Harper's Biochemistry Chapter 27 - Biosynthesis of the Nutritionally Nonessential Amino Acids PDF

S E C T I O N Metabolism of Proteins & VI Amino Acids Biosynthesis of the C H A P T E R Nutritionally...

S E C T I O N Metabolism of Proteins & VI Amino Acids Biosynthesis of the C H A P T E R Nutritionally Nonessential Amino Acids Victor W. Rodwell, PhD 27 O B J E C TI V E S Explain why the absence of certain amino acids that are present in most proteins from the human diet typically is not deleterious to human health. After studying this chapter, Appreciate the distinction between the terms “essential” and “nutritionally you should be able to: essential” amino acids, and identify the amino acids that are nutritionally nonessential. Name the intermediates of the citric acid cycle and of glycolysis that are precursors of aspartate, asparagine, glutamate, glutamine, glycine, and serine. Illustrate the key role of transaminases in amino acid metabolism. Explain the process by which the 4-hydroxyproline and 5-hydroxylysine of proteins such as collagen are formed. Describe the clinical presentation of scurvy, and provide a biochemical explanation for why a severe deprivation of vitamin C (ascorbic acid) results in this nutritional disorder. Appreciate that, despite the toxicity of selenium, selenocysteine is an essential component of several mammalian proteins. Define and outline the reaction catalyzed by a mixed-function oxidase. Identify the role of tetrahydrobiopterin in tyrosine biosynthesis. Indicate the role of a modified transfer RNA (tRNA) in the cotranslational insertion of selenocysteine into proteins. BIOMEDICAL IMPORTANCE significant nutritiona and metaboic abnormaities. Both the nutritiona disorder scurvy, a dietary deficiency of vitamin C, Amino acid deficiency states can resut if nutritionay essentia and specific genetic disorders are associated with an impaired amino acids are absent from the diet, or are present in inade- abiity of connective tissue to form peptidy 4-hydroxyproine quate amounts. In certain regions of West Africa, for exampe, and peptidy 5-hydroxyysine. The resuting conformationa kwashiorkor sometimes resuts when a chid is weaned onto instabiity of coagen is accompanied by beeding gums, a starchy diet poor in protein, whie marasmus may occur sweing joints, poor wound heaing, and utimatey in death. if both caoric intake and specific amino acids are deficient. Menkes syndrome, characterized by kinky hair and growth Patients with short bowe syndrome, if unabe to absorb suf- retardation, resuts from a dietary deficiency of copper, an ficient quantities of caories and nutrients, may suffer from essentia cofactor for the enzyme ysy oxidase that functions 273 274 SECTION VI Metabolism of Proteins & Amino Acids in formation of the covaent cross-inks that strengthen coa- Biosynthesis of the Nutritionally gen fibers. Genetic disorders of coagen biosynthesis incude severa forms of osteogenesis imperfecta, characterized by Essential Amino Acids Involves fragie bones, and Ehlers-Danlos syndrome, a group of con- Lengthy Metabolic Pathways nective tissue disorders that resut in mobie joints and skin The existence of nutritiona requirements suggests that depen- abnormaities due to defects in the genes that encode enzymes, dence on an external source of a specific nutrient can be of incuding procoagen-ysine 5-hydroxyase. greater surviva vaue than the abiity to biosynthesize it. Why? Because if the diet contains ampe quantities of a nutrient, retention of the abiity to biosynthesize it represents informa- NUTRITIONALLY ESSENTIAL & tion of negative surviva vaue, because ATP and nutrients are NUTRITIONALLY NONESSENTIAL not required to synthesize “unnecessary” DNA—even if spe- AMINO