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Information on EC 4.3.1.25 - phenylalanine/tyrosine ammonia-lyase
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4.3.1.25 phenylalanine/tyrosine ammonia-lyaseIUBMB Comments
This enzyme is a member of the aromatic amino acid lyase family, other members of which are EC 4.3.1.3 (histidine ammonia-lyase), EC 4.3.1.23 (tyrosine ammonia-lyase) and EC 4.3.1.24 (phenylalanine ammonia-lyase). The enzyme from some monocots, including maize, and from the yeast Rhodosporidium toruloides, deaminate L-phenylalanine and L-tyrosine with similar catalytic efficiency . The enzyme contains the cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO), which is common to this family . This unique cofactor is formed autocatalytically by cyclization and dehydration of the three amino-acid residues alanine, serine and glycine .
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Word Map
- 4.3.1.25
- synthesis
-
deamination
- glutinis
-
p-hydroxycinnamic
-
rhodotorula
- pharmacology
-
hydrolysate
- analysis
- medicine
- food industry
- nutrition
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
Reaction Schemes
Synonyms
PAL, PAL/TAL, PAL4, phenylalanine-tyrosine ammonia lyase, PTAL, RtPAL, Sb04g026510, Sb06g022740, SbPAL1, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
PAL
PAL/TAL
phenylalanine-tyrosine ammonia lyase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
L-tyrosine = trans-p-hydroxycinnamate + NH3
-
-
-
-
L-phenylalanine = trans-cinnamate + NH3
-
-
-
-
L-phenylalanine = trans-cinnamate + NH3
ordered uni-bi reaction sequence
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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PATHWAY SOURCE
PATHWAYS
MetaCyc
benzoate biosynthesis II (CoA-independent, non-beta-oxidative), cinnamoyl-CoA biosynthesis, coumarins biosynthesis (engineered), ephedrine biosynthesis, naringenin biosynthesis (engineered), phenylpropanoid biosynthesis, initial reactions, rosmarinic acid biosynthesis I, suberin monomers biosynthesis
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SYSTEMATIC NAME
IUBMB Comments
L-phenylalanine(or L-tyrosine):trans-cinnamate(or trans-p-hydroxycinnamate) ammonia-lyase
This enzyme is a member of the aromatic amino acid lyase family, other members of which are EC 4.3.1.3 (histidine ammonia-lyase), EC 4.3.1.23 (tyrosine ammonia-lyase) and EC 4.3.1.24 (phenylalanine ammonia-lyase). The enzyme from some monocots, including maize, and from the yeast Rhodosporidium toruloides, deaminate L-phenylalanine and L-tyrosine with similar catalytic efficiency [3]. The enzyme contains the cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO), which is common to this family [3]. This unique cofactor is formed autocatalytically by cyclization and dehydration of the three amino-acid residues alanine, serine and glycine [4].
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
2-chloro-trans-cinnamate + NH3
2-chloro-L-phenylalanine
51.4% conversion
-
-
?
2-fluoro-trans-cinnamate + NH3
2-fluoro-L-phenylalanine
94.3% conversion
-
-
?
2-hydroxy-trans-cinnamate + NH3
2-hydroxy-L-phenylalanine
15.7% conversion
-
-
?
2-methoxy-trans-cinnamate + NH3
2-methoxy-L-phenylalanine
64.9% conversion
-
-
?
3-chloro-trans-cinnamate + NH3
3-chloro-L-phenylalanine
71.6% conversion
-
-
?
3-fluoro-trans-cinnamate + NH3
3-fluoro-L-phenylalanine
61.5% conversion
-
-
?
3-hydroxy-trans-cinnamate + NH3
3-hydroxy-L-phenylalanine
30.3% conversion
-
-
?
3-methoxy-4-hydroxy-trans-cinnamate + NH3
3-methoxy-4-hydroxy-L-phenylalanine
60.3% conversion
-
-
?
3-methoxy-trans-cinnamate + NH3
3-methoxy-L-phenylalanine
77.8% conversion
-
-
?
4-fluoro-trans-cinnamate + NH3
4-fluoro-L-phenylalanine
57.5% conversion
-
-
?
4-hydroxy-trans-cinnamate + NH3
4-hydroxy-L-phenylalanine
61.1% conversion
-
-
?
4-methoxy-trans-cinnamate + NH3
4-methoxy-L-phenylalanine
0.7% conversion
-
-
?
