Amino acid ammonia lyases

Many amino acids can lose ammonia to give an unsaturated acid. The enzymes that catalyse these reactions are known as amino acid ammonia lyases. The one that concerns us at the end of the shikimic acid pathway is phenylalanine ammonia lyase, which catalyses the elimination of ammonia from phenylalanine to give the common metabolite cinnamic acid. 

PAL/TAL both belong to the L-amino acid ammonia lyase family, which catalyzes the formation of various a,/3-unsaturated acids by elimination of ammonia (ammonium ion) from the corresponding L-ct-amino acids. This family of proteins includes aspartate ammonia lyase (AAL), methylaspartate ammonia lyase (MAL), HAL,... 

Amino acid ammonia lyases [EC 4.3.1.n] Aminoacid - a, -unsaturated acid -1- NH3 Amino acid, unsaturated acid NH3 Potentiometric electrode, FET... 

Recently a number of enzymatic systems have been developed at several chemical companies including Upases (synthesis of enantiotrope alcohols, R-amid, S-amin), nitrilases (R-mandehc acid), amidases (non-proteinogenic L-amino acids), aspartic acid ammonia lyase (L-aspartic add), penicilin acylase (6-Aminopenicilanic acid), acylases (semisynthetic penicillins), etc.( Koeller and Wong, 2001 and references therin). 

A PNH3 electrode covered with this enzyme is used [123] for the determination of L-phenylalanine with very little interference fiom otho amino acids, notably L-tyrosine. A similar selectivity is obtained with phenylalanine decarboxylase [103] which, when attached to a pC02 electrode, enables the specific determination of phenylalanine. Other ammonia lyases are used te determine amino acids. Methionine lyase [124] and histidine ammonia lyase [12S] produce ammonia which is detected with a PNH3 electrode. 

Phenylalanine ammonia-lyase (PAL EC 4.3.1.5) is a pivotal enzyme in controlling flow of carbon from aromatic amino acids to secondary aromatic compounds (Figure 1) (28). PAL primarily deaminates phenylalanine to form t-cinnamic acid, however, in many species, it also less efficiently deaminates tyrosine to form -coumaric acid. Because PAL is restricted to plants and is an important enzyme in plant development, Jangaard (29) suggested that PAL inhibitors might make safe and effective herbicides, however, in his screen of several herbicides, he found no compound to have a specific effect on PAL. This was also the case in studies by Hoagland and Duke (30, 31.) in which 16 herbicides were screened. 

Watts KT, Mijts BN, Lee PC, Manning AJ, Schmidt-Dannert C (2006) Discovery of a substrate selectivity switch in tyrosine ammonia-lyase, a member of the aromatic amino acid lyase family. Chem Biol 13(12) 1317-1326... 

A specialized amino acid residue that serves as an essesn-tial electrophilic center in several enzymatic reactions, including those catalyzed by L-phenylalanine ammonia lyase (Reaction L-phenylalanine tranx-cinnamate + NH3) and L-histidine ammonia lyase (Reaction L-histi-dine urocanate + NH3). The former facilitates the elimination of ammonia and the pro-S hydrogen of phe-nylanine, and the initial step is nucleophilic attack of... 

This enzyme [EC 4.1.99.1], also known as L-tryptophan indole-lyase, catalyzes the hydrolysis of L-tryptophan to generate indole, pyruvate, and ammonia. The reaction requires pyridoxal phosphate and potassium ions. The enzyme can also catalyze the synthesis of tryptophan from indole and serine as well as catalyze 2,3-elimination and j8-replacement reactions of some indole-substituted tryptophan analogs of L-cysteine, L-serine, and other 3-substituted amino acids. 

PHENYLALANINE AMINOTRANSFERASE PHENYLALANINE AMMONIA-LYASE PHENYLALANINE DECARBOXYLASE PHENYLALANINE DEHYDROGENASE PHENYLALANINE MONOOXYGENASE PHENYLALANINE RACEMASE PHENYLALANINE AMINOTRANSFERASE AROMATIC AMINO ACID AMINOTRANSFERASE... 

Ammonia lyases catalyze the enantioselective addition of ammonia to an activated double bond. A one-pot, three-step protocol was developed for the enantioselective synthesis of L-arylalanines 50 using phenylalanine ammonia lyase (PAL) in the key step (Scheme 2.20). After formation of the unsaturated esters 48 in situ via a Wittig reaction from the corresponding aldehydes, addition of porcine Ever esterase and basification of the reaction mixture resulted in hydrolysis to the carboxylic acids 49. Once this reaction had gone to completion, introduction of PAL and further addition of ammonia generated the amino acids 50 in good yield and excellent optical purity [22]. 

Phenylalanine Ammonia-Lyase. The building units of lignin are formed from carbohydrate via the shikimic acid pathway to give aromatic amino acids. Once the aromatic amino acids are formed, a key enzyme for the control of lignin precursor synthesis is phenylalanine ammonia-lyase (PAL) (1). This enzyme catalyzes the production of cinnamic acid from phenylalanine. It is very active in those tissues of the plant that become lignified and it is also a central enzyme for the production of other phenylpropanoid-derived compounds such as flavonoids and coumarins, which can occur in many parts of the plant and in many different organs (35). Radioactive phenylalanine and cinnamic acid are directly incorporated into lignin in vascular tissue (36). 

When soybean leaves and pine needles were exposed to ozone, there was an initial decrease in the levels of soluble sugars followed by a subsequent increase. Ozone exposure also caused a decrease in the activity of the glycolytic pathway and the decrease in the activity was reflected in a lowered rate of nitrate reduction. Amino acids and protein also accumulated in soybean leaves following exposure. Ozone increased the activities of enzymes involved in phenol metabolism (phenylalanine ammonia lyase and polyphenoloxidase). There was also an increase in the levels of total phenols. Leachates from fescue leaves exposed to ozone inhibited nodulation. 

