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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 2-oxoglutarate (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 acetyl-CoA or acetoacetyl-CoA, 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

Digestion of Dietary Proteins

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 via the actions of the pepsins, and continues within the lumen of the duodenum. Within the small intestine there are two principal pancreatic enzymes involved in protein digestion; trypsin and chymotrypsin. Several additional pancreatic peptidases play a lesser role in peptide digestion and include the carboxypeptidases and the elastases.

The initial enzyme involved in protein digestion is gastric pepsins. Pepsins are derived from the precursor zymogen, pepsinogen. Pepsins are released from pepsinogen via acid-induced autocatalysis. 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 juice (chyme) passes from the stomach and is mixed with alkaline pancreatic juice 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 the pancreatic trypsins and the pancreatic chymotrypsins, and to a lesser extent by the pancreatic elastases, and by the pancreatic carboxypeptidases A1 and A2. Humans express three genes that encode members of the trypsin family of serine proteases. These genes are identified as protease, serine 1, 2, and 3 (PRSS1, PRSS2, and PRSS3). Expression of the PRSS1 and PRSS2 genes predominates in the pancreas while the PRSS3 gene is expressed in the pancreas and the brain. Humans express two genes encoding chymotrypsinogen identified as CTRB1 and CTRB2 with the CTRB1 encoded enzyme being the predominant pancreatic carboxypeptidase. Humans express a large family of 25 genes that encode enzymes of the carboxypeptidase family. The majority of these enzymes are involved in protein processing and are not involved in digestive processes. The term carboxypeptidase A refers to the fact that these enzymes hydrolyze peptide bonds where the amino acid on the C-terminal side of the bond is an aromatic or aliphatic amino acid. The carboxypeptidase A family includes six genes where the CPA1 and CPA2 genes encoded pancreatic digestive enzymes. Humans express eight genes that encode enzymes of the elastase family with the chymotrypsin-like elastase family members (excluding the CELA1 encoded enzyme) being pancreatic digesticve enzymes. The digestive elastases are chymotrypsin-like elastase 2A, 2B, 3A, and 3B (CELA2A, CELA2B, CELA3A, and CELA3B genes, respectively).

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 (apical) membranes of duodenal mucosal cells. Trypsin then cleaves more trypsinogen to trypsin, as well as chymotrypsinogens, proelastases, 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 colonic mucosal cells.

Amino Acid and Peptide Uptake

The absorption of most amino acids from the intestine requires an active transport process that is dependent upon Na+ or H+ co-transport. There are numerous amino acid transporters encompassing six major families of transport systems which are sometimes grouped into three broad categories. These three broad categories 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 that includes the SLC1, SLC6, SLC7, SLC36, SLC38, and SLC43 gene families. The transport of amino acids occurs in all other cells and so these transport systems are expressed throught the body. They are critically important within the context of the brain and the kidney. Many of the transporters that are required for intestinal amino acid uptake are also expressed in the proximal tubules of the kidneys where they are responsible for excretion and reabsorption of amino acids.

The neutral amino acid transporters were originally subdivided into at least eight subfamilies with all but one being Na+-dependent transporters. These original designations were the system A, ASC, N, beta (β), GLY, IMINO, PHE, B0, and L transporters. The system A and system B0 transporters were those defined by their preference for alanine and other small and polar neutral amino acids. The system ASC transporters were defined by their preference for alanine, serine, and cysteine. The system L transporters, which are Na+-independent, were defined by their preference for leucine and other large (bulky) hydrophobic neutral amino acids. The system N transporters show preference for glutamine, asparagine, and histine and are restricted to expression within hepatocytes. The acidic amino acid transporters were also subdivided into several subfamilies, all of which are Na+-dependent transporters. The acidic transporter subfamilies were the system B0,+, b+, y+, y+L, and b0,+ transporters. The anionic amino acid transporters were also referred to as the system X transporters. The XAG transporters are potassium-dependent glutamate and aspartate transporters. The XAG transporters (SLC1 family) are now more commonly called the excitatory amino acid transporters (EAAT) with there being five members EAAT1 (SLC1A3), EAAT2 (SLC1A2), EAAT3, (SLC1A1), EAAT4 (SLC1A6), and EAAT5 (SLC1A7). The Xc transporters are cystine and glutamate transporters that transport cystine in the opposite direction to that of glutamate (antiporter).

Due to the inconsistent usage of the varied nomenclature systems for amino acid transporters a nomenclature system encompassing five transport activities has been proposed. These five systems designations are: 1) the neutral system (or methionine preferring system) which transports all neutral amino acids; 2) the basic system which is responsible for the transport of cationic amino acids in addition to cystine; 3) the acidic system which transports glutamate and aspartate; 4) the iminoglycine system which transports proline, hydroxyproline, and glycine; and 5) the β-amino acid system which transports taurine and β-alanine.

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 basolateral membranes of enterocytes where they enter the superior mesenteric vein which feeds into the portal vein entering the liver.

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Essential vs. Nonessential Amino Acids

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

Glutamate Synthesis

Glutamate can be synthesized by two distinctly different reaction pathways. In one reaction glutamate is synthesized by the reductive amination of 2-oxoglutarate (α-ketoglutarate) catalyzed by glutamate dehydrogenase (GDH); it is thus a nitrogen-incorporating reaction. In the second type of reaction glutamate is formed from 2-oxoglutarate 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, a critical reaction in overall nitrogen homeostasis as discussed in detail in the Nitrogen Metabolism page.

Reactions catalyzed by glutamate dehydrogenase

Reactions catalyzed by glutamate dehydrogenase (GDH). Glutamate dehydrogenase represents an important "gateway" enzyme in that it can catalyze reactions in two different directions dependent upon overall cellular energy and metabolic needs. When energy and carbon levels are high glutamate can incorporate nitrogen (from NH4+) into 2-oxoglutarate which is driven by the increased levels of NADPH generated from oxidation of glucose in the Pentose Phosphate Pathway. Conversely, when energy levels are reduced glutamate can be oxidatively deaminated in the opposite direction allowing 2-oxoglutarate to be utilized in the TCA cycle for production of energy. Important to the reaction in this direction is that glutamine, which is the major circulating amino acid, effectively serves as the "carrier" of the carbons of 2-oxoglutarate.


Humans express two distinct glutamate dehydrogenase genes identified as GLUD1 and GLUD2. The GLUD1 gene encoded enzyme is the primary glutamate dehydrogenase (GDH1) activity in most tissues. This enzyme is localized to the mitochondrial matrix and functions as a homohexameric complex. The GLUD1 gene is located on chromosome 10q23.3 and is composed of 17 exons that encode a protein of 558 amino acids. The GLUD2 gene is thought to have arisen as a result of a retrotranspostitional event to the X chromosome. The GLUD2 gene is located at Xq24–q25 and is an intronless gene encoding a protein of 558 amino acids. The GLUD2 encoded protein (GDH2) also forms a homohexameric complex in the mitochondrial matrix. Expression of the GLUD2 gene is highest in neural tissues and the regulatory controls over this form of the enzyme are distinct from the GLUD1 encoded enzyme. The GDH2 complex is not inhibited by GTP which allows astrocyte GDH2 to continue to function under conditions of intense excitatory neurotransmission allowing these cells to handle the increased loads of the neurotransmitter glutamate.

Glutamate can also be derived from glutamine via the action of glutaminase. Indeed, the interconversion of glutamine and glutamate represents a critical pathway in overall nitrogen, acid-base, and energy homeostasis in the body as described in greater detail below. Glutaminase activity is present in many tissues such as the liver, small intestine, neurons, and the kidney tubule. There are two distinct glutaminase genes in humans identified as GLS (encoding the GLS1 enzyme) and GLS2 (encoding the GLS2 enzyme). The GLS gene is located on chromosome 2q32–q34 and is composed of 24 exons that undergo alternative splicing to yield several mRNAs generating two isoforms of the enzyme. These two GLS-derived isoforms are often referred to as glutaminase C (GAC) and kidney-type glutaminase (KGA) but are collectively the glutaminase 1 (GLS1) enzymes. The GLS encoded isoforms of glutaminase are primarily expressed in the kidneys. GLS encoded kidney-type glutaminase is a protein of 669 amino acids and GLS encoded glutaminase C is a protein of 598 amnio acids. The GLS2 gene encoded glutaminase was originally thought to be liver specific but is in fact expressed in numerous tissues and is important in the glutamate-glutamine cycle in the brain. The GLS2 encoded glutaminase was originally characterized as dependent on inorganic phosphate (Pi) for activity and is, therefore, also referred to as phosphate-activated glutaminase, PAG. However, both the GLS gene encoded enzymes and the GLS2 encoded enzymes require phosphate for activity with GLS enzymes being more sensitive. The GLS2 gene is located on chromosome 12q13.3 and is composed of 19 exons that undergo alternative splicing to yield several mRNAs that encode four different isoforms of the enzyme. The GLS encoded enzymes are inhibited by glutamate but the GLS2 encoded enzyme is not. The GLS2 encoded enzyme is activated by ammonia but the GLS encoded enzymes are not.

Glutamine Synthesis

Glutamine is synthesized from glutamate via the action of glutamine synthetase. The glutamine synthetase enzyme is encoded by the glutamate-ammonia ligase gene (symbol: GLUL) which is located on chromosome 1q31 and is composed of 9 exons that generate several alternatively spliced mRNAs, each of which encode the same 373 amino acid protein. Ultimately, however, glutamine is derived from 2-oxoglutarate via the sequential actions of amino transferases, or glutamate dehydrogenase, that yield glutamate from 2-oxoglutarate and then via the glutamine synthetase reaction acting on glutamate.

Reaction catalyzed by glutamine synthetase

Reaction catalyzed by glutamine synthetase


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Glutamine Metabolism in Growth and Cancer

Glutamine represents the most abundant amino acid in the blood with levels that are in the range of 500μM. This level of glutamine accounts for over 20% of the total pool of free amino acids in the blood. Although the diet serves as a principle source of glutamine from digested proteins that is then absorbed through the small intestine, another major source of blood glutamine is the ammonia scavanging reactions that take place in skeletal muscle and liver as well as many other tissues. By circulating in the plasma glutamine represents a major contributor to the energy needs of cells, as a major molecule for movement of ammonia in a non-toxic form, as a carbon source for the synthesis of glucose via gluconeogenesis in the kidney and small intestine, and as a critical substrate for the hexosamine biosynthesis pathway which synthesizes UDP-GlcNAc. UDP-GlcNAc is added to numerous cytoplasmic and nuclear proteins altering their activities and also represents a mode of epigenetic modification of histone proteins. The need for UDP-GlcNAc for glycoprotein synthesis also demonstrates the role of glutamine in endoplasmic reticulum (ER) homeostasis preventing the activation of ER stress pathways.