ACIDS cific encoded genes are no onger expressed. The number of enzymes required by prokaryotic ces to biosynthesize the Whie often empoyed with reference to amino acids, the terms nutritionay essential amino acids is arge reative to the num- “essentia” and “nonessentia” are miseading, since for human ber of enzymes required for the formation of the nutritionay subjects a 20 common amino acids are essentia to ensure nonessential amino acids (Table 27–2). This suggests a sur- heath. Of these 20 amino acids, 8 must be present in the human viva advantage for humans to retain the abiity to biosynthe- diet, and thus are best termed “nutritionally essential.” The other tize “easy” amino acids whie osing the abiity to make others 12 “nutritionally nonessential” amino acids, whie metabolically more difficut to biosynthesize. The reactions by which organ- essentia, need not be present in the diet (Table 27–1). The dis- isms such as pants and bacteria, but not human subjects, form tinction between these two casses of amino acids was estabished certain amino acids are not discussed. This chapter addresses in the 1930s by feeding human subjects a diet in which purified the reactions and intermediates invoved in the biosynthesis of amino acids repaced protein. Subsequent biochemica investiga- the 12 nutritionay nonessential amino acids in human tissues tions utimatey reveaed the reactions and intermediates invoved and emphasizes seected medicay significant disorders asso- in the biosynthesis of a 20 amino acids. Amino acid deficiency ciated with their metaboism. disorders are endemic in certain regions of West Africa where diets rey heaviy on grains that are poor sources of tryptophan and ysine. These nutritiona disorders incude kwashiorkor, TABLE 27–2 Enzymes Required for the Synthesis of which resuts when a chid is weaned onto a starchy diet poor in Amino Acids From Amphibolic Intermediates protein, and marasmus, in which both caoric intake and spe- cific amino acids are deficient. Number of Enzymes Required to Synthesize Nutritionally Essential Nutritionally Nonessential Arga 7 Ala 1 TABLE 27–1 Amino Acid Requirements of Humans His 6 Asp 1 Nutritionally Essential Nutritionally Nonessential Thr 6 Asnb 1 Argininea Alanine Met 5 (4 shared) Glu 1 Histidine Asparagine Lys 8 Glna 1 Isoleucine Aspartate Ile 8 (6 shared) Hylc 1 Leucine Cysteine Val 6 (all shared) Hypd 1 Lysine Glutamate Leu 7 (5 shared) Proa 3 Methionine Glutamine Phe 10 Ser 3 Phenylalanine Glycine Trp 5 (8 shared) Glye 1 Threonine Hydroxyprolineb 59 (total) Cysf 2 Tryptophan Hydroxylysineb Tyrg 1 Valine Proline 17 (total) Serine a From Glu. Tyrosine b From Asp. c From Lys. a d Nutritionally “semiessential.” Synthesized at rates inadequate to support growth of From Pro. e children. From Ser. b f Not necessary for protein synthesis, but is formed during posttranslational process- From Ser plus sulfate. g ing of collagen. From Phe.  CHAPTER 27 Biosynthesis of the Nutritionally Nonessential Amino Acids 275 + NH3 – O3PO O– O O FIGURE 27–3 γ-Glutamyl phosphate. Glutamate Dehydrogenase, Glutamine FIGURE 27–1 The reaction catalyzed by glutamate dehydro- Synthetase, & Aminotransferases genase (EC 1.4.1.3). Play Central Roles in Amino Acid Biosynthesis The combined action of the enzymes gutamate dehydrogenase, gutamine synthetase, and the aminotransferases (see Figures 27–1, BIOSYNTHESIS OF THE 27–2, and 27–4) resuts in the incorporation of potentiay cyto- NUTRITIONALLY NONESSENTIAL toxic ammonium ion into nontoxic amino acids. AMINO ACIDS Asparagine Glutamate The conversion of aspartate to asparagine, catayzed by aspara- Gutamate, the precursor of the so-caed “gutamate famiy” of gine synthetase (Figure 27–5), resembes the gutamine syn- amino acids, is