Serine-202 is the putative precursor of the active site dehydroalanine of phenylalanine ammonia lyase. Site-directed mutagenesis studies on the enzyme from parsley (Petroselinum crispum L.)

Molecular cloning, functional characterization and expression of a drought inducible phenylalanine ammonia-lyase gene (ObPAL) from Ocimum basilicum L

Phenylalanine ammonia-lyase (PAL) is a control point for branched phenylpropanoid and terpenoid pathways. It represents the first regulatory step to provide a metabolic flux to produce of the precursors needed for biosynthesizing main volatile phenylpropanoid compounds (methyleugenol and methylchavicol) in basil. It is crucial during the stage of the environmental and development stimulants. To obtain better knowledge of the biosynthesis of these phenylpropene compounds, characterization and cloning of Ocimum basilicum PAL (ObPAL) cDNA and its heterologous expression and enzyme activity were assessed. The almost full-length ObPAL was 2064 bp in size encoding a 687-amino-acid polypeptide with molecular weight of 74.642 kDa and theoretical pI of 8.62. Phylogenetic analysis revealed a significant evolutionary relatedness of ObPAL with the PAL sequence reported in different species of Lamiaceae. To further confirm its function, ObPAL was cloned into pET28a (+) vector and expressed in E. coli. The recombinant protein exhibited high PAL activity and could catalyze the L-Phe conversion to trans-cinnamic acid. Expression analysis of PAL gene showed that ObPAL manifested various transcription ratios exposed to drought stress. Overall, our results demonstrated the ObPAL regulation gene is possibly a mechanism dependent on cultivar and drought stress.

Expression of Genes Related to Phenylpropanoid Biosynthesis in Different Organs of Ixeris dentata var. albiflora

Members of the genus Ixeris have long been used in traditional medicines as stomachics, sedatives, and diuretics. Phenylalanine ammonia-lyase (PAL), cinnamate-4-hydroxylase (C4H), 4-coumarate: coenzyme-A (CoA) ligase (4CL), chalcone synthase (CHS), and dihydroflavonol 4-reductase (DFR) are important enzymes in the phenylpropanoid pathway. In this study, we analyzed seven genes from Ixeris dentata var. albiflora that are involved in phenylpropanoid biosynthesis, using an Illumina/Solexa HiSeq 2000 platform. The amino acid sequence alignments for IdPALs, IdC4H, Id4CLs, IdCHS, and IdDFR showed high identity to sequences from other plants. We also investigated transcript levels using quantitative real-time PCR, and analyzed the accumulation of phenylpropanoids in different organs of I. dentata var. albiflora using high-performance liquid chromatography. The transcript levels of IdC4H, Id4CL1, IdCHS, and IdDFR were highest in the leaf. The catechin, chlorogenic acid, ferulic acid, and quercetin contents were also highest in the leaf. We suggest that expression of IdC4H, Id4CL1, IdCHS, and IdDFR is associated with the accumulation of phenylpropanoids. Our results may provide baseline information for elucidating the mechanism of phenylpropanoid biosynthesis in different organs of I. dentata var. albiflora.

Phenylalanine ammonia-lyase, a key component used for phenylpropanoids production by metabolic engineering

Phenylalanine ammonia-lyase, a versatile enzyme with industrial and medical applications.

Molecular cloning and characterization of genes involved in rosmarinic acid biosynthesis from Prunella vulgaris

Prunella vulgaris L., commonly known as "self-heal" or "heal-all," is a perennial herb with a long history of medicinal use. Phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), and 4-coumarate:coenzyme-A (CoA) ligase (4CL) are important enzymes in the phenylpropanoid pathway and in the accumulation of rosmarinic acid (RA), which is a major secondary metabolite in P. vulgaris. In this study, we isolated cDNAs encoding PvPAL, PvC4H, and Pv4CL from P. vulgaris using rapid amplification of cDNA ends polymerase chain reaction (PCR). The amino acid sequence alignments of PvPAL, PvC4H, and Pv4CL showed high sequence identity to those of other plants. Quantitative real-time PCR analysis was used to determine the transcript levels of genes involved in RA biosynthesis in the flowers, leaves, stems, and roots of P. vulgaris. The transcript levels of PvPAL, PvC4H, and Pv4CL1 were the highest in flowers, whereas Pv4CL2 was the highest in roots. High-performance liquid chromatography analysis also showed the highest RA content in the flowers (3.71 mg/g dry weight). We suggest that the expression of the PvPAL, PvC4H, and Pv4CL1 genes is correlated with the accumulation of RA. Our results revealed that P. vulgaris flowers are appropriate for medicinal usage, and our findings provide support for increasing RA production in this plant.