Coumaroyl-CoA is produced from the amino acid phenylalanine by what has been termed the general phenylpropanoid pathway, through three enzymatic conversions catalyzed by phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), and 4-coumarate CoA ligase (4CL). Malonyl-CoA is formed from acetyl-CoA by acetyl-CoA carboxylase (ACC) (Figure 3.2). Acetyl-CoA may be produced in mitochondria, plastids, peroxisomes, and the cytosol by a variety of routes. It is the cytosolic acetyl-CoA that is used for flavonoid biosynthesis, and it is produced by the multiple subunit enzyme ATP-citrate lyase that converts citrate, ATP, and Co-A to acetyl-CoA, oxaloacetate, ADP, and inorganic phosphate. ... 

FIGURE 18-26 Catabolic pathways for arginine, histidine, glutamate, glutamine, and proline. These amino acids are converted to a-ketoglutarate. The numbered steps in the histidine pathway are catalyzed by histidine ammonia lyase, urocanate hydratase, imida-zolonepropionase, and glutamate formimino transferase. 

Some of the pathways of animal and bacterial metabolism of aromatic amino acids also are used in plants. However, quantitatively more important are the reactions of the phenylpropanoid pathway,173-1743 which is initiated by phenylalanine ammonia-lyase (Eq. 14-45).175 As is shown at the top of Fig. 25-8, the initial product from phenylalanine is trails-cinnam-ate. After hydroxylation to 4-hydroxycinnamate (p-coumarate) and conversion to a coenzyme A ester,1753 the resulting p-coumaryl-CoA is converted into mono-, di-, and trihydroxy derivatives including anthocyanins (Box 21-E) and other flavonoid compounds.176 The dihydroxy and trihydroxy methylated products are the starting materials for formation of lignins and for a large series of other plant products, many of which impart characteristic fragrances. Some of these are illustrated in Fig. 25-8. 

A large number of a, 3-didehydro-a-amino acids have been identified as constituents of relatively low molecular weight cyclic compounds from microbial sources. However, the presence of a,p-didehydroalanine in bacterial as well as in mammalian histidine ammonia lyase and in phenylalanine ammonia lyase shows that the occurrence of a,p-didehydro-a-amino acids is not limited to small molecules alone 8 These residues are incorporated in natural sequences by posttranslation modification. a,p-Didehydro-a-amino acids have also been postulated to be precursors in the biosynthesis of several heterocyclic metabolites including penicillin and cephalosporin 9 Other well-known compounds containing ,( -di-dehydro-a-amino acids are nisin 10,11 (a food preservative112 ), subtilin (a broad spectrum antibiotic) 13 and some of the metabolites isolated from Streptomyces strains such as gri-seoviridin 14 ... 

Free amino acids are further catabolized into several volatile flavor compounds. However, the pathways involved are not fully known. A detailed summary of the various studies on the role of the catabolism of amino acids in cheese flavor development was published by Curtin and McSweeney (2004). Two major pathways have been suggested (1) aminotransferase or lyase activity and (2) deamination or decarboxylation. Aminotransferase activity results in the formation of a-ketoacids and glutamic acid. The a-ketoacids are further degraded to flavor compounds such as hydroxy acids, aldehydes, and carboxylic acids. a-Ketoacids from methionine, branched-chain amino acids (leucine, isoleucine, and valine), or aromatic amino acids (phenylalanine, tyrosine, and tryptophan) serve as the precursors to volatile flavor compounds (Yvon and Rijnen, 2001). Volatile sulfur compounds are primarily formed from methionine. Methanethiol, which at low concentrations, contributes to the characteristic flavor of Cheddar cheese, is formed from the catabolism of methionine (Curtin and McSweeney, 2004 Weimer et al., 1999). Furthermore, bacterial lyases also metabolize methionine to a-ketobutyrate, methanethiol, and ammonia (Tanaka et al., 1985). On catabolism by aminotransferase, aromatic amino acids yield volatile flavor compounds such as benzalde-hyde, phenylacetate, phenylethanol, phenyllactate, etc. Deamination reactions also result in a-ketoacids and ammonia, which add to the flavor of... 

In addition to resolution approaches, there are three main methods to prepare amino acids by biological methods addition of ammonia to an unsaturated carboxylic acid the conversion of an a-keto acid to an amino acid by transamination from another amino acid, and the reductive animation of an a-keto acid. These approaches are discussed in Chapter 19 and will not be discussed here to avoid duplication. The use of a lyase to prepare L-aspartic acid is included in this chapter as is the use of decarboxylases to access D-glutamic acid. 

Lyases are an attractive group of enzymes from a commercial perspective, as demonstrated by then-use in many industrial processes.240 They catalyze the cleavage of C-C, C-N, C-O, and other bonds by means other than hydrolysis, often forming double bonds. For example, two well-studied ammonia lyases, aspartate ammonia lyase (aspartase) (E.C. 4.3.1.1) and phenylalanine ammonia lyase (PAL) (E.C. 4.3.1.5), catalyze the trans-elimination of ammonia from the amino acids, l-aspartate and L-phenylalanine, respectively. Most commonly used in the synthetic mode, the reverse reaction has been used to prepare the L-amino acids at the ton scale (Schemes 19.30 and 19.31).240 242 These reactions are conducted at very high substrate concentrations such that the equilibrium is shifted, resulting in very high conversion to the amino acid products. 

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