metabolic pathways of glutmaine use in proliferating/cancer cells

Metabolic pathways that utilize glutamine in proliferating and cancer cells. Glutamine is the most abundant amino acid in the blood and it is tranported into cells through the actions or various transporters such as the one encoded by the SLC1A5 gene (also known as ASCT2: Alanine Serine Cysteine Transporter 2). Within the cytosol glutamine and aspartate combine through the action of asparagine synthase to form aspragine and glutamate. Cytosolic glutamine is also a required substrate for the synthesis of UDP-GlcNAc in the hexosamine biosynthesis pathway. UDP-GlcNAc is used to O-GlcNAcylate numerous cytoplasmic and nuclear proteins resulting in changes in transcription profiles and epigenetic modifications of histone proteins. In the mitochondria glutamine is deaminated by the glutaminase encoded by the GLS2 gene forming glutamate. In numerous cancer cells the GLS encoded enzyme (often referred to as KGA for kidney-type glutaminase) is found in the cytosol allowing for high levels of glutamate to be formed in this location. The glutamate can be used in a series of transamination reactions ultimately contributing to the synthesis of proline, alanine, and aspartate. In addition, glutmate is used to make glutathione which serves a potent anti-oxidant function in proliferating and cancer cells. Within the mitochondria the glutamate can be converted to 2-oxoglutarate (α-ketoglutarate) via transamination reactions or through the action of glutamate dehydrogenase (encoded by the GLUD1 gene). Within the cytosol the glutamate is also converted to 2-oxoglutarate via transamination reactions. In cancer cells the cytosolic IDH1 encoded enzyme can convert 2-oxoglutarate to isocitrate which then contributes to the cytoplasmic pool of citrate. In the mitochindria the 2-oxoglutarate can enter the TCA cycle where it can be oxidized to malate and oxaloacetic acid (OAA). The malate can be transported to the cytosol and converetd to pyruvate through the action of malic enzyme (encoded by the ME1 gene). This latter reaction has the benefit of contributing to the NADPH pool which cancer cells can use for reductive biosynthetic reactions such as fatty acid and nucleotide biosynthesis. The OAA generated from glutamine can be transaminated to aspartate and transported to the cytosol where its can be used in the process of nucleotide biosynthesis. In many cancer cells expression of the IDH2 gene is enhanced and, like the cytosolic IDH1 encoded enzyme, can carry out the reverse TCA cycle reaction, converting 2-oxoglutarate to isocitrate. It should be pointed out that in this context these are normal activities of the wild-type IDH1 and IDH2 encoded enzymes. Mutant forms of IDH1 and IDH2 are also found in cancer cells but catalyze distinct reactions as a result of mutations. Many cancer cells also activate a reductive oxidation process that allows isocitrate to be converted to citrate. The citrate can be transported into the cytosol and hydrolyzed to acetyl-CoA and OAA. The acetyl-CoA can serve as a precursor for the synthesis of fatty acids promoting the ability of cancer cells to generate membranes for rapid cell division. The glutamine and the asparate that result from the transamination of OAA, as well as by the routes utilizing glutamate, both serve in the processes of nucleotide biosynthesis. In addition to the carbons of glutamine, the nitrogen is critical to the formation of carbamoyl phosphate which is the first step in pyrimidine nucleotide biosynthesis. Glutamine can also be effluxed from cells, through the action of the LAT1 antiporter, in exchange for leucine. TRhe increased intracellular levels of leucine can activate the mTOR complex 1 (mTORC1) which prevents apoptosis. Efflux of glutamine can also occur through the action of the xCT antiporter allowing cystine uptake (not shown but discussed in text). The cystine is reduced to cysteine which contributes to glutathione synthesis as well as overall protein synthesis.


The release of ammonia from glutamine, within the proximal tubule, represents a major mechanism linking metabolism to the role of the kidneys in the maintenance of acid-base homeostasis. In rapidly dividing cells such as small intestinal enterocytes, lymphocytes, and especially cancer cells, glutamine is rapidly consumed and used for both energy generation and as a source of carbon and nitrogen for the synthesis of biomass. The high level of glutamine that is maintained in the plasma provides a readily accessible source of carbon and nitrogen that can support the metabolic demands of cancer cells. In the small intestine and in the kidney the deamination of glutamine to 2-oxoglutarate allows the carbon skeleton to be diverted into the TCA cycle and ultimately diverted, via oxaloacetic acid, to the gluconeogenesis pathway for the de novo synthesis of endogenous glucose. The removal of the nitrogens from glutamine within the kidney proximal tubule epithelial cells allows the kidney to release excess acid in the from of ammonium ion (NH4+).

Glutamine is transported into cells through the actions on one of the several glutamine transporters such as SLC1A5 (also known as ASCT2), SLC38A1, SLC38A3, SLC38A5, and SLC38A7. Intracellular glutamine can be effluxed from cells for other amino acids through the action of several antiporter-type transporters such as the L-type amino acid transporter that is a heterodimer of the SLC3A2 and SLC7A5 encoded proteins forming what is commonly identified as LAT1. Glutamate, that is formed via glutaminase action on glutamine, can be effluxed from cells, in exchage for cystine, through the action of the antiporter commonly identified as xCT. The xCT rtansporter is a heterodimer of the SLC3A2 and SCL7A11 encoded proteins. Within cells cytine is rapidly reduced to two molecules of the amino acid cysteine. This represents a major link between glutamine and the sulfur necessary for biomass synthesis, particularly in rapidly dividine tumor cells. Even in nutrient deprived states cancer cells can gain access to nutrients, such as proteins, in the blood through the upregulation of macropinocytosis. The increased protein uptake allows for their degradation and release of amino acids including glutamine. Some RAS-transformed cancer cells have been shown to acquire needed glutamine through autophagic degradation of intracellular proteins.

In order to support energy generation the glutamine that is transported into cells, such as rapidly proliferating cells and cancer cells, is deaminated through the action of glutaminase and the resulting glutamate is further deaminated through the actions of aminotransferases or through the action of glutamate dehydrogenase. The resulting 2-oxoglutarate is fed into the TCA cycle and oxidized generating the reduced electron carriers, NADH and FADH2 which fuel oxidative phosphorylation and the synthesis of ATP. In some tumor cells, a portion of glutamine that is converted to oxaloacetic acid via the TCA cycle, is converted to pyruvate through the activity of malic enzymes. Humans express three malic enzymes, one cytoplasmic that requires NADP+ and two mitochondrial enzymes, one that requires NADP+ and one that requires NAD+. The cytoplasmic enzyme is called malic enzyme 1 and is encoded by the ME1 gene. The NAD+-dependent mitochondrial enzyme is called malic enzyme 2 and is encoded by the ME2. The NADP+-dependent mitochondrial enzyme is called malic enzyme 3 and is encoded by the ME3 gene. The significance of the NADP+ requiring malic enzymes is that in addition to pyruvate, NADPH is also generated. The NADPH can then be used in biomass producing reductive biosynthetic reactions such as fatty synthesis and phospholipid synthesis.

Glutamine is also critical in the biosynthesis of nucleotides for RNA and DNA synthesis as is required in rapidly proliferating cells and cancer cells. Glutamine can serve as a precursor for aspartate through the concerted actions of glutaminase, yielding glutamate, followed by transfer of the nitrogen from glutamate of oxaloacetic acid forming aspartate. The oxaloacetic acid can also be derived from glutamine, thus indicating this pivotal role of glutamine in overall nucleotide homeostasis. The asparate that can be derived from glutamine is required as a source of carbon for both purine and pyrimidine nucleotide synthesis. In addition, glutamine serves as the amino donor in the formation of carbamoyl phosphate through the actions of the tri-functional enzyme carbamoyl-phosphate synthetase 2, aspartate transcarbamoylase, and dihydroorotase. This enzyme is encoded by the CAD gene. The resulting carbamoyl phosphate is the initiating precursor for the synthesis of the pyrimidine nucleotides. Thus, it should be obvious that the carbons and the nitrogen of glutamine are critical components of overall nucleotide homeostasis.

In cancer cells, the expression of enzymes involved in glutamine metabolism varies widely and is related to factors such as tissue of origin and the overall genotype of the specific cancer. As indicated in the previous section, humans express two gene encoding glutaminase enzymes. The GLS gene is more widely expressed and is the glutaminse encoding gene believed to be of more significance in cancer cell metabolism. Sirtuins, which are NAD+-dependent deacetylases, paly a role in the regulation of expression of numerous genes. In cancer cells the sirtuin encoded by the SIRT3 gene has been shown to deacetylate the GLS2 gene resulting in increased expression under conditions of caloric restriction. The glutaminase C isoform (GAC) is more active than the kidney-type glutaminase (KGA) and the levels of GAC have been found to be increased in numerous cancers. Glutamate dehydrogenase activity is also altered in cancer cells. Glutamate dehydrogenase is allosterically activated by leucine, the levels of which will be higher in cancer cells due to increased activity of various amino acid transporters. In the direction of glutamate deamination, glutamate dehydrogenase is activated by ADP. Therefore, low cellular energy states will lead to induction of 2-oxoglutarate production via the glutamate dehydrogenase reaction allowing for increased ATP synthesis from the TCA cycle-derived NADH and FADH2.

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Aspartate and Asparagine

Aspartate can be formed in a transamination reaction or via the deamination of asparagine. The transamination reaction is catalyzed by aspartate transaminase, AST. This reaction uses the α-keto acid oxaloacetate as the amino acceptor and glutamate as the primary amino group donor. Humans express two AST enzymes, one that is localized in the cytosol and the other is localized to the mitochondria. The cytosolic AST enzyme is encoded by the glutamate oxaloacetic transaminase 1 gene (GOT1). The GOT1 gene is located on chromosome 10q24.2 and is composed of 9 exons that encode a 413 amino acid protein. The mitochondrial AST enzyme is encoded by the GOT2 gene which is located on chromosome 16q21 and is composed of 10 exons that generate two alternatively spliced mRNAs, both of which encode different isoforms.

Reaction catalyzed by aspartate transaminase (AST)

Reaction catalyzed by aspartate transaminase (AST)


Aspartate, formed by deamination of asparagine, is catalyzed by asparaginase. Humans express at least three enzymes that can catalyze the deamination of asparagine to aspartate. However, the true primary physiologic substrates for these enzymes may not be asparagine. One enzyme was originally identified as a lysophospholipase due to its ability to hydrolyze lysophospholipids in addition to it being subsequently shown to harbor asparaginase activity. The enzyme is encoded by the asparaginase gene (ASPG) which is located on chromosome 14q32.33 and is composed of 20 exons that encode a 573 amino acid protein. A second human enzyme with asparaginase activity is the enzyme N-aspartyl-β-glucosaminidase (also called aspartylglucosaminidase) which is encoded by the AGA gene. The AGA encoded protein has as its primary function the hydrolysis of carbohydrates linked to asparagine residues in glycoproteins. Defects in the AGA gene result in aspartylglucoasminuria which is a lysosomal storage disease. The third human enzyme with asparaginase activity is called asparaginase like 1 (encoded by the ASRGL1 gene). In addition to being able to hydrolyze asparagine to aspartate, the ASRGL1 encoded enzyme hydrolyzes isoaspartyl peptide linkages. The ASRGL1 gene is located on chromosome 11q12.3 and is composed of 10 exons that generate two alternatively spliced mRNAs that express the same 308 amino acid protein. Asparaginases from bacteria have significant clinical utility as they are used in the treatment of several forms of hematopoietic malignancies that rely on extracellular asparagine for their rapid growth.

Reaction catalyzed by asparaginase

Reaction catalyzed by asparaginase


Asparagine is synthesized from aspartate via an amidotransferase reaction catalyzed by asparagine synthetase. Asparagine synthetase is encoded by the ASNS gene which is located on chromosome 7q21.3 and is composed of 15 exons that generate several alternatively spliced mRNAs.

Reaction catalyzed by asparagine synthetase

Reaction catalyzed by asparagine synthetase


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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 two 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)

Reaction catalyzed by alanine transaminase (ALT)


The glucose-alanine cycle

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, Methionine, and S-Adenosylmethionine

The sulfur for cysteine synthesis comes from the essential amino acid methionine through a series of interelated reaction pathways. Initially a condensation of ATP and methionine, catalyzed by methionine adenosyltransferase (MAT), yields S-adenosylmethionine (SAM or AdoMet). 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. MAT is also called S-adenosylmethionine synthetase. There are three MAT genes in humans identified as MAT1A, MAT2A and MAT2B. The MAT enzymes encoded by the MAT1A gene function as either a homotetramer identified as MAT I (called the alpha form), or as a homodimer identifed as MAT III (called the beta form). The MAT I and MAT III isoforms are only expressed in the liver. The MAT enzyme encoded by the MAT2A gene is identified as MAT II (called the gamma form). The MAT II enzyme is expressed in several non-hepatic tissues. The MAT1A gene is located on chromosome 10q22 and is composed of 10 exons that encode a protein of 395 amino acids. The MAT2A gene is located on chromosome 2p11.2 and is composed of 9 exons that encode a protein of 395 amino acids. The MAT2B gene is located on chromosome 5q34 and is composed of 8 exons that generate two alternatively spliced mRNAs encoding the MAT 2 beta isoform 1 (334 amino acids) and the MAT 2 beta isoform 2 (323 amino acids) enzymes.