Expression and properties of the highly alkalophilic phenylalanine ammonia-lyase of thermophilic Rubrobacter xylanophilus

The sequence of a phenylalanine ammonia-lyase (PAL; EC: 4.3.1.24) of the thermophilic and radiotolerant bacterium Rubrobacter xylanophilus (RxPAL) was identified by screening the genomes of bacteria for members of the phenylalanine ammonia-lyase family. A synthetic gene encoding the RxPAL protein was cloned and overexpressed in Escherichia coli TOP 10 in a soluble form with an N-terminal His6-tag and the recombinant RxPAL protein was purified by Ni-NTA affinity chromatography. The activity assay of RxPAL with l-phenylalanine at various pH values exhibited a local maximum at pH 8.5 and a global maximum at pH 11.5. Circular dichroism (CD) studies showed that RxPAL is associated with an extensive α-helical character (far UV CD) and two distinctive near-UV CD peaks. These structural characteristics were well preserved up to pH 11.0. The extremely high pH optimum of RxPAL can be rationalized by a three-dimensional homology model indicating possible disulfide bridges, extensive salt-bridge formation and an excess of negative electrostatic potential on the surface. Due to these properties, RxPAL may be a candidate as biocatalyst in synthetic biotransformations leading to unnatural l- or d-amino acids or as therapeutic enzyme in treatment of phenylketonuria or leukemia.

Characterization, high-resolution mapping and differential expression of three homologous PAL genes in Coffea canephora Pierre (Rubiaceae)

Phenylalanine ammonia lyase (PAL) is the first entry enzyme of the phenylpropanoid pathway producing phenolics, widespread constituents of plant foods and beverages, including chlorogenic acids, polyphenols found at remarkably high levels in the coffee bean and long recognized as powerful antioxidants. To date, whereas PAL is generally encoded by a small gene family, only one gene has been characterized in Coffea canephora (CcPAL1), an economically important species of cultivated coffee. In this study, a molecular- and bioinformatic-based search for CcPAL1 paralogues resulted successfully in identifying two additional genes, CcPAL2 and CcPAL3, presenting similar genomic structures and encoding proteins with close sequences. Genetic mapping helped position each gene in three different coffee linkage groups, CcPAL2 in particular, located in a coffee genome linkage group (F) which is syntenic to a region of Tomato Chromosome 9 containing a PAL gene. These results, combined with a phylogenetic study, strongly suggest that CcPAL2 may be the ancestral gene of C. canephora. A quantitative gene expression analysis was also conducted in coffee tissues, showing that all genes are transcriptionally active, but they present distinct expression levels and patterns. We discovered that CcPAL2 transcripts appeared predominantly in flower, fruit pericarp and vegetative/lignifying tissues like roots and branches, whereas CcPAL1 and CcPAL3 were highly expressed in immature fruit. This is the first comprehensive study dedicated to PAL gene family characterization in coffee, allowing us to advance functional studies which are indispensable to learning to decipher what role this family plays in channeling the metabolism of coffee phenylpropanoids.

Molecular cloning and characterization of phenylalanine ammonia-lyase and cinnamate 4-hydroxylase in the phenylpropanoid biosynthesis pathway in garlic (Allium sativum)

The cDNAs encoding phenylalanine ammonia-lyase (PAL) and cinnamate 4-hydroxylase (C4H) were cloned from garlic (Allium sativum) using reverse transcription-polymerase chain reaction (RT-PCR) with degenerate primers and 5' and 3' rapid amplification of cDNA ends (RACE) PCR. Amino acid sequence alignments showed that AsPAL and AsC4H have more than 70% amino acid identity with their homologues in other plants. The expression of AsPAL and AsC4H transcripts was highest in the roots but surprisingly low in the bulbils, where phenylpropanoid compounds are most concentrated. These results suggest that some phenylpropanoids are synthesized in the roots and subsequently transported to the bulbils of A. sativum .