L-tyrosine methyl ester
p-hydroxycinnamic acid methyl ester + NH3
-
-
-
-
?
L-phenylalanine
trans-cinnamate + NH3
-
key gateway enzyme linking the phenylpropanoid secondary pathway to primary metabolism
-
-
r
L-phenylalanine
trans-cinnamate + NH3
the bifunctional enzyme shows KM-values for L-Phe and L-Tyr in the same order of magnitude
-
-
r
L-phenylalanine
trans-cinnamate + NH3
enzyme of the phenylpropanoid pathway
-
-
?
L-tyrosine
p-coumarate + NH3
-
substrate binding is cooperative, nH 2.6
-
-
?
L-tyrosine
trans-p-hydroxycinnamate + NH3
the bifunctional enzyme shows KM-values for L-Phe and L-Tyr in the same order of magnitude
-
-
?
additional information
?
-
wild type enzyme and mutants show no catalytic activity with His
-
-
-
additional information
?
-
wild type enzyme and mutants show no catalytic activity with His
-
-
-
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NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
L-phenylalanine
trans-cinnamate + NH3
-
key gateway enzyme linking the phenylpropanoid secondary pathway to primary metabolism
-
-
r
L-phenylalanine
trans-cinnamate + NH3
C5XXT8, C5YCD6
enzyme of the phenylpropanoid pathway
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3,5-dihydro-5-methylidene-4H-imidazol-4-one
-
the cofactor is regenerated during the reaction cycle and thus does not require external cofactor regeneration
3,5-dihydro-5-methylidene-4H-imidazol-4-one
prosthetic group; prosthetic group
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
m-cresol/glycine
-
0.387 mM, 50% inhibition, strong synergistic inhibition
-
o-cresol/glycine
-
0.078 mM, 50% inhibition, strong synergistic inhibition
-
phenol/glycine
-
0.056 mM 50% inhibition, strong synergistic inhibition
-
CN-
-
the substrate analog DL-2-hydroxyphenylalanine or cinnamate protects
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
8.5
8.8
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
enzyme expression is induced up to 3fold by presence of L-isoleucine, L-phenylalanine or L-tyrosine in growth medium. The presence of trans-cinnamic acid suppresses enzyme expression
-
-
brenda
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
in shoot and branch shoot, mainly loclaized to sclerenchymal cells
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
metabolism
enzyme of the phenylpropanoid pathway; enzyme of the phenylpropanoid pathway
metabolism
-
key gateway enzyme linking the phenylpropanoid secondary pathway to primary metabolism
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
Sequence
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
tetramer
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CRYSTALLIZATION/commentary
ORGANISM
UNIPROT
LITERATURE
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
R123A
-
modest improvements in resistance against protease inactivation
R123H
-
modest improvements in resistance against protease inactivation
R123Q
-
modest improvements in resistance against protease inactivation
Y110A
-
modest improvements in resistance against protease inactivation
Y110H
-
modest improvements in resistance against protease inactivation
Y110L
-
modest improvements in resistance against protease inactivation
F102Y
the turnover rate for L-Tyr is improved 3.6fold, whereas the turnover rate for L-Phe is unaffected. Km values for both L-Tyr and L-Phe are increased by 7.6- and 24fold, respectively, which causes reduced enzyme efficiency for both substrates
H123F
the mutant shows 6.2fold elevation in catalytic efficiency (kcat/Km) for L-Phe, mainly due to a 5.7fold decrease in Km. The mutant enzyme loses activity for L-Tyr. The loss of polarity in the H123F mutant orients both L-Tyr and L-Phe in similar positions, where the ortho-carbon is closer to the methylidene carbon of 4-methylidene-imidazole-5-one
H123Y
the catalytic efficiency of the mutant enzyme for L-Phe is reduced, mainly due to a 10fold decrease in the turnover rate. The H123Y mutant also loses activity against L-Tyr
K443E
the mutant enzyme shows no measurable activity against any of the three substrates, L-Phe, L-Tyr, and L-His
Y96F
the mutant enzyme displays only trace amounts of activity for both L-Tyr and L-Phe
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
60
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
0-2°C, 50 mM Tris/HCl, 0.01% Mn2+, pH 8.8, whole cells retain 85% of initial enzyme activity for at least 12 weeks
-
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PURIFICATION/commentary
ORGANISM
UNIPROT
LITERATURE
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CLONED/commentary
ORGANISM
UNIPROT
LITERATURE
controlled expression in Escherichia coli to mitigate product toxicity
expression in Escherichia coli
controlled expression in Escherichia coli to mitigate product toxicity