Synthesis of S-adenosylmethionine (SAM)

Biosynthesis of S-adenosylmethionine, SAM

SAM serves as a precurosor for several methyl transfer reactions where one the most physiologically significant reaction is 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. Transmethylation reactions employing SAM are extremely important, but in the context of cysteine biosynthesis, the role of S-adenosylmethionine in transmethylation is secondary to the production of homocysteine (essentially a by-product of transmethylase activity).

S-adenosylhomocysteine is then cleaved by adenosylhomocyteinase (also called S-adenosylhomocysteine hydrolase) to yield homocysteine and adenosine. Adenosylhomocysteinase is encoded by the AHCY gene located on chromosome 20q11.22 and is composed of 17 exons that generate two alternatively spliced mRNAs encoding adenosylhomocysteinase isoform 1 (432 amino acids) and adenosylhomocysteinase isoform 2 (404 amino acids).

Homocysteine can be converted back to methionine by methionine synthase (also called homocysteine methyltransferase). This reaction was also discussed in the context of vitamin B12-requiring enzymes in the Vitamins page. The methionine synthase reaction represents the clinically most significant of only two vitamin B12-requiring enzymes in human cells. Methionine synthase, in addition to B12, requires the folate-derived vitamin co-factor, N5-methyltetrahydrofolate (N5-methyl THF). Methionine synthase is encoded by the MTR gene (5-methyltetrahydrofolate-homocysteine methyltransferase) located on chromosome 1q43 and is composed of 34 exons that generate three alternatively spliced mRNAs.

Deficiency in B12, or folate, or defects in the MTR gene all will result in the development of megaloblastic anemias. The anemia develops due to the trapping of folate in the reduced form (N5-methyl-THF) which results in depletion of the active folate pool. The active folate pool is required for purine and thymine nucleotide biosynthesis needed for DNA synthesis. Bone marrow erythroblasts begin to enlarge in preparation for cell division but, due to loss of nucleotide synthesis, they remain as megaloblasts.

In cysteine synthesis, homocysteine condenses with serine to produce cystathionine which is catalyzed by cystathionine β-synthase (cystathionine beta synthase: CBS). The details of CBS are discussed below. Cystathionine is subsequently cleaved by cystathionine γ-lyase (also called cystathionase; also discussed in more detail below) 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 sulfur from the essential amino acid, methionine, is required for the synthesis of cysteine. The synthesis of cysteine represents an extremely important and clinically relevant biochemical pathway. Several vitamins are required for this metabolic pathway to proceed emphasizing the nutritional impact. Folate, pyridoxal phosphate (PLP, B6), and B12 are all necessary for cysteine synthesis. The enzyme methionine synthase requires both folate and B12 for activity. Deficiency in either of these vitamins contributes to homocysteinemia and also to the development of macrocytic (megaloblastic) anemias. Cystathionine β-synthase is a PLP requiring enzyme demonstrating why B6 deficiency is also associated with the development of homocysteinemia.

In addition to methionine synthase, two other key enzymes of the methionine to cysteine biosynthesis pathway are cystathionine β-synthase (cystathionine beta synthase: CBS) and cystathionine γ-lyase (cystathionase). Both of these enzymes require pyridoxal phosphate (PLP: derived from vitamin B6) as a cofactor, and both are under regulatory control. Cystathionine γ-lyase is also negatively regulated by cysteine-mediated allosteric control. In addition, cysteine inhibits the expression of the cystathionine β-synthase gene. Cystathionine β-synthase is encoded by the CBS gene located on chromosome 21q22.3 which is composed of 24 exons which generate at least three alternatively spliced mRNAs. Cystathionine γ-lyase is encoded by the CTH gene located on chromosome 1p31.1 and is composed of 13 exons that undergo alternative splicing generating three isoform encoding mRNAs. Genetic defects are known for both the CBS gene (see next section) and the cystathionine γ-lyase gene. Missing or impaired cystathionine γ-lyase leads to excretion of cystathionine in the urine but does not have any other untoward effects. Rare cases are known in which cystathionine γ-lyase is defective and operates at a low level. This genetic disease leads to methioninuria with no other consequences.

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Homocysteinemia / Homocystinuria

Homocysteinemias (homocystinemias) 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 and homocystine in the blood, where the elevated urine output of the metabolite is referred to as homocysteinurina or homocystinuria. Homocystine is a disulfide-bonded homodimer of two homocysteines. This is similar to the formation of cystine from two cysteines as diagrammed in the Figure below. In addition to homocysteinuria, patients excrete elevated levels of methionine and metabolites of homocysteine. The most common causes of homocystinuria (classic 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 (ectopia lentis), osteoporosis, lengthening and thinning of the long bones, and an increased risk of abnormal blood clotting (thromboembolism). The nature of the lens dislocation (subluxation), evident in homocysteinemia patients, can serve as a differential diagnostic tool. Lens dislocation is also found in patients suffering from Marfan syndrome, which is a connective tissue disorder caused by defects in the fibrillin gene (FBN1). In homocystinuria the lens subluxation occurs in a downward and inward direction, whereas in Marfan syndrome the lens subluxation occurs upward and outward. Some instances of genetic homocysteinemia respond favorably to pyridoxine therapy suggesting, that in these cases the defect in CBS is a decreased affinity for the cofactor, pyridoxal phosphate.

Homocysteinemia 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 cystathionine γ-lyase and the homocysteinemia 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 homocysteinemia presenting with reduced levels of plasma methionine. The enzyme methylmalonyl-CoA mutase also requires B12 and so a homocysteinuria 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 homocysteinemia allows for a differential diagnosis of the nutritional (non-genetic) cause.

Another related disorder, referred to as hyperhomocysteinemia, is most often associated with manifestation of symptoms much later in life. The characteristic pathology of hyperhomocysteinemia is coronary artery disease (CAD) and an increased risk for deep vein thromboses, DVT. In addition there is an increased risk for mild cognitive impairment and dementia. Evidence suggests a link between hyperhomocysteinemia and Alzheimer disease. Similar to the dietary causes of homocystinuria, hyperhomocysteinemia can result from deficiencies in vitamin B6, vitamin B12, and folate. An inherited form of hyperhomocysteinemia results from mutations in the methylene tetrahydrofolate reductase (MTHFR) gene. The most common mutation in this gene that results in hyperhomocysteinemia is a C to T change at nucleotide position 677 (C677T). Mutations in the methionine synthase (MTR) gene are also associated with inherited hyperhomocysteinemia. In the case of the MTR gene the most common mutation is a change of an A for a G at nucleotide position 2756 (A2756G).

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.

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Functions of S-Adenosylmethionine (SAM or AdoMet)

S-adenosylmethione (abbreviated SAM or AdoMet), synthesized as described in the previous section, is utilized in a wide array of methyl transfer reactions involving nucleic acids, lipids, proteins, neurotransmitters, and small molecules. During the course of the transfer of the methyl group from SAM to an appropriate acceptor, S-adenosylhomocysteine (abbreviated SAH or AdoHcy) is generated. The resultant SAH is catabolized to adenosine and homocysteine through the action of adenosylhomocysteinase (also called S-adenosylhomocysteine hydrolase) which is encoded by the AHCY gene. The AHCY gene is located on chromosome 20q11.22 and is composed of 17 exons that generate five alternatively spliced mRNAs encoding three distinct proteins isoforms of 432 amino acids (isoform 1), 404 amino acids (isoform 2), and 434 amino acids (isoform 3). Mutations in the AHCY gene are one of the causes of hypermethioninemia.

The role of SAM in nucleotide and protein methylation contributes to several epigenetic processes and points to the role of nutritional components, in this case methionine, in the control of gene expression. The DNA methyltransferases encoded by the DNMT1 and DNMT3 genes utilize SAM in the methylation of cytidine residues found in CpG dinucleotides in DNA. The RNA methyltransferase encoded by the RNMT gene utilizes SAM as a substrate for the N7-methylation of the guanine residue present in the mRNA 5'-cap structure. The RNA methyltransferases encoded by the METTL3 and METTL4 genes incorporate methyl groups into adenine and cytidine residues in mRNA molecules utilizing SAM as the methyl donor. These latter mRNA methylation events represent important posttranscriptional mechanisms for the regulation of gene expression.

Numerous SAM-dependent methyltransferases are involved in the methylation of histone proteins which represents another mode of epigenetic regulation of gene expression. These methyltransferases all utilize SAM as the methyl donor and incorporate the methyl group onto lysine residues, arginine residues, and histidine residues in proteins. Several histone lysine and histone arginine N-methyltransferases have been identified including all of the HMT (histone lysine methyltransferase) gene family enzymes and the PRMT (protein arginine methyltransferase) gene family enzymes. Humans express 34 genes that encode protein lysine methyltransferases and nine genes that encode protein arginine methyltransferases. Many of the proteins that are targets for enzymes of the PRMT family are involved in the processes of signal transduction or regulation of transcription. In addition to members of the histone protein family and transcription factor family, numerous other proteins are subject to either lysine or arginine methylation. Additional enzymes that utilize SAM as a methyl donor are involved in the modification of proteins that serve functions in diverse processes such as protein damage repair, protein stability, and protein function. The enzyme identified as protein-L-isoaspartate (D-aspartate) O-methyltransferase (encoded by the PCMT1 gene) is required for the repair of deamidated aspartate and asparagine residues in proteins. and it utilizes SAM in these reactions. The function of the enzyme, isoprenylcysteine carboxyl methyltransferase (encoded by the ICMT gene) is to methylate the cysteine residues in the C-terminus of proteins following their prenylation. Humans express three genes that catalyze the SAM-dependent cysteine methylation reaction on prenylated proteins with the ICMT gene being the most abundantly expressed. The SAM-dependent protein methyltransferase encoded by the LCMT1 gene (leucine carboxyl methyltransferase 1) catalyzes the methylation of a C-terminal leucine residue in the Ser/Thr phosphatase identified as PP2A, a modification required for its proper function. The synthesis of the diphthamide residue found on His715 in human translation elongation factor eEF2 requires a methylation step involving SAM as the methyl donor.

Numerous reaction pathways involved in the synthesis of small molecules, as well as the synthesis and catabolism of neurotransitters involve enzymes that are SAM-dependent methyltransferases. These methyltransferases are classified as either N-methyltransferases or O-methyltransferases dependent on whether the acceptor of the methyl group is nitrogen or an oxygen, respectively. The synthesis of epinephrine from norepinephrine requires the SAM-dependent enzyme phenylethanolamine N-methyltransferase encoded by the PNMT gene. The conversion of serotonin to melatonin requires the enzyme acetylserotonin O-methyltransferase encoded by the ASMT gene. Creatine synthesis also requires SAM-dependent methylation in a reaction catalyzed by guanidinoacetate N-methyltransferase (encoded by the GAMT gene). The catabolism of the catecholamines, epinephrine, norepinephrine, and dopamine involves the SAM-dependent enzyme catechol O-methyltransferase (encoded by the COMT gene). The catabolism of histamine occurs either through oxidation or methylation. The methylation pathway involves the SAM-dependent enzyme histamine N-methyltransferase which is encoded by the HNMT gene.