Characterization and differential expression analysis of artichoke phenylalanine ammonia-lyase-coding sequences

Sequences encoding phenylalanine ammonia-lyase were isolated from artichoke, by using a sequence homology strategy, by screening a genomic library and by 3'-rapid amplification of cDNA end (RACE) technology. These analyses and Southern blots suggested that, in artichoke, phenylalanine ammonia-lyase (PAL) is encoded by a small gene family. The sequences isolated from genomic DNA possess two exons and one intron at the conserved position as in most plant pal characterized to date. The 3'-RACE analysis also indicated that each member of the artichoke pal gene family was present as a pool of transcripts, different in the length of 3'-untranslated region. The deduced amino acid sequences were highly similar to those of PAL from lettuce and sunflower. One of the artichoke pal genes was completely sequenced, and its 5' upstream region contained TATA, CAAT box and cis regulatory elements identified in other phenylpropanoid pathway genes as playing a role in UV and elicitor induction. The expression of three of the identified artichoke pal sequences was evaluated in different plant parts, in developmental stages and after wounding, using gene-specific primers/probe combinations in real-time polymerase chain reaction assays. The three putative genes were differentially expressed in the plant parts analysed and were developmentally regulated. Moreover, after leaf mechanical injury, all of them were differentially regulated. The possible involvement of the single pal genes in different physiological processes is discussed.

Friedel-Crafts-type mechanism for the enzymatic elimination of ammonia from histidine and phenylalanine

The surprisingly high catalytic activity and selectivity of enzymes stem from their ability to both accelerate the target reaction and suppress competitive reaction pathways that may even be dominant in the absence of enzymes. For example, histidine and phenylalanine ammonia-lyases (HAL and PAL) trigger the abstraction of the nonacidic beta protons of these amino acids while leaving the much more acidic ammonium hydrogen atoms untouched. Both ammonia-lyases have a catalytically important electrophilic group, which was believed to be dehydroalanine for 30 years but has now been revealed by X-ray crystallography and UV spectroscopy to be a highly electrophilic 5-methylene-3,5-dihydroimidazol-4-one (MIO) group. Experiments suggest that the reaction is initiated by the electrophilic attack of MIO on the aromatic ring of the substrate. This incomplete Friedel-Crafts-type reaction leads to the activation of a beta proton and its stereospecific abstraction, followed by the elimination of ammonia and regeneration of the MIO group. The plausibility of such a mechanism is supported by a synthetic model. The application of the PAL reaction in the biocatalytic synthesis of enantiomerically pure alpha-amino beta-aryl propionates from aryl acrylates is also discussed.

Isolation and genetic mapping of a Coffea canephora phenylalanine ammonia-lyase gene (CcPAL1) and its involvement in the accumulation of caffeoyl quinic acids

Biosynthesis of caffeoylquinic acids occurs via the phenylpropanoid pathway in which the phenylalanine ammonia-lyase (PAL) acts as a key-control enzyme. A full-length cDNA (pF6), corresponding to a PAL gene (CcPAL1), was isolated by screening a Coffea canephora fruit cDNA library and its corresponding genomic sequence was characterized. Amplification of total DNA from seven Coffea species revealed differences in intronic length. This interspecific polymorphism was used to locate the gene on a genetic map established for a backcross progeny between Coffea pseudozanguebariae and C. dewevrei. The CcPAL1 gene was found on the same linkage group, but genetically independent, as a caffeoyl-coenzyme A-O-methyltransferase gene, another gene intervening in the phenylpropanoid pathway. In the same backcross, a lower caffeoylquinic acid content was observed in seeds harvested from plants harbouring the C. pseudozanguebariae CcPAL1 allele. Involvement of the CcPAL1 allelic form in the differential accumulation of caffeoylquinic acids in coffee green beans is then discussed.

The interaction of heteroaryl-acrylates and alanines with phenylalanine ammonia-lyase from parsley

Acrylic acids and alanines substituted with heteroaryl groups at the beta-position were synthesized and spectroscopically characterized (UV, HRMS, (1)H NMR, and (13)C NMR spectroscopy). The heteroaryl groups were furanyl, thiophenyl, benzofuranyl, and benzothiophenyl and contained the alanyl side chains either at the 2- or 3-positions. While the former are good substrates for phenylalanine ammonia-lyase (PAL), the latter compounds are inhibitors. Exceptions are thiophen-3-yl-alanine, a moderate substrate and furan-3-yl-alanine, which is inert. Possible reasons for these exceptions are discussed. Starting from racemic heteroaryl-2-alanines their D-enantiomers were prepared by using a stereodestructive procedure. From the heteroaryl-2-acrylates, the L-enantiomers of the heteroaryl-2-alanines were prepared at high ammonia concentration. These results can be best explained by a Friedel-Crafts-type electrophilic attack at the aromatic part of the substrates as the initial step of the PAL reaction.