formed by the reductive amidation of the citric thetase reaction (see Figure 27–2), but gutamine, rather than acid cyce intermediate α-ketogutarate, a reaction catayzed ammonium ion, provides the nitrogen. Bacteria asparagine by mitochondria gutamate dehydrogenase (Figure 27–1). synthetases can, however, aso use ammonium ion. The reac- The reaction both strongy favors gutamate synthesis and tion invoves the intermediate formation of asparty phosphate owers the concentration of cytotoxic ammonium ion. (Figure 27–6). The couped hydroysis of PPi to Pi by pyro- phosphatase, EC 3.6.1.1, ensures that the reaction is strongy favored. Glutamine The amidation of gutamate to gutamine catayzed by gutamine Serine synthetase (Figure 27–2) invoves the intermediate formation of Oxidation of the α-hydroxy group of the gycoytic interme- γ-gutamy phosphate (Figure 27–3). Foowing the ordered bind- diate 3-phosphogycerate, catayzed by 3-phosphogycerate ing of gutamate and ATP, gutamate attacks the γ-phosphorus of dehydrogenase, converts it to 3-phosphohydroxypyruvate. ATP, forming γ-gutamy phosphate and ADP. NH4+ then binds, Transamination and subsequent dephosphoryation then and uncharged NH3 attacks γ-gutamy phosphate. Reease of Pi form serine (Figure 27–7). and of a proton from the γ-amino group of the tetrahedra inter- mediate then aows reease of the product, gutamine. Glycine Gycine aminotransferases can catayze the synthesis of gy- Alanine & Aspartate cine from gyoxyate and gutamate or aanine. Unike most Transamination of pyruvate forms aanine (Figure 27–4). Simi- aminotransferase reactions, is strongy favored gycine syn- ary, transamination of oxaoacetate forms aspartate. thesis. Additiona important mammaian routes for gycine formation are from choine (Figure 27–8) and from serine (Figure 27–9). NH3+ NH3+ – O O– H2N O– O O O O L-Glutamate L-Glutamine NH4+ Mg-ATP Mg-ADP + Pi FIGURE 27–4 Formation of alanine by transamination of FIGURE 27–2 The reaction catalyzed by glutamine synthetase pyruvate. The amino donor may be glutamate or aspartate. The other (EC 6.3.1.2). product thus is α-ketoglutarate or oxaloacetate. 276 SECTION VI Metabolism of Proteins & Amino Acids + + O NH 3 O NH 3 – – O O – O H 2N O O L-Aspartate L-Asparagine H2O + Gln Glu Mg-ATP Mg-AMP + PPi FIGURE 27–5 The reaction catalyzed by asparagine synthe- tase (EC 6.3.5.4). Note similarities to and differences from the gluta- mine synthetase reaction (Figure 27–2). FIGURE 27–7 Serine biosynthesis. Oxidation of Proline 3-phosphoglycerate is catalyzed by 3-phosphoglycerate dehydroge- The initia reaction of proine biosynthesis converts the nase (EC 1.1.1.95). Transamination converts phosphohydroxypyruvate γ-carboxy group of gutamate to the mixed acid anhydride of to phosphoserine. Hydrolytic removal of the phosphoryl group cata- lyzed by phosphoserine hydrolase (EC 3.1.3.3) then forms l-serine. gutamate γ-phosphate (see Figure 27–3). Subsequent reduc- tion forms gutamate γ-semiadehyde, which foowing spon- taneous cycization is reduced to l-proine (Figure 27–10). Cysteine Whie not itsef nutritionay essentia, cysteine is formed from methionine, which is nutritionay essentia. Foowing con- version of methionine to homocysteine (see Figure 29–18), homocysteine and serine form cystathionine, whose hydroy- sis forms cysteine and homoserine (Figure 27–11). Tyrosine Phenyaanine hydroxyase converts phenyaanine to tyro- sine (Figure 27–12). If the diet contains adequate quantities of the nutritionay essentia amino acid phenyaanine, tyrosine is nutritionay nonessentia. However, since the phenyaanine hydroxyase reaction is irreversibe, dietary tyrosine cannot repace phenyaanine. Cataysis by this mixed-function oxidase incorporates one atom of O2 into the para