Lipid metabolism is another important process that involves SAM-dependent methylation. The conversion of phosphatidylethanolamine (PE) to phosphatidylcholine (PC) requires the enzyme phosphatidylethanolamine N-methyltransferase (encoded by the PEMT gene) which carries out three successive SAM-dependent methylation reactions. This reaction is a critically important reaction of membrane lipid homeostasis. Lipid synthesis and remodeling is important in all cell membranes but is particularly critical in the homeostasis of the myelin sheath protecting neurons in the nervous system. Reduced capacity to carry out the methionine synthase reaction, due to nutritional or disease mediated deficiency of vitamin B12, results in reduced SAM production. In turn, reduced levels of SAM in the brain are a contributor to the neural degeneration (i.e. depression, peripheral neuropathy) seen in chronic B12 deficiency.

The metabolism and detoxification of numerous xenobiotic compounds is also known to require SAM-dependent methyltransferase family enzymes. The anti-cancer drugs of the thiopurine class, such as 6-mercaptopurine, are metabolized by the enzyme thiopurine S-methyltransferase which is encoded by the TPMT gene.

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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 daily requirement for phenylalanine is for the production of tyrosine; if the diet is rich in tyrosine itself, the requirements for phenylalanine can be reduced by about 50%.

Phenylalanine hydroxylase (more specifically phenylalanine 4-hydroxylase) is a mixed-function monooxygenase that is one of three enzymes belonging to the biopterin-dependent aromatic amino acid hydroxylase (AAAH) family. Phenylalanine hydroxylase is encoded by the PAH gene located on chromosome 12q22–q24.2 and is composed of 13 exons that encode a protein of 452 amino acids. The required biopterin is in the form of tetrahydrobiopterin (often designated BH4 or H4B). The other two enzymes in this family are tyrosine hydroxylase and tryptophan hydroxylase. Phenylalanine hydroxylase transfers one atom from molecular oxygen (O2) into the hydroxyl of tyrosine and the other hydroxylates tetrahydrobiopterin forming an intermediate identifed as pterin 4α-carbinolamine (also called 4α-hydroxypterin or 4α-hydroxydihydrobiopterin). The tetrahydrobiopterin can be regenerated in a salvage pathway that involves the enzymes pterin 4α-carbinolamine dehydratase 1 and dihydropteridine reductase. The pterin 4α-carbinolamine dehydratase 1 enzyme is encoded by the PCBD1 gene. The PCBD1 gene is located on chromosome 10q22.1 and is composed of 6 exons that generate three alternatively spliced mRNA, each of which encode a distinct protein isoform. The product of the PCBD1 encoded enzyme, acting on pterin 4α-carbinolamine, is the quinoid molecule identified as dihydrobiopterin. Dihydrobiopterin is then converted to tetrahydrobiopterin by the NADH-dependent enzyme commonly referred to as dihydropteridine reductase. Human dihydropteridine reductase is produced by the quinoid dihydropteridine reductase gene (symbol: QDPR) located on chromosome 4p15.31 and which is composed of 7 exons that encode a protein of 244 amino acids.

Reaction catalyzed by phenylalanine hydroxylase in the synthesis of tyrosine

Biosynthesis of tyrosine from phenylalanine. Phenylalanine serves as the precursor for tyrosine. The conversion of phenylalanine to tyrosine can also be considered the first step in the catabolism of phenylalanine as this conversion reaction is necessary to catabolize phenylalanine. PCBD1 is pterin 4α-carbinolamine dehydratase.

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, however, the precise mechanism by which this enzyme deficiency leads to the severe neural degeneration is not fully understood. One theory suggests that the accumulation of phenylalanine interferes with the transport of tyrosine into the brain. A reduction in brain tyrosine levels would then result in reduced synthesis of the neurotransmitters dopamine and norepinephrine. Another theory suggests that the mental retardation is caused by the accumulation of phenylalanine in the brain, which becomes a major donor of amino groups in aminotransferase activity and depletes neural tissue of 2-oxoglutarate (α-ketoglutarate). This absence of 2-oxoglutarate in the brain shuts down the TCA cycle and the associated production of aerobic energy. Although both theories are plausible no direct evidence for either has been demonstrated.

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, mutations in the PCBD1 gene or the QDPR gene can manifest with hyperphenylalaninemia. Mutations in the PCBD1 gene and the QDPR gene are causes of a family of disorders termed tetrahydrobiopterin deficiency syndromes. At least nine different mutations in the PCBD1 gene have been found to be associated with inherited tetrahydrobiopterin deficiency. However, the mutations in PCBD1 are not associated with significant pathology. It is thought that other enzymes can compensate for the reduced activity of PCBD1. At least 30 different mutations in the QDPR gene are associated with inherited tetrahydrobiopterin deficiencies and these mutations account for approximately 30% of all the cases of these related disorders. Because the function of the QDPR gene


Ornithine and Proline Biosynthesis

Glutamate is the precursor of both proline and ornithine with Δ1-pyrroline-5-carboxylate serving as a branch point intermediate leading to one or the other of these two 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. The synthesis of ornithine from glutamate occurs only in the intestines. The conversion of glutamate to Δ1-pyrroline-5-carboxylate is catalyzed by a bi-functional enzyme that is a member of the aldehyde dehydrogenase family. This enzyme, aldehyde dehydrogenase 18 family, member A1 (encoded by the ALDH18A1 gene), possess both γ-glutamyl kinase activity and an NADPH-dependent γ-glutamylphosphate reductase activity. The ALDH18A1 encoded enzyme is also known as delta-1-pyrroline-5-carboxylate synthase (P5CS). The Δ1-pyrroline-5-carboxylate intermediate in this pathway can exist as the open-chain tautomeric compound glutamate γ-semialdehyde which can be transaminated to ornithine via the action of ornithine aminotransferase. Ornithine aminotransferase utilizes glutamate as the amino donor and releases 2-oxoglutarate (α-ketoglutarate). The ALDH18A1 gene is located on chromosome 10q24.3 and is composed of 18 exons that generate two alternatively spliced mRNAs encoding isoform 1 (795 amino acids) and isoform 2 (793 amino acids) versions of the enzyme. Mutations in the ALDH18A1 gene result is a disorder charaterized by hyperammonemia, hypoornithinemia, hypocitrullinemia, hypoargininemia and hypoprolinemia. This disorder is also associated with CNS degeneration, connective tissue disruption, and cataract formation. Ornithine aminotransferase is encoded by the OAT gene located on chromsome 10q26 and is composed of 12 exons that generate two alternatively spliced mRNAs.

The fate of Δ1-pyrroline-5-carboxylate (and its open-chain tautomer, glutamate γ-semialdehyde) depends on prevailing cellular conditions. Ornithine production occurs from the semialdehyde compound via a simple glutamate-dependent transamination, producing ornithine. When arginine concentrations become elevated, the ornithine contributed from the urea cycle plus that from Δ1-pyrroline-5-carboxylate inhibit the aminotransferase reaction, with accumulation of Δ1-pyrroline-5-carboxylate as a result. The accumulating Δ1-pyrroline-5-carboxylate can then be reduced to proline by the NAD(P)H-dependent enzyme pyrroline-5-carboxylate reductase 1 (PYCR1). The PYCR1 gene is located on chromosome 17q25.3 and is composed of 9 exons that generate five alternatively spliced mRNAs that encode four different isoforms of the enzyme.

Ornithine and proline synthesis

Synthesis of ornithine and proline. Glutamate serves as the precursor for the synthesis of both ornithine and proline which are derived from the Δ1-pyrroline-5-carboxylate intermediate in the pathway. Formation of Δ1-pyrroline-5-carboxylate occurs via the action of the bi-functional enzyme, aldehyde dehydrogenase 18 family, member A1 (also known as delta-1-pyrroline-5-carboxylate synthase). The transamination of the tautomeric form of Δ1-pyrroline-5-carboxylate (glutamate γ-semialdehyde) results in the generation of ornithine. The reduction of Δ1-pyrroline-5-carboxylate to proline occurs via the action of pyrroline-5-carboxylate reductase 1 (PYCR1). PRODH is proline dehydrogenase, the first enzyme in the pathway of proline catabolism which converts proline back to Δ1-pyrroline-5-carboxylate.

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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 (3-phosphoglycerate dehydrogenase) converts 3-phosphoglycerate into a keto acid, 3-phosphohydroxypyruvate, suitable for subsequent transamination. The aminotransferase, phosphoserine aminotransferase 1, utilizing glutamate as a donor, produces 3-phosphoserine, which is converted to serine by phosphoserine phosphatase. The phosphoserine phosphatase gene (symbol: PSPH) is located on chromsome 7p11.2 which is in a region of chromosome 7 that is deleted in Williams-Beuren syndrome, WBS (also called Williams syndrome, WS). WBS is associated with multiple organ system involvement typically showing supravalvular aortic stenosis (SVAS), mental retardation, and distinctive facial features. Phosphoglycerate dehydrogenase is encoded by the PHGDH gene which is located on chromosome 1p12 and is composed of 17 exons that generate a protein of 533 amino acids. Phosphoserine aminotransferase 1 is encode by the PSAT1 gene located on chromosome 9q21.2 and is composed of 9 exons that generate two alternatively spliced mRNAs encoding isoform 1 (370 amino acids; also called PSAT1β beta) and isoform 2 (324 amino acids; also called PSAT1α alpha). The PSPH gene is composed of 12 exons that encode a 225 amino acid protein.

As indicated below, serine can be derived from glycine (and visa versa) by a single step reaction that involves serine hydroxymethyltransferase (SHMT; also called glycine hydroxymethyltransferase) and tetrahydrofolate (THF). Indeed, the interconversion of serine and glycine via the involvement of THF represents the major pathway for the generation of N5,N10-methylene-THF which of a member of the active pool of folate derivatives. N5,N10-methylene-THF is required for purine nucleotide and thymine nucleotide biosynthesis.

Humans express two serine hydroxymethyltransferase genes, one is a cytosolic enzyme while the other is located in the mitochondria. The cytosolic enzyme is derived from the SHMT1 gene located on chromosome 17p11.2 which is composed of 13 exons that generate three alternatively spliced mRNAs. The mitochondrial enzyme is derived from the SHMT2 gene located on chromosome 12q12–q14 which is composed of 14 exons that generate five altrernatively spliced mRNAs that encode three distinct isoforms of the enzyme. The location of the SMHT1 gene (17p11.2) resides within the 3.7 Mb region of chromosome 17 that is deleted in Smith-Magenis syndrome, SMS, a disorder associated with behavioral problems, psychomotor retardation, growth delay, speech delay, brachycephaly, midface hypoplasia, and a hoarse voice. One of the major functions of the SHMT2 encoded enzyme is in mitochondrial thymidylate synthesis pathway via its role in glycine and tetrahydrofolate metabolism. Mitochondrial thymidylate synthesis is required to prevent uracil accumulation in mitochondrial DNA (mtDNA).

Synthesis of serine

Reactions of serine biosynthesis. Serine can be derived from the glycolytic intermediate, 3-phosphoglycerate, in a three-step reaciton pathway. The first reaction is catalyzed by phosphoglycerate dehydrogenase (PHGDH). The second reaction is a simple transamination catalyzed by phosphoserine aminotransferase 1 (PSAT1) which utilizes glutamate as the amino donor and releases 2-oxoglutarate (α-ketoglutarate). The last step in the reaction pathway is catalyzed by phosphoserine phosphatase (PSPH).


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Glycine Biosynthesis

The main pathway to glycine is a one-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. As pointed out in the previous section, there are mitochondrial and cytosolic versions of serine hydroxymethyltransferase. The cytosolic enzyme is encoded by the SHMT1 gene on chromosome 17 and the mitochondrial enzyme is encoded by the SHMT2 gene on chromosome 12. The major glycine biosynthetic enzyme is the cytosolic form of SHMT.

