehydrogenase activity. The ultimate end-product of lysine catabolism, via this pathway, is acetoacetyl-CoA.

Genetic deficiencies in either of the first two reactions of the saccharopine pathway of lysine catabolism result in familial hyperlysinemia. Since these two reactions are catalyzed by the bifunctional enzyme AASS, defects can be found in either the N-terminal lysine:2-oxoglutarate reductase activity or the saccharopine dehydrogenase activity. These deficiencies are observed in individuals who excrete large quantities of urinary lysine and some saccharopine. The lysinemia and associated lysinuria are benign.

One of the other minor pathways of lysine catabolism, yet clinically significant, is the pipecolic acid pathway. L-pipecolic acid (2-carboxypiperdine) was known to be a widely distributed non-protein amino acid in plants and to be derived from lysine catabolism in mammals. Originally it was thought that the degradation of lysine to pipecolate was the major catabolic pathway for this amino acid. Although it is now known that this product of lysine catabolism reflects a minor catabolic pathway, there is clinical significance to this pathway. In addition, lysine catabolism via the pipecolic acid pathway may play a significant role in the central nervous system. Lysine catabolism via this pathway involves conversion to α-keto-ε-amino-caproic acid and then to pipecolic acid. Pipecolic acid then is ultimately converted to α-aminoadipic semialdehyde which is also a product of the saccharopine pathway of lysine catabolism. Formation of α-aminoadipic semialdehyde from pipecolic acid is catalyzed by α-aminoadipic semialdehyde dehydrogenase (AASA dehydrogenase). AASA dehydrogenase is also known as antiquitin (ATQ1) and is encoded by the aldehyde dehydrogenase 7 family member A1 gene (ALDH7A1). The ALDH7A1 gene is located on chromosome 5q23.2 composed of 18 exons encoding a protein of 510 amino acids. Mutations in the ALDH7A1 gene are associated with pyridoxine-dependent epilepsy.

Other serious disorders associated with lysine metabolism are due to failure of the transport systems for lysine and the other dibasic amino acids across the intestinal wall. Lysine is essential for protein synthesis; and deficiencies of its transport into the body can cause seriously diminished levels of protein synthesis. Probably more significant however, is the fact that arginine is transported on the same dibasic amino acid carrier, and resulting arginine deficiencies limit the quantity of ornithine available for the urea cycle. The result is severe hyperammonemia after a meal rich in protein. The addition of citrulline to the diet prevents the hyperammonemia.

Lysine is also important as a precursor for the synthesis of carnitine, required for the transport of fatty acids into the mitochondria for oxidation. Free lysine does not serve as the precursor for this reaction, rather the modified lysine found in certain proteins. Some proteins modify lysine to trimethyllysine using SAM as the methyl donor to transfer methyl groups to the ε-amino of the lysine side chain. Hydrolysis of proteins containing trimethyllysine provides the substrate for the subsequent conversion to carnitine.

Structure of carnitine


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Histidine Catabolism

Histidine catabolism begins with release of the α-amino group catalyzed by histidase, introducing a double bond into the molecule. As a result, the deaminated product, urocanate, is not the usual α-keto acid associated with loss of α-amino nitrogens. The end product of histidine catabolism is glutamate, making histidine one of the glucogenic amino acids.

Another key feature of histidine catabolism is that it serves as a source of ring nitrogen to combine with tetrahydrofolate (THF), producing the 1-carbon THF intermediate known as N5-formiminoTHF. The latter reaction is one of two routes to N5-formiminoTHF. Urocanate is converted to 4-imidazolone-5-propionate via the action of urocanate hydratase. The latter product is then converted to N-formiminoglutamte via the action of imidazolone propionase. Glutamate formiminotransferase then transfers the fomimino group to THF yielding glutamate and N5-formiminoTHF.

The principal genetic deficiency associated with histidine metabolism is absence or deficiency of the first enzyme of the pathway, histidase. The resultant histidinemia is relatively benign. The disease, which is of relatively high incidence (1 in 10,000), is most easily detected by the absence of urocanate from skin and sweat, where it is normally found in relative abundance.

Decarboxylation of histidine in the intestine by bacteria gives rise to histamine. Similarly, histamine is synthesized in numerous tissues by the decarboxylation of histidine catalyzed by histidine decarboxylase. Histamine exerts multiple activities but the two most significant are its roles in immunologic response to antigen and inducing the release of hydrogen ion (H+) by parietal cells of the stomach to generate the HCl necessary for gastric digestion. The largest amount of histamine produced in the body is that made by mast cells and basophils. If these cells are sensitized by the presentation of IgE on their surfaces they will degranulate in response to antigen binding, releasing histamine into the circulation. The response to this release is bronchoconstriction and vasodialtion which are the general symptoms associated with asthma and various allergic reactions. Within the gastrointestinal system, histamine is produced in the enterochromaffin-like cells of the stomach and when release in response to vagal nerve stimulation bind to receptors on parietal cells triggering the mobilization of the proton pumb of the parietal cell to the apical membrane allowing for increased H+ transport into the lumen of the stomach. All of the actions of histamine are the result of binding to one of four cell surface receptors (H1–H4) all of which are G-protein coupled receptors (GPCRs). The H1 receptor is coupled to a Gq-type G-proteins and is responsible for triggering bronchoconstriction and vasodilation. The H2 receptor is a Gs-type G-protein and is present on parietal cells and vascular smooth muscle cells.

Synthesis of histamine

Synthesis of Histamine


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Tryptophan Catabolism

A number of important side reactions occur during the catabolism of tryptophan on the pathway to acetoacetate. The first enzyme of the catabolic pathway is an iron porphyrin oxygenase that opens the indole ring. The latter enzyme is highly inducible, its concentration rising almost 10-fold on a diet high in tryptophan.

Kynurenine is the first key branch point intermediate in the catabolic pathway leading to 3 fates:

Kynurenine can undergo deamination in a standard transamination reaction yielding kynurenic acid. Kynurenic acid and metabolites have been shown to act as antiexcitotoxics and anticonvulsives. High levels of kynurenic acid have been found in the urine of individuals suffering from schizophrenia. Kynurenic acid has been shown to act as a non-competetive antagonist at the glycine binding site of the NMDA receptor (NMDA = N-methyl-D-aspartate) which is an ionotropic (ligand-gated ion channel) receptor for glutamate. The NMDA receptor is a key component of the glutaminergic neurotransmission system believed to be involved in the pathophysiology of schizophrenia, thus explaining the potential role of kynurenic acid in schizophrenia.

Structures of kynurenine and kynurenic acid

Kynurenine can also undergo a series of catabolic reactions producing 3-hydroxyanthranilic acid plus alanine. Another equivalent of alanine is produced from kynurenine in a single step reaction leading to anthranilic acid. It is the production of these alanine residues that allows tryptophan to be classified among the glucogenic amino acids. Oxidation of 3-hydroxyanthranilate converts it into 2-amino-3-carboxymuconic 6-semialdehyde, which has two fates. The main flow of carbon elements from this intermediate leads to acetoacetate which is why tryptophan is also a ketogenic amino acid. An important side reaction in liver involves a non-enzymatic cyclization to quinolate then via a transamination and several rearrangements yields limited amounts of nicotinic acid, which leads to production of a small amount of NAD+ and NADP+.

Aside from its role as an amino acid in protein biosynthesis, tryptophan also serves as a precursor for the synthesis of serotonin and melatonin. These products are discussed in Specialized Products of Amino Acids.

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Last modified: March 8, 2014