Genomic evidences for the existence of a phenylpropanoid metabolic pathway in Aspergillus oryzae

Plants interact with their environment by producing a diverse array of secondary metabolites. A majority of these compounds are phenylpropanoids and flavonoids which are valued for their medicinal and agricultural properties. The phenylpropanoid biosynthesis pathway proceeds with the basic C6-C3 carbon skeleton of phenylalanine, and involves a wide range of enzymes viz., phenylalanine ammonia lyase, coumarate hydroxylase, coumarate ligase, chalcone synthase, chalcone reductase and chalcone isomerase. Recently, bacteria have also been shown to contain homodimeric polyketide synthases belonging to the plant chalcone synthase superfamily linking the capabilities of plants and bacteria in the biosynthesis of flavonoids. We report here the presence of genes encoding the core enzymes of the phenylpropanoid pathway in an industrially useful fungus, Aspergillus oryzae. Although the assignment of enzyme function must be confirmed by further biochemical evidences, this work has allowed us to anticipate the phenylpropanoid metabolism profile in a filamentous fungus for the first time and paves way for research on identifying novel fungal flavonoid-like metabolites.

Inhibitors of phenylalanine ammonia-lyase: 1-aminobenzylphosphonic acids substituted in the benzene ring

Dextrorotatory 1-amino-3',4'-dichlorobenzylphosphonic acid was found to be a potent inhibitor of the plant enzyme phenylalanine ammonia-lyase both in vitro and in vivo from among the ring-substituted 1-aminobenzylphosphonic acids and other analogues of phenylglycine. A structure activity relationship analysis of the results obtained permits predictions on the geometry of the pocket of the enzyme and is a basis in the strategy of better inhibitor synthesis.

Characterization of the active site of histidine ammonia-lyase from Pseudomonas putida

Elucidation of the 3D structure of histidine ammonia-lyase (HAL, EC 4.3.1.3) from Pseudomonas putida by X-ray crystallography revealed that the electrophilic prosthetic group at the active site is 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) [Schwede, T.F., Rétey, J., Schulz, G.E. (1999) Biochemistry, 38, 5355-5361]. To evaluate the importance of several amino-acid residues at the active site for substrate binding and catalysis, we mutated the following amino-acid codons in the HAL gene: R283, Y53, Y280, E414, Q277, F329, N195 and H83. Kinetic measurements with the overexpressed mutants showed that all mutations resulted in a decrease of catalytic activity. The mutants R283I, R283K and N195A were approximately 1640, 20 and 1000 times less active, respectively, compared to the single mutant C273A, into which all mutations were introduced. Mutants Y280F, F329A and Q277A exhibited approximately 55, 100 and 125 times lower activity, respectively. The greatest loss of activity shown was in the HAL mutants Y53F, E414Q, H83L and E414A, the last being more than 20 900-fold less active than the single mutant C273A, while H83L was 18 000-fold less active than mutant C273A. We propose that the carboxylate group of E414 plays an important role as a base in catalysis. To investigate a possible participation of active site amino acids in the formation of MIO, we used the chromophore formation upon treatment of HAL with l-cysteine and dioxygen at pH 10.5 as an indicator. All mutants, except F329A showed the formation of a 338-nm chromophore arising from a modified MIO group. The UV difference spectra of HAL mutant F329A with the MIO-free mutant S143A provide evidence for the presence of a MIO group in HAL mutant F329A also. For modelling of the substrate arrangement within the active site and protonation state of MIO, theoretical calculations were performed.

Methylidene-imidazolone: a novel electrophile for substrate activation

The recent three-dimensional structure of histidine ammonia-lyase revealed that the enzyme contains a 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO) ring, which forms autocatalytically from an Ala-Ser143-Gly triad. This novel prosthetic group, which is also present in phenylalanine ammonia-lyase, activates substrates by electrophilic interaction. Modern analytical methods, theoretical calculations and molecular biology tools have given further insight into the mode of action of MIO.

1,4-Dihydro-l-phenylalanine-its synthesis and behavior in the phenylalanine ammonia-lyase reaction

1,4-Dihydro-l-phenylalanine, a nonaromatic derivative of l-phenylalanine, has been isolated for the first time. It was synthesized as a yet unobserved minor product in the Birch reduction of l-phenylalanine. This is unexpected because it has an electron donor substituent at a reduced sp(3)-carbon atom of the ring system. Kinetic measurements with phenylalanine ammonia-lyase showed that 1,4-dihydro-l-phenylalanine is no substrate but a moderately good competitive inhibitor of the enzymatic reaction. This is in agreement with its predicted behavior and provides further evidence for the plausibility of the recently proposed mechanism of action of phenylalanine ammonia-lyase.