position of phenyaa- nine and reduces the other atom to water. Reducing power, pro- vided as tetrahydrobiopterin, derives utimatey from NADPH. Hydroxyproline & Hydroxylysine FIGURE 27–8 Formation of glycine from choline. Catalysts Hydroxyproine and hydroxyysine occur principay in coagen. include choline dehydrogenase (EC 1.1.3.17), betaine aldehyde dehy- Since there is no tRNA for either hydroxyated amino acid, nei- drogenase (EC 1.2.1.8), betaine-homocysteine N-methyltransferase (EC 2.1.1.157), sarcosine dehydrogenase (EC 1.5.8.3), and dimethylgly- ther dietary hydroxyproine nor dietary hydroxyysine is incor- cine dehydrogenase (EC 1.5.8.4). porated during protein synthesis. Peptidy hydroxyproine and hydroxyysine arise from proine and ysine, but ony after these Methylene amino acids have been incorporated into peptides. Hydroxyation H4 folate H4 folate of peptidy proy and peptidy ysy residues, catayzed by prolyl NH3+ NH3+ hydroxylase and lysyl hydroxylase of skin, skeeta musce, and O – O– + HO O O O NH 3 – Serine H2O Glycine O –O PO 3 O FIGURE 27–9 Interconversion of serine and glycine, cata- lyzed by serine hydroxymethyltransferase (EC 2.1.2.1). The reac- FIGURE 27–6 Aspartyl phosphate. tion is freely reversible. (H4 folate, tetrahydrofolate.)  CHAPTER 27 Biosynthesis of the Nutritionally Nonessential Amino Acids 277 FIGURE 27–11 Conversion of homocysteine and serine to homoserine and cysteine. The sulfur of cysteine derives from methio- nine and the carbon skeleton from serine. The catalysts are cystathionine β-synthase (EC 4.2.1.22) and cystathionine γ-lyase (EC 4.4.1.1). Valine, Leucine, & Isoleucine Whie eucine, vaine, and isoeucine are a nutritionay essentia amino acids, tissue aminotransferases reversiby interconvert a three amino acids and their corresponding α-keto acids. FIGURE 27–10 Biosynthesis of proline from glutamate. Catalysts for these reactions are glutamate-5-kinase (EC 2.7.2.11), glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41), and pyrroline- 5-carboxylate reductase (EC 1.5.1.2). Ring closure of glutamate semi- aldehyde is spontaneous. granuating wounds requires, in addition to the substrate, moec- uar O2, ascorbate, Fe2+, and α-ketogutarate (Figure 27–13). For every moe of proine or ysine hydroxyated, one moe of α-ketogutarate is decarboxyated to succinate. The hydroxyases are mixed-function oxidases. One atom of O2 is incorporated into proine or ysine, the other into succinate (see Figure 27–13). A FIGURE 27–12 Conversion of phenylalanine to tyrosine by deficiency of the vitamin C required for these two hydroxyases phenylalanine hydroxylase (EC 1.14.16.1). Two distinct enzymatic activities are involved. Activity II catalyzes reduction of dihydrobiop- resuts in scurvy, in which beeding gums, sweing joints, and terin by NADPH, and activity I the reduction of O2 to H2O and of phe- impaired wound heaing resut from the impaired stabiity of co- nylalanine to tyrosine. This reaction is associated with several defects agen (see Chapters 5 and 50). of phenylalanine metabolism discussed in Chapter 29. 278 SECTION VI Metabolism of Proteins & Amino Acids Subsequent repacement of the serine oxygen by seenium invoves seenophosphate formed by seenophosphate synthe- tase (see Figure 27–14). Successive enzyme-catayzed reactions convert cystey-tRNASec to aminoacryy-tRNASec and then to seenocystey-tRNASec. In the presence of a specific eongation factor that recognizes seenocystey-tRNASec, seenocysteine FIGURE 27–13 Hydroxylation of a proline-rich peptide. can then be incorporated into proteins. Molecular oxygen is incorporated into both succinate and proline. Procollagen-proline 4-hydroxylase (EC 1.14.11.2) thus is a mixed- function oxidase. Procollagen-lysine 5-hydroxylase (EC 