Reaction catalyzed by serine hydroxymethyltransferase

Reaction catalyzed by serine hydroxymethyltransferase


Glycine as a Neurotransmitter

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 (pentameric) complex consisting of a complex of either three or four α-subunits and one β-subunit. There are four different α-subunit genes (GLRA1, GLRA2, GLRA3, GLRA4) and a single β-subunit gene (GLRB) in the human genome. The GlyR is a ligand-gated ionotropic receptor that is a chloride channel. In addition to glycine, the 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) type glutamate receptors.

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Amino Acid Catabolism

Glutamine/Glutamate and Asparagine/Aspartate Catabolism

Glutaminase is an important kidney tubule enzyme involved in the process of renal ammoniagenesis. Glutaminase converts glutamine (predominantly derived from the liver but also from many other tissues) to glutamate and NH4+, with the NH4+ being excreted in the urine. Glutaminase activity is present in many other tissues in addition to the kidney, such as the liver, small intestine, and neurons where its role is nearly as significant as it is within the kidney tubule. The glutamate produced from glutamine is converted to 2-oxoglutarate (α-ketoglutarate) via the action of glutamate dehydrogenase (making glutamine a glucogenic amino acid) and yielding another mole of NH4+.

There are two distinct glutaminase genes in humans identified as GLS (encoding the GLS1 enzyme) and GLS2 (encoding the GLS2 enzyme). The GLS gene is located on chromosome 2q32–q34 and is composed of 24 exons that undergo alternative splicing to yield several mRNAs generating two isoforms of the enzyme. These two GLS-derived isoforms are often referred to as glutaminase C (GAC) and kidney-type glutaminase (KGA) but are collectively the glutaminase 1 (GLS1) enzymes. The GLS encoded isoforms of glutaminase are primarily expressed in the kidneys. GLS encoded kidney-type glutaminase is a protein of 669 amino acids and GLS encoded glutaminase C is a protein of 598 amnio acids. The GLS2 gene encoded glutaminase was originally thought to be liver specific but is in fact expressed in numerous tissues and is important in the glutamate-glutamine cycle in the brain. The GLS2 encoded glutaminase was originally characterized as dependent on inorganic phosphate (Pi) for activity and is, therefore, also referred to as phosphate-activated glutaminase, PAG. However, both the GLS gene encoded enzymes and the GLS2 encoded enzymes require phosphate for activity with GLS enzymes being more sensitive. The GLS2 gene is located on chromosome 12q13.3 and is composed of 19 exons that undergo alternative splicing to yield several mRNAs that encode four different isoforms of the enzyme. The GLS encoded enzymes are inhibited by glutamate but the GLS2 encoded enzyme is not. The GLS2 encoded enzyme is activated by ammonia but the GLS encoded enzymes are not.

Reaction catalyzed by glutaminase

Reaction catalyzed by glutaminase

Asparaginase (see above) is also widely distributed within the body, where it converts asparagine into ammonia and aspartate. Aspartate can serve as an amino donor in transamination reacions yielding 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 2-oxoglutarate (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) that delivers waste nitrogen from skeletal muscle to the liver where it can be incorporated into urea. The alanine catabolic pathway involves a simple aminotransferase reaction that directly produces pyruvate. The transamination is carried out by alanine transaminase, ALT (also called alanine aminotranserase). Generally, the pyruvate produced from alanine has two distinct fates that are controlled by the energy demands of the liver and the metabolic needs of the organism as a whole. When energy needs are high in hepatocytes the pyruvate is oxidized by the PDH complex (PDHc) to acetyl-CoA and diverted into the TCA cycle. Altrenatively, during the fasted state when blood glucose levels are low, the pyruvate is diverted into the gluconeogenic pathway so that the liver can release glucose to the blood. 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 ultimately hydrolyzed to urea and ornithine by arginase.

Ornithine, in excess of urea cycle needs, is transaminated to form glutamate γ-semialdehyde which is in equilibrium with its tautomeric compound, Δ1-pyrroline-5-carboxylate. Catabolism of Δ1-pyrroline-5-carboxylate back to glutamate is catalyzed by aldehyde dehydrogenase 4 family, member A1 (also called delta-1-pyrroline-5-carboxylate dehydrogenase, P5CDH). The dehydrogenase is encoded by the ALDH4A1 gene located on chromosome 1p36 and is composed of 17 exons that generate three alternativley spliced mRNAs, two of which encode the same protein.

Proline catabolism involves a two-step process that is essentially a reversal of its synthesis process outlined above. Proline is first converted back to Δ1-pyrroline-5-carboxylate by the enzyme proline dehydrogenase (gene symbol: PRODH). The PRODH gene is located on chromosome 22q11.21 and is composed of 16 exons that generate two alternatively spliced mRNAs. As for the catabolism of ornithine, the resulting Δ1-pyrroline-5-carboxylate is converted to glutamate via the action of ALDH4A1.

The glutamate that results from ornithine and proline catabolism can then be converted to 2-oxoglutarate (α-ketoglutarate) in a transamination reaction. Therefore, ornithine and proline are both glucogenic. Since arginine is metabolized to urea and ornithine, and the resulting ornithine is a glucogenic precursor, arginine is also a glucogenic amino acid.

Catabolic pathways for arginine, ornithine, and proline

Catabolism of arginine, ornithine, and proline. The catabolism of ornithine and proline is essentially a reversal of their synthesis from glutamate. Proline is oxidized back to Δ1-pyrroline-5-carboxylate via the action of proline dehydrogenase (PRODH). Ornithine can be deaminated to Δ1-pyrroline-5-carboxylate via a reversal of the ornithine aminotransferase (OAT) reaction. The resulting Δ1-pyrroline-5-carboxylate is oxidized to glutamate via the action of aldehyde dehydrogenase 4 family, member A1, ALDH4A1 (also called delta-1-pyrroline-5-carboxylate dehydrogenase, P5CDH). Arginine catabolism/metabolism involves several pathways, with the major catabolic pathway being its role in the urea cycle. In some tissues arginine serves as the precursor for nitric oxide (NO) production via the action of nitric oxide synthases (NOS). The citrulline byproduct of the NOS reaction can feed back into arginine synthesis via the hepatic urea cycle enzymes argininosuccinate synthetase (ASS1) and argininosuccinate lyase (ASL). Arginine also serves as the precursor for creatine synthesis and, therefore, arginine can be excreted in the urine as creatine byproduct, creatinine. The cycling of citrulline back to arginine involves the urea cycle enzymes, argininosuccinate synthetase (ASS1) and argininosuccinate lyase (ASL).


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Serine Catabolism

The catabolism of serine in humans involves the conversion of serine to glycine and then glycine oxidation to CO2 and NH3, with the production of two equivalents of N5,N10-methyleneTHF, as 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 serine deamination activity of the enzyme appears to be lacking in humans even though the activity is involved in the catabolism of threonine in humans as described in the next section.

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Threonine Catabolism

There are at least three pathways for threonine catabolism that have been identified in yeasts, insects, and vertebrates including mammals. The principal threonine catabololizing pathway in humans involves a glycine-independent serine/threonine dehydratase (also known as serine dehydratase/threonine deaminase) yielding α-ketobutyrate (2-ketobutyrate) which is further catabolized to propionyl-CoA. Serine/threonine dehydratase is derived from the SDS gene which is located on chromosome 12q24.13 and is composed of 8 exons that encode a protein of 328 amino acids. 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 resulting propionyl-CoA is converted, via a mitochondrially-localized three reaction ATP-dependent pathway, to succinyl-CoA. The succinyl-CoA can then enter the TCA cycle for further oxidation. The enzymes required for this conversion are propionyl-CoA carboxylase, methylmalonyl-CoA epimerase, and methylmalonyl-CoA mutase, respectively. Propionyl-CoA carboxylase is called an ABC enzyme due to the requirements for ATP, Biotin, and CO2 for the reaction. This propionyl-CoA conversion pathway is also required for the metabolism of the amino acids valine, isoleucine, and methionine (see below), and odd-chain fatty acids. For this reason this three-step reaction pathway is often remembered by the mnemonic as the VOMIT pathway, where V stands for valine, O for odd-chain fatty acids, M for methionine, I for isoleucine, and T for threonine.

Propionyl-CoA carboxylase functions as a heterododecameric enzyme (subunit composition: α6β6) and the two different subunits are encoded by the PCCA and PCCB genes, respectively. The PCCA gene is located on chromosome 13q32 and is composed of 27 exons that generate three alternatively spliced mRNAs. The PCCB gene is located on 3q21–q22 and is composed of 17 exons that generate two alternatively spliced mRNAs. Methylmalony-CoA epimerase is encoded by the MCEE gene located on chromosome 2p13.3 and is composed of 4 exons that encode a 176 amino acid protein. Methylmalonyl-CoA mutase is encoded by the MUT gene located on chromosome 6p12.3 and ius composed of 13 exons that encode a protein of 750 amino acids. Mutations in the MUT gene are one cause of the methylmalonic acidemias.

The second pathway of threonine catabolism utilizes serine hydroxymethyltransferase (SHMT). As indicated above in the Glycine Biosynthesis section, 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 of threonine catabolism in mammals occurs in the mitochondria and is initiated by threonine dehydrogenase (TDH) 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 enzyme that is most important for 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, 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 enzyme, glycine dehydrogenase (decarboxylating) which is also called the glycine cleavage complex, GCC. The GCC is composed of four mitochondrial proteins encoded by four genes. The protein components of the GCC are the actual glycine dehydrogenase subunit (identified as the P subunit: pyridoxal phosphate-dependent), a lipoic acid-containing subunit (the H subunit), a tetrahydrofolate-requiring enzyme called aminomethyltransferase (the T subunit), and dihydrolipoamide dehydrogenase (the L subunit). The P subunit is encoded by the GLCD gene located on chromosome 9p22 and is composed of 25 exons that encode a protein of 1020 amino acids. The H subunit is encoded by the GCSH gene located on chromosome 16q23.2 and is composed of 5 exons that generate two splice variant mRNAs, only one of which encodes a functional protein of 173 amino acids. The T subunit (aminomethyltransferase) is encoded by the AMT gene located on chromosome 3p21.31 and is composed of 9 exons that generate four alternatively spliced mRNAs generating four isoforms of the enzyme. The L subunit is encoded by the DLD gene located on chromosome 7q31–q32 and is composed of 14 exons that generate multiple alternatively spliced mRNAs. The DLD encoded protein is also found as a subunit of several other important dehydrogenase complexes: the pyruvate dehydrogenase complex (PDHc), the 2-oxoglutarate (α-ketoglutarate) dehydrogenase complex, and the branched-chain keto-acid dehydrogenase (BCKD) complex. 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.

Reaction catalyzed by glycine decarboxylase

Reaction catalyzed by the glycine cleavage complex, GCC


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Cysteine Catabolism

There are several pathways for non-protein disposition of cysteine that include both metabolism and catabolism. The major cysteine catabolic pathway in humans occurs via the action of cysteine dioxygenase type 1 (gene symbol: CDO1). CDO1 oxidizes the sulfhydryl group of cysteine to sulfinate, producing the intermediate cysteine sulfinate. The CDO1 gene is located on chromosome 5q23.2 and is composed of 6 exons that encode a 200 amino acid protein.