-
controlled expression in Escherichia coli to mitigate product toxicity
-
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
-
rapid quantization of Phe and Tyr in plasma and serum from subjects with phenylketonuria
food industry
medicine
-
enzyme substitution therapy for the treatment of phenylketonuria
nutrition
pharmacology
synthesis
food industry
-
the enzyme is a useful biocatalyst for removal of L-phenylalanine from protein hydrolysates, which can be evaluated as potential ingredients in foodstuffs for phenylketonuria patients. The enzyme is also capable to catalyze the deamination of L-tyrosine to p-coumaric acid but at a substantially low reaction rate. Therefore, the final content of L-Tyr in samples treated with L-phenylalanine ammonia-lyase should be analyzed in each case and taken in consideration to avoid its deficiency in phenylketonuria patients
food industry
Rhodotorula toruloides NBRC 0559
-
the enzyme is a useful biocatalyst for removal of L-phenylalanine from protein hydrolysates, which can be evaluated as potential ingredients in foodstuffs for phenylketonuria patients. The enzyme is also capable to catalyze the deamination of L-tyrosine to p-coumaric acid but at a substantially low reaction rate. Therefore, the final content of L-Tyr in samples treated with L-phenylalanine ammonia-lyase should be analyzed in each case and taken in consideration to avoid its deficiency in phenylketonuria patients
-
nutrition
-
the enzyme is a useful biocatalyst for removal of L-phenylalanine from protein hydrolysates, which can be evaluated as potential ingredients in foodstuffs for phenylketonuria patients. The enzyme is also capable to catalyze the deamination of L-tyrosine to p-coumaric acid but at a substantially low reaction rate. Therefore, the final content of L-Tyr in samples treated with L-phenylalanine ammonia-lyase should be analyzed in each case and taken in consideration to avoid its deficiency in phenylketonuria patients
nutrition
Rhodotorula toruloides NBRC 0559
-
the enzyme is a useful biocatalyst for removal of L-phenylalanine from protein hydrolysates, which can be evaluated as potential ingredients in foodstuffs for phenylketonuria patients. The enzyme is also capable to catalyze the deamination of L-tyrosine to p-coumaric acid but at a substantially low reaction rate. Therefore, the final content of L-Tyr in samples treated with L-phenylalanine ammonia-lyase should be analyzed in each case and taken in consideration to avoid its deficiency in phenylketonuria patients
-
pharmacology
-
the enzyme is a useful biocatalyst for removal of L-phenylalanine from protein hydrolysates, which can be evaluated as potential ingredients in foodstuffs for phenylketonuria patients. The enzyme is also capable to catalyze the deamination of L-tyrosine to p-coumaric acid but at a substantially low reaction rate. Therefore, the final content of L-Tyr in samples treated with L-phenylalanine ammonia-lyase should be analyzed in each case and taken in consideration to avoid its deficiency in phenylketonuria patients
pharmacology
-
enzyme substitution therapy for the treatment of phenylketonuria
pharmacology
Rhodotorula toruloides NBRC 0559
-
the enzyme is a useful biocatalyst for removal of L-phenylalanine from protein hydrolysates, which can be evaluated as potential ingredients in foodstuffs for phenylketonuria patients. The enzyme is also capable to catalyze the deamination of L-tyrosine to p-coumaric acid but at a substantially low reaction rate. Therefore, the final content of L-Tyr in samples treated with L-phenylalanine ammonia-lyase should be analyzed in each case and taken in consideration to avoid its deficiency in phenylketonuria patients
-
synthesis
-
immobilization of Escherichia coli cells stably expressing the enzyme on calcium alginate beads for use in batch coversion of L-tyrosine to p-hydroxycinnamic acid. Immobilization and controlling of pH value to 9.8 results in stabilization. In 1 l batch reactions, 50 g/l tyrosine can be converted to 39 g/l p-hydroxycinnamic acid
synthesis
-
use of enzyme for synthesis of optically pure L-phenylalanine from trans-cinnamate
synthesis
-
synthesis of p-hydroxycinnamic acid methyl ester, which shows antibacterial activity
synthesis
-
reconstructed phenylpropanoid pathway in engineered Escherichia coli or Saccharomyces cerevisiae leads to the biosynthesis of a wide range of phenylpropanoid-derived compounds, including pinocembrin, naringenin, styrene, 2',4',6'-trihydroxydihydrochalcone, trans-resveratrol, trans-cinnamic acid, p-coumarate, p-hydroxystyrene
synthesis
-
use of enzyme for synthesis of optically pure L-phenylalanine from trans-cinnamate
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Camm, E.L.; Towers, G.H.N.