Purification and characterization of beta-methylaspartase from Fusobacterium varium

Beta-methylaspartase (EC 4.3.1.2) was purified 20-fold in 35% yield from Fusobacterium varium, an obligate anaerobe. The purification steps included heat treatment, fractional precipitation with ammonium sulfate and ethanol, gel filtration, and ion exchange chromatography on DEAE-Sepharose. The enzyme is dimeric, consisting of two identical 46 kDa subunits, and requires Mg2+ (Km = 0.27+/-0.01 mM) and K+ (Km = 3.3+/-0.8 mM) for maximum activity. Beta-methylaspartase-catalyzed addition of ammonia to mesaconate yielded two diastereomeric amino acids, identified by HPLC as (2S,3S)-3-methylaspartate (major product) and (2S,3R)-3-methylaspartate (minor product). Optimal activity for the deamination of (2S,3S)-3-methylaspartate (Km = 0.51+/-0.04 mM) was observed at pH 9.7. The N-terminal protein sequence (30 residues) of the F. varium enzyme is 83% identical to the corresponding sequence of the clostridial enzyme.

Novel photoreactive cinnamic acid analogues to elucidate phenylalanine ammonia-lyase

4-[3-(Trifluoromethyl) diazirinyl] cinnamic acid derivatives were synthesized to elucidate properties of phenylalanine ammonia-lyase (PAL). 2-Methoxy and 2-biotinylated alkoxy compounds have inhibitory activity on the formation of phenylalanine from cinnamic acid. Specific photolabeling of the enzyme was detected using biotinylated derivatives without the use of radioisotopes. The results indicated that the 4-[3-(trifluoromethyl) diazirinyl] skeleton will be a suitable photoreactive compound to elucidate regulation of phenylpropanoid biosynthesis.

Novel cofactors via post-translational modifications of enzyme active sites

Recent crystallographic and biochemical studies have revealed the existence of numerous novel post-translational modifications within enzyme active sites. These modifications create structural and functional diversity. Although the function and biosynthesis of some of these modifications are well understood, others need further investigation.

The behavior of substrate analogues and secondary deuterium isotope effects in the phenylalanine ammonia-lyase reaction

Metacresol and glycine can be thought as a dissection of metatyrosine, which is an excellent substrate of phenylalanine ammonia-lyase (PAL) (B. Schuster and J. Rétey, PNAS 92, 8433, 1995). Whereas metacresol was a very weak inhibitor and glycine was inert, simultaneous addition of both compounds led to synergistic inhibition of PAL. [2H5]Phenylalanine as a substrate showed a kinetic deuterium isotope effect of 9% (kH/k2H = 1.09 +/- 0.01) while its Km value was identical to that of the unlabeled substrate. The following substrate analogues were synthesized and assayed with PAL: cyclooctatetraenyl (COT)-d,l)-alanine as well as 2-pyridyl-, 3-pyridyl-, and 4-pyridyl-(l)-alanines. While COT-(d,l)-alanine turned out to be a rather reluctant substrate, all three isomers of pyridyl-(l)-alanines were converted with a comparable or even higher Vmax than l-phenylalanine into the corresponding pyridyl acrylic acids. Their Km values were, however, an order of magnitude higher than that of the natural substrate. These results are discussed in terms of the novel mechanism which implies an electrophilic attack of the prosthetic dehydroalanine at the aromatic ring. The heats of formation of the putative sigma complexes of the electrophilic substitution at the pyridine ring have been calculated using semiempirical force-field methods. The results show the feasibility of the proposed mechanism also with the substrate analogues.

Identification of essential amino acids in phenylalanine ammonia-lyase by site-directed mutagenesis

The postulated precursor of the prosthetic dehydroalanine of phenylalanine ammonia-lyase (PAL), serine 202, was changed to cysteine by site-directed mutagenesis. After cloning and heterologous expression in Escherichia coli, the gene product was assayed for PAL activity. Mutant S202C showed full catalytic activity, and its kinetic constants and the amount of thiol groups were identical to those of wild-type PAL. It must be concluded that in a posttranslational modification both water and hydrogen sulfide can be eliminated from the amino acid in position 202 to form dehydroalanine. In an attempt to identify further amino acids essential either for the posttranslational modification or for catalysis, arginine 174, glutamine 425, and lysine 499 were changed to isoleucine. Analysis of the heterologously expressed mutated gene products revealed that only the R174I mutant showed a significantly lower Vmax value (1/450) identifying this arginine as important. This finding was supported by treatment of wild-type PAL and mutant R174I with phenylglyoxal and 2,3-butandione. Both react specifically with the guanidino group of arginine. They irreversibly inhibited wild-type PAL but had no influence of the Vmax value of mutant R174I. Preincubation with l-phenylalanine protected wild-type PAL from inhibition by phenylglyoxal indicating that arginine 174 is close to the active site. Incubation with KCN irreversibly abolished the remaining activity of mutant R174I leading to the conclusion that arginine 174 is important in catalysis.