1.14.11.4) SUMMARY catalyzes an analogous reaction. A vertebrates can form certain amino acids from amphiboic intermediates or from other dietary amino acids. The These α-keto acids thus can repace their corresponding amino intermediates and the amino acids to which they give rise are acids in the diet. α-ketogutarate (Gu, Gn, Pro, Hyp), oxaoacetate (Asp, Asn), and 3-phosphogycerate (Ser, Gy). Selenocysteine, the 21st Amino Acid Cysteine, tyrosine, and hydroxyysine are formed from nutritionay essentia amino acids. Serine provides the carbon Whie the occurrence of seenocysteine (Figure 27–14) in pro- skeeton and homocysteine the sufur for cysteine biosynthesis. teins is reativey uncommon, at east 25 human seenoproteins In scurvy, a nutritiona disease that resuts from a deficiency are known. Seenocysteine is present at the active site of severa of vitamin C, impaired hydroxyation of peptidy proine and human enzymes that catayze redox reactions. Exampes incude peptidy ysine resuts in a faiure to provide the substrates for thioredoxin reductase, gutathione peroxidase, and the deiodinase cross-inking of maturing coagens. that converts thyroxine to triiodothyronine. Where present, Phenyaanine hydroxyase converts phenyaanine to tyrosine. seenocysteine participates in the cataytic mechanism of these Since the reaction catayzed by this mixed function oxidase is enzymes. Significanty, the repacement of seenocysteine by irreversibe, tyrosine cannot give rise to phenyaanine. cysteine can actuay reduce cataytic activity. Impairments in Neither dietary hydroxyproine nor hydroxyysine is human seenoproteins have been impicated in tumorgenesis incorporated into proteins because no codon or tRNA dictates and atheroscerosis, and are associated with seenium deficiency their insertion into peptides. cardiomyopathy (Keshan disease). Peptidy hydroxyproine and hydroxyysine are formed Biosynthesis of seenocysteine requires serine, seenate by hydroxyation of peptidy proine or ysine in reactions (SeO42−), ATP, a specific tRNA, and severa enzymes. Serine pro- catayzed by mixed-function oxidases that require vitamin C as vides the carbon skeeton of seenocysteine. Seenophosphate, cofactor. formed from ATP and seenate (see Figure 27–14), serves as the Seenocysteine, an essentia active site residue in severa seenium donor. Unike 4-hydroxyproine or 5-hydroxyysine, mammaian enzymes, arises by cotransationa insertion from a seenocysteine arises cotranslationally during its incorporation previousy modified tRNA. into peptides. The UGA anticodon of the unusua tRNA caed tRNASec normay signas STOP. The abiity of the protein syn- thetic apparatus to identify a seenocysteine-specific UGA REFERENCES codon invoves the seenocysteine insertion eement, a stem- Gadyshev VN, Arner ES, Brigeius FR, et a: Seenoprotein gene oop structure in the untransated region of the mRNA. tRNASec nomencature. J Bio Chem 2016;291:20436. is first charged with serine by the igase that charges tRNASer. Kiberg MS: Asparagine synthetase chemotherapy. Annu Rev Biochem 2006;75:629. Rayman RP: Seenium and human heath. Lancet H 2012;379;9822;1256. H Se CH2 C COO– Ruzzo EK, Capo-Chichi JM, Ben-Zeev B, et a: Deficiency of NH3+ asparagine synthetase causes congenita microcephay and a O progressive form of encephaopathy. Neuron 2013;80:429. Sticke F, Inderbitzin D, Candinas D: Roe of nutrition in iver Se + ATP + H2O AMP + Pi + H Se P O– transpantation for end-stage chronic iver disease. Nutr Rev O– 2008;66:47. Turanov AA, Shchedrina VA, Everey RA, et a: Seenoprotein S FIGURE 27–14 Selenocysteine (top) and the reaction cata- is invoved in maintenance and transport of mutiprotein lyzed by selenophosphate synthetase (EC 2.7.9.3) (bottom). compexes. Biochem J 2014;462:555.