Catabolism of cysteine sulfinate proceeds through transamination (catalyzed by cytosolic AST) to β-sulfinylpyruvate (3-sulfinylpyruvate) which then undergoes desulfuration yielding pyruvate and bisulfite, (HSO3) which is in equilibrium with sulfite (SO32–) at pH 7.2. The enzyme sulfite oxidase (gene symbol: SUOX) then catalyzes the conversion of sulfite to sulfate. The SUOX encoded enzyme is somewhat unique in that it uses the oxygen atom from H2O to convert sulfite to sulfate, (SO42–) and releases two protons (H+). The SUOX gene is located on chromosome 12q13.2 and is composed of 7 exons that encode a protein of 545 amino acids. The enzyme cysteine desulfurase (encoded by the NFS1 gene) is another important enzyme associated with cysteine catabolism. Cysteine desulfurase removes the sulfur from cyteine yielding alanine. The sulfur remains associated with cysteine desulfurase and is subsequently transferred to numerous enzymes that possess iron-sulfur clusters for their activity. Cysteine desulfurase is a member of the pyridoxal phosphate (B6)-dependent aminotransferase family. The NFS1 gene is located on chromosome 20q11.22 and is composed of 14 exons. In addition to alternative splicing (generating two mRNAs), there are alternative in-frame translational start sites in the NFS1 derived mRNAs. The use of these alternative translational start sites generates mitochondrial and cytoplasmic or nuclear forms of the enzyme.

Other than protein, the most important metabolic products derived from cysteine are glutathione (GSH), the bile salt modifying compound, taurine, and as a source of the sulfur for coenzyme-A synthesis. Taurine is used to form the bile acid conjugates taurocholate and taurochenodeoxycholate. Taurine synthesis occurs primarily in the liver since this is the only bile acid synthesizing tissue in the body However, taurine can be transported to the blood and disseminated to other tissues. Taurine is derived from the cysteine catabolism intermediate, cysteine sulfinate. Cysteine sulfinate is converted to hypotaurine by the rate-limiting enzyme in taurine synthesis, cysteine sulfinic acid decarboxylase, CSAD (also called sulfinoalanine decarboxylase). The CSAD gene is located on chromosome 12q13.11–q14.3 and is composed of 21 exons that generate three alternatively spliced mRNAs each of which encode a unique isoform of the enzyme. Oxidation of hypotaurine to taurine is thought to occur spontaneously, i.e non-enzymatically.

Pathways of cysteine catabolism

Pathways of cysteine catabolism. Catabolism of cysteine is responsible for the release and or transfer of the sulfur from this amino acid. The catabolism of cysteine can also involve a metabolic pathway as is the case for taurine synthesis. Cysteine catabolism and taurine synthesis both begin with the oxidation to cysteine sulfinic acid catalyzed by cysteine dioxygenase. Cysteine sulfinate is converted to taurine via the action of cysteinesulfinate decarboxylase. Catabolism of cysteine sulfinate to sulfate ion first involves a transamination that releases 3-sulfinpyruvate that spntaneously decomposes to bisulfite ion and pyruvate. The transaminase responsible for this reaction is the soluble form of aspartate transaminase which is encoded by the GOT1 gene. The bisulfite ion is in ionic equilibrium with sulfite ion which is then converted to the sulfate ion via the action of sulfite oxidase. The released sulfate can be used for PAPS synthesis as described in the following Figure.

The enzyme cystathionase (cystathionine γ-lyase) 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 sulfurtransferases to incorporate sulfur into cyanide ion, (CN), thereby detoxifying the cyanide to thiocyanate. These sulfurtransferase enzymes contain domains called rhodanese domains since they were first identifed in a mitochondrial enzyme that was originally called rhodanese (thiosulfate sulfurtransferase, TST). Another rhodanese domain-containing enzyme that is located in the cytosol is called mercaptopyruvate sulfurtransferase (MPST). MPST transfers the sulfur group from 3-mercaptopyruvate to CN and other thiol compounds.

One of the important uses of the sulfate that is derived from the catabolism of cysteine is 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

Two-step reaction for synthesis of PAPS. The synthesis of PAPS involves the addition of sulfate at the β (beta) position of the phosphates of ATP with the resultant loss of the γ (gamma) phosphate generating adenosine 5'-phosphosulfate, APS. APS is then phosphorylated at the 3'-position of the ribose moiety forming the ultimate product, PAPS. Synthesis of PAPS in humans is catalyzed by the bi-functional enzyme 3'-phosphoadenosine 5'-phosphosulfate synthase, PAPSS. PAPSS possesses both the ATP sulfurylase and APS kinase activities that are associated with two separate enzymes in yeasts, bacteria, and plants. Humans express two PAPSS genes identified as PAPSS1 and PAPSS2.

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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 cysteine and α-ketobutyrate via the reaction pathway involving the synthesis of SAM and cysteine 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.

In the catbolism of methionine the α-ketobutyrate is converted to propionyl-CoA. The propionyl-CoA is converted, via a mitochondrially-localized three reaction ATP-dependent pathway, to succinyl-CoA. The succinyl-CoA can then enter the TCA cycle for further oxidation. The enzymes required for this conversion are propionyl-CoA carboxylase, methylmalonyl-CoA epimerase, and methylmalonyl-CoA mutase, respectively. Propionyl-CoA carboxylase is called an ABC enzyme due to the requirements for ATP, Biotin, and CO2 for the reaction. The clinical significance of methylmalonyl-CoA mutase in this pathway is that it is one of only two enzymes that requires a vitamin B12-derived co-factor for activity. The other B12-requiring enzyme is methionine synthase (see the Cysteine Synthesis section above). This propionyl-CoA conversion pathway is also required for the metabolism of the amino acids valine, isoleucine, and threonine and fatty acids with an odd number of carbon atoms. For this reason this three-step reaction pathway is often remembered by the mnemonic as the VOMIT pathway, where V stands for valine, O for odd-chain fatty acids, M for methionine, I for isoleucine, and T for threonine.

Propionyl-CoA carboxylase functions as a heterododecameric enzyme (subunit composition: α6β6) and the two different subunits are encoded by the PCCA and PCCB genes, respectively. The PCCA gene is located on chromosome 13q32 and is composed of 27 exons that generate three alternatively spliced mRNAs. The PCCB gene is located on chromosome 3q21–q22 and is composed of 17 exons that generate two alternatively spliced mRNAs. Methylmalonyl-CoA epimerase is encoded by the MCEE gene located on chromosome 2p13.3 and is composed of 4 exons that encode a 176 amino acid protein. Methylmalonyl-CoA mutase is encoded by the MUT gene located on chromosome 6p12.3 and is composed of 13 exons that encode a protein of 750 amino acids. Mutations in the MUT gene are one of the causes of the methylmalonic acidemias.

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 β-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 β-synthase activity. Under these conditions accumulated homocysteine is remethylated to methionine, using N5-methyl-THF as the methyl donor.

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

This group of essential amino acids is 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 amino acids occurs in most cells but at highest rates in skeletal muscle. BCAA catabolism yields both NADH and FADH2 which can be utilized for ATP generation which is a primary reason for their high rates of catabolism in skeletal muscle. 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 pyridoxal phosphate-dependent BCAA aminotransferase (termed a branched-chain aminotransferase, BCAT), with 2-oxoglutarate (α-ketoglutarate) as amine acceptor.

Humans express two genes that encode BCAT activity. These two genes are identified as BCAT1 and BCAT2. The primary protein encoded by the BCAT1 gene is a cytosolic version of the enzyme and the protein is identified as BCATc. The primary protein encoded by the BCAT2 gene is a mitochondrial version of the enzyme and this protein is designated BCATm. The BCAT1 gene is located on chromosome 12p12.1 and is composed of 13 exons that generate five alternatively spliced mRNAs, each of which encode a distinct isoform. BCAT1 isoform 1 is a 386 amino acid protein. BCAT1 isoform 2 is a 349 amino acid protein. BCAT1 isoform 3 is a 325 amino acid protein. BCAT1 isoform 4 is a 398 amino acid protein. BCAT1 isoform 5 is a 385 amino acid protein. The BCAT2 gene is located on chromosome 19q13 and is composed of 12 exons that generate three alternatively spliced mRNAs that encode three different isoforms. BCAT2 isoform a is a 392 amino acid protein which is also referred to as PP18a. BCAT2 isoform b is a 300 amino acid protein which is also referred to as PP18b. The isoform b protein is found in the cytosol. BCAT2 isoform c is a 352 amino acid protein. Expression of the BCAT1 gene is restricted to only a few tissues types. The BCAT1 gene represents the primary BCAT expressing gene in the brain. Expression of BCAT2 is widely distributed among numerous tissues. Although detectable in the fetal liver, the adult liver does not express either BCAT gene.

The metabolism of the branched-chain amino acids is critical to overall nitrogen homeostasis in the brain and to the maintenance of proper levels of the excitatory neurotransmitter, glutamate. The critical enzymes that are necessary for this homeostatic process are the BCATc and BCATm isoforms of the BCAA aminotransferases. Within the brain different populations of cells express predominantly BCATc while others express predominantly BCATm and this differential distribution is what is important in overall neuronal nitrogen homeostasis.

As a result of the BCAT reaction, three different α-keto acids are produced and are oxidized using a common branched-chain α-keto acid dehydrogenase (BCKD) complex, yielding the three different CoA derivatives. Subsequently the metabolic pathways diverge, producing many intermediates. The BCKD complex is one of three dehydrogenase complexes whose vitamin-derived cofactor requirements can be remembered by the mnemonic: Tender Loving Care For Nancy, where the T stands for thiamine, the L for lipoic acid, the C for coenzyme A (CoA), the F for riboflavin, and the N for niacin. The other two dehydrogenase complexes are the PDHc and the 2-oxoglutarate dehydrogenase complexes associated with the TCA cycle.

The BCKD complex is a multimeric enzyme composed of three catalytic subunits. The E1 portion of the complex is a thiamine pyrophosphate (TPP)-dependent decarboxylase with a subunit structure of α2β2. The E2 portion is a dihydrolipoamide branched-chain transacylase composed of 24 lipoic acid-containing polypeptides. The E3 portion is a homodimeric flavoprotein identified as dihydrolipoamide dehydrogenase, DLD. The activity of BCKD is regulated by two additional subunits, a kinase and a phosphatase that reversibly phosphorylate/dephosphorylate, respectively, the complex. The phosphorylated enzyme is inactive. The E1α gene (symbol: BCKDHA) is located on chromosome 19q13.1–q13.2, spans 55 kb and contains 9 exons that generate two alternatively spliced mRNAs that encode alpha subunit isoform 1 (445 amino acids) and alpha subunit isoform 2 (444 amino acids). The E1β gene (symbol: BCKDHB) is located on chromosome 6q14.1 and is composed of 16 exons that genereate two alternatively spliced mRNAs that encode the same 392 amino acid protein. The E2 gene (symbol: DBT) is located on chromosome 1p31, spans 68 kb and contains 13 exons that encode a protein of 482 amino acids. The E3 gene (symbol: DLD) is located on chromosome 7q31–q32, spans 20 kb and contains 14 exons that generate several alternatively spliced mRNAs. The DLD gene encodes the same dihydrolipoamide dehydrogenase subunits found in the PDHc and the 2-oxoglutarate dehydrogenase complexes.