Enzymatic catalysis by Friedel-Crafts-type reactions

Although most enzymes work in aqueous medium, at their active sites they can adjust the polarity to meet the requirements of the reactions they catalyse. Thus, a Friedel-Crafts-type electrophilic substitution which is normally conducted in water-free media, can be used to activate the substrate for chemically difficult transformations. It is shown that histidine and phenylalanine ammonia lyases which contain the rare prosthetic group dehydroalanine, make use of a Friedel-Crafts-type reaction which was formerly thought to occur only in rather abiotic conditions. While histidine ammonia-lyase catalyses the first step of histidine degradation in most cells, phenylalanine ammonia-lyase is an important plant enzyme, producing cinnamic acid which is the precursor of lignins, coumarins and flavonoids responsible for the marvelous colours of many flowers.

On the nature of the irreversible inhibition of histidine ammonia lyase by cysteine and dioxygen

The irreversible inhibition of histidine ammonia lyase by L-cysteine and dioxygen has been reexamined. After denaturation and consecutive digestion of the inhibited enzyme by trypsin and endoproteinase Glu-C, the generated chromophoric system (lambda max = 340 nm) remained intact and was isolated in an octapeptide containing amino acids 138-145, as previously described (Hernandez, D.; Stroh, J.G.; Phillips, A. T. Arch. Biochem. Biophys. 1993, 307, 126). Conducting the inhibition in the presence of 18O2 did not result in the incorporation of the heavy isotope into the isolated octapeptide. Total hydrolysis followed by amino acid analysis of the octapeptide revealed the presence of one arginine in addition to those expected from the deduced sequence (G3SVAD). 1H NMR spectroscopy of the octapeptide confirmed the presence of the amino acids GSVAD and showed no signals for olefinic or aromatic protons. To account for the excess mass of the octapeptide, we propose an oxidative degradation of the dehydroalanine prosthetic group, followed by reaction of the resulting dicarbonyl system with a nearby arginine residue.

Expression of poplar phenylalanine ammonia-lyase in insect cell cultures

A cDNA encoding one of the phenylalanine ammonia-lyase genes from Populus trichocarpa x deltoides was inserted into a baculovirus expression vector and the PAL protein was successfully expressed in insect cell cultures. High levels of active holoenzyme were obtained that could be purified in a single chromatographic step. Site-directed mutagenesis and expression of the mutant enzyme confirmed that conversion of the putative active site serine202 residue to alanine is sufficient to destroy the catalytic activity of PAL.

The mechanism of action of phenylalanine ammonia-lyase: the role of prosthetic dehydroalanine

Phenylalanine ammonia-lyase (EC 4.3.1.5) from parsley is posttranslationally modified by dehydrating its Ser-202 to the catalytically essential dehydroalanine prosthetic group. The codon of Ser-202 was changed to those of alanine and threonine by site-directed mutagenesis. These mutants and the recombinant wild-type enzyme, after treatment with sodium borohydride, were virtually inactive with L-phenylalanine as substrate but catalyzed the deamination of L-4-nitrophenylalanine, which is also a substrate for the wild-type enzyme. Although the mutants reacted about 20 times slower with L-4-nitrophenylalanine than the wild-type enzyme, their Vmax for L-4-nitrophenylalanine was two orders of magnitude higher than for L-phenylalanine. In contrast to L-tyrosine, which was a poor substrate, DL-3-hydroxyphenylalanine (DL-m-tyrosine) was converted by phenylalanine ammonia-lyase at a rate comparable to that of L-phenylalanine. These results suggest a mechanism in which the crucial step is an electrophilic attack of the prosthetic group at position 2 or 6 of the phenyl group. In the resulting carbenium ion, the beta-HSi atom is activated in a similar way as it is in the nitro analogue. Subsequent elimination of ammonia, concomitant with restoration of both the aromatic ring and the prosthetic group, completes the catalytic cycle.