Catabolism of the branched-chain amino acids, isoleucine, leucine, and valine

Catabolism of the branched-chain amino acids. The three branched-chain amino acids, isoleucine, leucine, and valine enter the catabolic pathway via the action of the same two enzymes. The initial deamination of all three amino acids is catalyzed by one of two branched-chain amino acid transaminases (BCATc or BCATm). The resulting α-ketoacids are then oxidatively decarboxylated via the action of the enzyme complex, branched-chain ketoacid dehydrogenase (BCKD). The BCKD reaction generates the CoA derivatives of the decarboxylated ketoacids while also generating the reduced electron carrier, NADH. After these first two reactions the remainder of the catabolic pathways for the three amino acids diverges. The third reaction of branched-chain amino acid catabolism involves a dehydrogenation step that involve three distinct enzymes, one for each of the CoA derivatives generated via the BCKD reaction. This latter dehydrogenation step also yields additional reduced electron carrier as FADH2. The third reaction of isoleucine catabolism involves the enzyme short/branched-chain acyl-CoA dehydrogenase (SBCAD). The SBCAD enzyme is encoded by the ACADSB gene. The third reaction of leucine catabolism involves the enzyme isovaleryl-CoA dehydrogenase (IVD). The third reaction of valine catabolism involves the enzyme isobutyryl-CoA dehydrogenase (IBD). The IBD enzyme is encoded by the acyl-CoA dehydrogenase family, member 8 (ACAD8) gene.

The principal catabolic by-product from valine is propionylCoA, the glucogenic precursor of succinyl-CoA. Isoleucine catabolism terminates with production of acetyl-CoA and propionyl-CoA; thus isoleucine is both glucogenic and ketogenic. Leucine gives rise to acetyl-CoA and acetoacetyl-CoA, and is thus classified as strictly ketogenic. As pointed out above for the catabolism of methionine, the resulting propionyl-CoA is converted, via a mitochondrially-localized, three reaction, ATP-dependent pathway, to succinyl-CoA. The succinyl-CoA can then enter the TCA cycle for further oxidation. The enzymes required for this conversion are the ABC enzyme propionyl-CoA carboxylase, methylmalonyl-CoA epimerase, and the B12-dependent enzyme methylmalonyl-CoA mutase. This propionyl-CoA conversion pathway is often remembered by the mnemonic as the VOMIT pathway, where V stands for valine, O for odd-chain fatty acids, M for methionine, I for isoleucine, and T for threonine.

Propionyl-CoA carboxylase functions as a heterododecameric enzyme (subunit composition: α6β6) and the two different subunits are encoded by the PCCA and PCCB genes, respectively. The PCCA gene is located on chromosome 13q32 and is composed of 27 exons that generate three alternatively spliced mRNAs. The PCCB gene is located on chromosome 3q21–q22 and is composed of 17 exons that generate two alternatively spliced mRNAs. Methylmalonyl-CoA epimerase is encoded by the MCEE gene located on chromosome 2p13.3 and is composed of 4 exons that encode a 176 amino acid protein. Methylmalonyl-CoA mutase is encoded by the MUT gene located on chromosome 6p12.3 and is composed of 13 exons that encode a protein of 750 amino acids. Mutations in the MUT gene are one cause of the methylmalonic acidemias.

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Disorders of Branched-Chain Amino Acid Metabolism

There are a number of genetic diseases associated with faulty catabolism of the branched-chain amino acids (BCAA). The most common defect is in the branched-chain α-keto acid dehydrogenase (BCKD) complex. 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.

Additional disorders that are associated with defects in BCAA metabolism include isovaleric acidemia and 3-methylcrotonylglycinuria. Both of these disorders are the result of defects in leucine catabolism. Isovaleric acidemia results from mutations in the gene encoding the enzyme isovaleryl-CoA dehydrogenase (IVD) which converts isovaleryl-CoA to 3-methylcrotonyl-CoA. The IVD gene is located on chromosome 15q15.1 and is composed of 16 exons that generate two alternatively spliced mRNAs encoding isoform 1 precursor (426 amino acids) and isoform 2 precursor (396 amino acids). Mutations in the IVD gene lead to the accumulation of isovaleryl-CoA which is toxic to the central nervous system and is a fatal disorder in its most severe form if not correctly diagnosed. Although there are variabilities in the symptoms of isovaleric acidemia, in the infantile severe form the symptoms initially present as poor feeding, vomiting, seizures, and lethargy. These symptoms can progress to seizures, coma, and death. Isovaleric acidemia is inherited as an autosomal recessive disorder.

The other major leucine metabolic defect is 3-methylcrotonylglycinuria which results from defects in either of the two subunits of 3-methylcrotonyl-CoA carboxylase (3MCC). The function of 3-methylcrotonyl-CoA carboxylase is to catalyze the carboxylation of 3-methylcrotonyl-CoA to 3-methylglutaconyl-CoA during the catabolism of leucine. The 3-methylcrotonyl-CoA is the product of isovaleryl-CoA dehydrogenase which catalyzes the previous reaction in leucine catabolism. As indicated 3MCC is composed of two subunits in a heterododecameric configuration composed of six α-subunits and six β-subunits (α6β6). The activity of 3MCC is dependent on biotin. The α-subunit covalently binds biotin while the carboxyltransferase activity is encoded by the β-subunit. The structure of 3MCC and its dependence on biotin make it highly similar in structure and catalytic activity to propionyl-CoA carboxylase, PCC. The α-subunit of 3MCC is encoded by the MCCC1 gene and the β-subunit is encoded by the MCCC2 gene. Mutations in the MCCC1 gene cause 3-methylcrotonylglycinuria type I, while mutations in the MCCC2 gene cause 3-methylcrotonylglycinuria type II. The MCCC1 gene is located on chromosome 3q27.1 and is composed of 22 exons that generate two alternatively spliced mRNAs encoding isoform 1 precursor (725 amino acids) and isoform 2 precursor (608 amino acids). The MCCC2 gene is located on chromosome 5q13.2 and is composed of 19 exons that encode a 563 amino acid protein. Inheritance of 3-methylcrotonylglycinuria (also referred to as 3MCC deficiency) occurs in an autosomal recessive manner. The symptoms that result from defects in either of the two genes encoding 3MCC can range from benign to profound metabolic acidosis and early death. In the more severe forms of 3MCC deficiency infants appear normal at birth but will develop symptoms during the first year of life or possibly not until early childhood. The characteristic features of the severe forms of 3MCC deficiency include difficulty feeding, recurrent episodes of vomiting and diarrhea, lethargy, and hypotonia. If left undiagnosed or untreated, 3MCC deficiency can lead to delayed development, seizures, and coma and ultimately death.

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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 hydroxylation to tyrosine via the tetrahydrobiopterin-requiring phenylalanine hydroxylase (PAH) reaction. Thus, phenylalanine catabolism always ensues in the pathway of tyrosine biosynthesis followed by tyrosine catabolism. Tyrosine is equally important for protein biosynthesis as well as an intermediate in the biosynthesis of the catecholamines: dopamine, norepinephrine and epinephrine (see Specialized Products of Amino Acids).

The pathway of tyrosine degradation involves conversion to fumarate and acetoacetate, allowing phenylalanine and tyrosine to be classified as both glucogenic and ketogenic. The catabolism of tyrosine involves five reactions, four of which have been shown to associated with inborn errors in metabolism and three of these result in clinically significant disorders. The first reaction of tyrosine catabolism involves the nuclear genome encoded mitochondrial enzyme tyrosine aminotransferase and generates the corresponding ketoacid, p-hydroxyphenylpyruvic acid. Like most aminotransferase reaction, tyrosine aminotransferase utilizes 2-oxoglutarate (α-ketoglutarate) as the amino acceptor with the consequent generation of glutamate. Tyrosine aminotransferase is encoded by the TAT gene on chromosome 16q22.1 which is composed of 12 exons that generate a protein of 454 amino acids. The second reaction of tyrosine catabolism is catalyzed by p-hydroxyphenylpyruvate dioxygenase which is encoded by the HPD gene located on chromosome 12q24.31 which is composed of 17 exons that generate two alternatively spliced mRNAs. The product of the HPD reaction is homogentisic acid. Homogentisate is oxidized by the second dioxygenase enzyme of tyrosine catabolism, homogentisate oxidase. Homogentisate oxidase is encoded by the homogentisate 1,2-dioxygenase gene (symbol: HDG) located on chromosome 3q13.33 and composed of 16 exons that encode a protein of 445 amino acids. Oxidation of homogentisate yields 4-maleylacetoacetate which is isomerized to 4-fumarylacetoacetate by the enzyme glutathione S-transferase zeta (ζ) 1 which is encoded by the GSTZ1 gene. Glutathione S-transferase zeta 1 was formerly called 4-maleylacetoacetate isomerase or maleylacetoacetate cis-trans-isomerase. The GSTZ1 gene is located on chromosome 14q24.3 and is composed of 12 exons that generate three alternatively spliced mRNAs. Fumarylacetoacetate is hydrolyzed to fumarate and acetoacetate by the enzyme fumarylacetoacetate hydrolase which is encoded by the FAH gene located on chromosome 15q25.1 and is composed of 14 exons that generate a 419 amino acid protein. The fumarate end product of tyrosine catabolism feeds directly into the TCA cycle for further oxidation. The acetoacetate is activated to acetoacetyl-CoA via the action of the mitochondrial ketone body utilization enzyme, succinyl-CoA:3-oxoacid-CoA transferase (SCOT) which is encoded by the OXCT1 (3-oxoacid-CoA transferase 1) gene. Acetoacetate can also be activated in the cytosol by the cytosolic enzyme, acetoacetyl-CoA synthetase (AACS).

Catabolism of phenylalanine and tyrosine

Pathway of phenylalanine and tyrosine catabolism. Phenylalanine becomes tyrosine via the action of phenylalanine hydroxylase as discussed in the Tyrosine Biosynthesis section. Therefore, the phenylalanine and tyrosine catabolic pathways are the same. Tyrosine is ultimately degraded to fumarate and acetoacetate througgh a series of five reactions. HPD: hydroxyphenylpyruvate dioxygenase. GSTZ1: glutathione S-transferase zeta 1 which was formerly called 4-maleylacetoacetate isomerase. FAH: fumarylacetoacetate hydrolase.

Inherited mutations in the TAT gene lead to hypertyrosinemia type II (TYRSN2; also called Richner-Hanhart syndrome) which, as the name implies, is associated with elevated tyrosine levels in the blood and, consequently the urine. This form of tyrosinemia is associated with mental retardation, painful corneal eruptions, photophobia, keratitis, and painful palmoplantar hyperkeratosis. Mutations in the HPD gene result in hypertyrosinemia type IIII (TYRSN3). TYRSN3 is an autosomal recessive disease that, in addition to hypertyrosinemia, is associated with mild mental retardation and/or convulsions but these patients do not display hepatic damage as is characteristic of type I hypertyrosinemia. Mutations in the FAH gene result in hypertyrosinemia type I (TYRSN1). TYRSN1 is an autosomal recessive disorder characterized by hypertyrosinemia and progressive liver disease. This disorder also leads to a secondary renal tubular dysfunction resulting in hypophosphatemic rickets. 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 which is the third enzyme in the tyrosine catabolic pathway. 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 of indeterminant etiology.

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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 where this specific lysine transporter is encoded by the SLC7A1 gene. There are actually at least three transporter mechanisms for lysine transport. One is the aforementioned y+ system that functions as a uniporter. The other two lysine transporters are Na+-dependent antiporter systems that are heterodimeric transporters composed of a heavy chain and a light chain forming transporters of the y+L system. The common heavy chain of these two different transporters is encoded by the SLC3A2 gene (often referred to as 4F2hc for 4F2 cell-surface antigen heavy chain). The light chains are encoded by the SLC7A6 and SLC7A7 genes both of which encode the y+LAT2 and y+LAT1 proteins, respectively. 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. Mammalian α-aminoadipic semialdehyde synthase is encoded by the AASS gene found on chromosome 7q31.3 and is composed of 26 exons encoding a protein of 926 amino acids. The N-terminal half of the AASS protein harbors the lysine:2-oxoglutarate reductase activity and the C-terminal half harbors the saccharopine dehydrogenase activity. The ultimate end-product of lysine catabolism, via this saccharopine pathway, is acetoacetyl-CoA.

Genetic deficiencies in either of the first two reactions of the saccharopine pathway of lysine catabolism result in familial hyperlysinemia associated with psychomotor retardation. 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 C-terminal saccharopine dehydrogenase activity. These deficiencies are observed in individuals who excrete large quantities of urinary lysine and some saccharopine.

One of the other minor pathways of lysine catabolism 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 5q31 composed of 19 exons that generate three alternatively spliced mRNAs generating three isoforms of the enzyme. 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.

Carnitine Synthesis from Lysine

Lysine is also important as a precursor for the synthesis of carnitine (γ-trimethyl-hydroxybutyrobetaine), 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 (6-N-trimethyllysine), found in certain proteins, is the precursor. Protein lysine methylation is catalyzed by one of a family of 27 lysine methyltransferases (KMT) expressed in humans. Some of the most critical proteins that are methylated on lysine residues are the histone proteins in chromatin, the consequences of which are regulation of gene expression. The methyl donor for KMT proteins is S-adenosylmethionine (AdoMet of SAM). Hydrolysis of proteins containing trimethyllysine provides the substrate for the subsequent conversion to carnitine. Once trimethyllysine is released from proteins within the lysosomal compartment, the overall pathway to carnitine synthesis requires four separate reactions. Most human tissues can convert trimethyllysines to γ-butyrobetaine (the compound prior to carnitine) but only the liver, kidney, brain, and testes express the γ-butyrobetaine dioxygenase enzyme (also called γ-butyrobetaine 2-oxoglutarate dioxygenase or γ-butyrobetaine hydroxylase) that hydroxylates γ-butyrobetaine forming carnitine. The gene encoding γ-butyrobetaine dioxygenase is identified as BBOX1. The γ-butyrobetaine dioxygenase enzyme as well as the first enzyme of carnitine synthesis (trimethyllysine hydroxylase) are members of the large family of 2-oxoglutarate and ferrous (Fe2+) iron-dependent dioxygenases. Although the liver, kidney, brain, and testes can synthesize carnitine, only the liver and the kidneys can transport carnitine to the blood.

Synthesis of carnitine from trimethyllysine

Synthesis of carnitine. Carnitine is synthesized from the trimethylated lysine released from proteins following their degradation in the lysosome. A series of four reactions converts trimethyllysine to carnitine (γ-trimethyl-hydroxybutyrobetaine). The first and last reactions of carnitine synthesis are catalyzed by enzymes that are members of the large family of 2-oxoglutarate and ferrous (Fe2+) iron-dependent dioxygenases. The two enzymes have also been shown to utilize ascorbate as co-factor. The first reaction is catalyzed by trimethyllysine hydroxylase, epison (also called trimethyllysine dioxygenase) which is encoded by the TMLEH gene. The second reaction is an aldolase-like cleavage reaction that releases glycine. The activity has been given the name 3-hydroxytrimethyllysine aldolase, however, no distinct human gene has been identified as encoding this specific activity. There is speculation that the reaction may in fact be catalyzed by serine hydroxymethyltransferase (SHMT). Humans express a cytosolic SHMT (encoded by the SHMT1 gene) and a mitochondrial SHMT (encoded by the SHMT2 gene). The third reaction is catalyzed by aldehyde dehydrogenase 9 family, member A1 (ALDH9A1). The ALDH9A1 encoded enzyme was formerly known as 4-N-trimethylaminobutyraldehyde dehydrogenase (TMABADH). The last reaction is catalyzed by γ-butyrobetaine dioxygenase (also called γ-butyrobetaine 2-oxoglutarate dioxygenase and γ-butyrobetaine hydroxylase) encoded by the BBOX1 gene.


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Histidine Catabolism

Histidine catabolism begins with release of the α-amino group catalyzed by histidine ammonia-lyase (also called 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 histidase enzyme is encoded by the HAL gene located on chromosome 12q22-q24.1 and is composed of 21 exons generating three alternatively spliced mRNAs. 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-formimino-THF. The latter reaction is one of two routes to N5-formimino-THF. Urocanate is converted to 4-imidazolone-5-propionate via the action of urocanate hydratase 1 (encoded by the UROC1 gene). The UROC1 gene is located on chromosome 3q21.3 and is composed of 21 exons that generate two alternatively spliced mRNAs. The 4-imidazolone-5-propionate is then converted to N-formimidoyl-L-glutamte via the action of an imidazolone propionase activity. The imidazolone propionase activity is encoded by the amidohydrolase domain-containing 1 gene (symbol: AMDHD1). The AMDHD1 gene is located on chromosome 12q23.1 and is composed of 9 exons that encode a 426 amino acid protein. The enzyme formimidoyltransferase cyclodeaminase (also called glutamate formiminotransferase) then transfers the formimino group from N-formimidoyl-L-glutamte to THF yielding N5-formimino-THF and glutamate. Formimidoyltransferase cyclodeaminase is encode by the FTCD gene located on chromosome 21q22.3 which is composed of 16 exons that generate two alternatively spliced mRNAs, both of which encode the same 541 amino acid protein.

Catabolism of histidine and forminiotetrahydrofolate synthesis

Catabolism of histidine. Histidine catabolism proceeds via a 4-step pathway to glutamate. The process of histidine catabolism represents, not only a catabolic reaction pathway, but a major folic acid derivative biosynthesis pathway. In the course of the catabolism, a portion of the carbon skeleton of histidine is transferred to tetrahydrofolate (THF) forming the folate derivative, N5-formimino-THF.


The principal genetic deficiencies associated with histidine metabolism are associated with mutations in the HAL, UROC1, and FTCD gene. Mutations in the HAL gene result in histidinemia which 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. UROC1 mutations have only been reported in a few individuals who inherited compound heterozygous missense mutations. These individuals exhibited mental retardation, short stature, and episodic aggressiveness and affection-seeking behaviors. Inherited defects in the FTCD gene represent the second most common cause of inborn errors in folate metabolism. Potential for severe mental retardation is the main clinical feature associated with FTCD deficiency. Patients with FTCD defects will also present with megaloblastic anemia due to the role of folate derivatives in the synthesis of purine and thymine nucleotides.

Histamine Synthesis and Functions

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 which is a pyridoxal phosphate-requiring (B6) enzyme. The histidine decarboxylase gene (symbol: HDC) is located on chromosome 15q21.1 and is composed of 14 exons that encode a protein of 662 amino acids.

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 vasodilation 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. When histamine is released from these cells, in response to vagal nerve stimulation, it binds to specific receptors on parietal cells triggering the mobilization of the proton pump 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 (H1R–H4R), all of which are G-protein coupled receptors (GPCRs). The H1 receptor is coupled to a Gq-type G-protein 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

Catabolism of tryptophan in humans results in the formation of acetoacetate. The first enzyme of the tryptophan catabolic pathway opens the indole ring. This enzyme is tryptophan 2,3-dioxygenase which is encoded by the TDO2 gene located on chromosome 4q31–q32 and is composed of 12 exons that encode a protein of 406 amino acids. The product of the TDO2 reaction is N-formyl-kynurenine. The TDO2 gene is highly inducible, leading to increasing concentrations of the enzyme, of up to 10-fold, on a diet high in tryptophan. Tryptophan catabolism can also be initiated by the enzyme indoleamine 2,3-dioxygenase 1 encoded by the IDO1 gene. The activity of the IDO1 enzyme also results in the generation of N-formyl-kynurenine. The IDO1 gene is located on chromosome 8p12–p11 and is composed of 10 exons that generate a protein of 403 amino acids. N-formyl-kynurenine is then converted to kynurenine by the enzyme, arylformamidase (also called kynurenine formamidase), encoded by the AFMID gene.

Kynurenine is the first key branch point intermediate in the catabolic pathway leading to three distinct catabolic fates for tryptophan. Kynurenine can undergo deamination in a transamination reaction. The transamination reaction can be catalyzed by several different transaminases. One of these enzymes is the human homolog of mouse kynurenine aminotransferase II, yielding kynurenic acid. The human kynurenine aminotransferase II (KAT II, KAT2) enzyme is called aminoadipate aminotransferase which is encoded by the AADAT gene. The enzyme encoded by the AADAT gene has two aminotransferase activities, one of which is utilized in the saccharopine pathway of lysine catabolism, the other is used in the transamination of kynurenine. Another kynurenine transaminase is cysteine conjugate-beta lyase 2 encoded by the CCBL2 gene. The CCBL2 encoded protein was formerly known as kynurenine aminotransferase III (KAT III, KAT3). Another, related enzyme, that was once called kynurenine aminotransferase I (KAT I, KAT1) is cysteine conjugate-beta lyase encoded by the CCBL1 gene. The CCBL1 encoded protein is a cytosolic enzyme that, as its name implies, metabolizes cysteine conjugates.

Kynurenic acid and metabolites have been shown to act as anti-excitotoxics and anti-convulsives. 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 glutamatergic neurotransmission system believed to be involved in the pathophysiology of schizophrenia, thus explaining the potential role of kynurenic acid in schizophrenia.

Catabolism of tryptophan

Catabolic pathways for tryptophan. Tryptophan catabolism to acetoacetate also involves functional metabolism to several important bioactive compounds. These compounds include the nicotinamide adenine dinucleotide co-factors, NAD+ and NADP+, kynurenic acid, and quinolinic acid. TDO2: tryptophan 2,3-dioxygenase. IDO1: indoleamine 2,3-dioxygenase 1. AADAT: aminoiadipate aminotransferase. HAAO: 3-hydroxyanthranilate 3,4-dioxygenase. ACMS: α-amino-β-carboxymuconate-ε-semialdehyde.


Kynurenine can also undergo a series of catabolic reactions resulting in complete oxidation to acetoacetyl-CoA or this pathway can also be utilized to allow kynurenine to serve as an important intermediate in the pathway for the synthesis of the nicotinamide adenine dinucleotide co-factors, NAD+ and NADP+. The first reaction in this pathway of kynurenine metabolism is catalyzed by kynurenine hydroxylase (kynurenine 3-monooxygenase) forming 3-hydroxykynurenine. Kynurenine hydroxylase is encoded by the KMO gene located on chromosome 1q42–q44 and is composed of 16 exons that generate a protein of 486 amino acids. The next step in the pathway is catalyzed by kynureninase and produces 3-hydroxyanthranilic acid and the amino acid alanine. It is the production of alanine residues that allows tryptophan to be classified among the glucogenic amino acids. Kynureninase is a pyridoxal phosphate (vitamin B6)-requiring enzyme encoded by the KNYU gene. The KYNU gene is located on chromosome 2q22.2 and is composed of 23 exons that generate several alternatively spliced mRNAs that encode two distinct isoforms of the enzyme. Kynureninase can also act directly on kynurenine to produce anthranilic acid with the release of alanine. The anthranilic acid subsequently is converted to 3-hydroxyanthranilic acid. This latter two-step reaction is a minor component of overall tryptophan catabolism. The next step in the pathway is the conversion of 3-hydroxyanthranilic acid to quinolinic acid catalyzed by the enzyme 3-hydroxyanthranilate 3,4-dioxygenase which is encoded by the HAAO gene. Quinolinic acid is ultimately converted, via several steps, to the nicotinamide adenine dinucleotide co-factors. Quinolinic acid is also an excitatory neurotoxic compound that functions via its ability to activate the glutamate NMDA receptors. An intermediate in the HAAO catalyzed reaction is α-amino-β-carboxymuconate-ε-semialdehyde (ACMS). This intermediate can be metabolized via the action of the enzyme ACMS decarboxylase. This latter reaction is important for the prevention of over accumulation of quinolinic acid from ACMS. The product of the ACMS decarboxylase reaction goes on to be further metabolized to acetoacetyl-CoA, the end product of complete tryptophan catabolism.

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

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Last modified: December 1, 2017