Phenylalanine ammonia lyase
Phytochemistry
12
961-973
1973
Sporidiobolus pararoseus, Triticum aestivum
-
brenda
Hanson, K.R.; Havir, E.A.
Phenylalanine ammonia-lyase
Biochem. Plants
7
577-625
1981
Rhodotorula glutinis
-
brenda
Jorrin, J.; Lopez-Valbuena, R.; Tena, M.
Purification and properties of phenylalanine ammonia-lyase from sunflower (Helianthus annuus L.) hypocotyls
Biochim. Biophys. Acta
964
73-82
1988
Helianthus annuus
-
brenda
Abell, C.W.; Shen, R.S.
Phenylalanine ammonia-lyase from the yeast Rhodotorula glutinis
Methods Enzymol.
142
242-249
1987
Rhodotorula glutinis
brenda
Fritz, R.R.; Hodgins, D.S.; Abell, C.W.
Phenylalanine ammonia-lyase. Induction and purification from yeast and clearance in mammals
J. Biol. Chem.
251
4646-4650
1976
Rhodotorula glutinis
brenda
Jangaard, N.O.
The characterization of phenylalanine ammonia-lyase from several plant species
Phytochemistry
13
1765-1768
1974
Cyperus rotundus, Echinochloa crus-galli, Glycine max, Sorghum halepense, Zea mays
-
brenda
Parkhurst, J.R.; Hodgins, D.S.
Yeast phenylalanine ammonia-lyase. Properties of the enzyme from Sporobolomyces pararoseus and its catalytic site
Arch. Biochem. Biophys.
152
597-605
1972
Sporidiobolus pararoseus
brenda
Hodgins, D.S.
Properties of yeast L-phenylalanine ammonia-lyase
Arch. Biochem. Biophys.
149
91-96
1972
Rhodotorula glutinis
brenda
Vance, C.P.; Bandoni, R.J.; Towers, G.H.N.
Further observations on phenylalanine ammonia-lyase in fungi
Phytochemistry
14
1513-1514
1975
Nectria cinnabarina
-
brenda
Adachi, O.; Matsushita, K.; Shinagawa, E.; Ameyama, M.
Crystallization and properties of L-phenylalanine ammonia-lyase from Rhodosporidium toruloides
Agric. Biol. Chem.
54
2839-2843
1990
Rhodotorula toruloides
-
brenda
Dahiya, J.S.
Isolation and characterization of phenylalanine ammonia-lyase enzyme from the fungus Leptosphaeria maculans
Indian J. Exp. Biol.
31
874-877
1993
Leptosphaeria maculans
-
brenda
Alunni, S.; Cipiciani, A.; Fioroni, G.; Ottavi, L.
Mechanisms of inhibition of phenylalanine ammonia-lyase by phenol inhibitors and phenol/glycine synergistic inhibitors
Arch. Biochem. Biophys.
412
170-175
2003
Rhodotorula glutinis
brenda
Khan, W.; Prithiviraj, B.; Smith, D.L.
Chitosan and chitin oligomers increase phenylalanine ammonia-lyase and tyrosine ammonia-lyase activities in soybean leaves
J. Plant Physiol.
160
859-863
2003
Glycine max
brenda
Trotman, R.J.; Camp, C.E.; Ben-Bassat, A.; DiCosimo, R.; Huang, L.; Crum, G.A.; Sariaslani, F.S.; Haynie, S.L.
Calcium alginate bead immobilization of cells containing tyrosine ammonia lyase activity for use in the production of p-hydroxycinnamic acid
Biotechnol. Prog.
23
638-644
2007
Rhodotorula glutinis
brenda
Vannelli, T.; Xue, Z.; Breinig, S.; Qi, W.W.; Sariaslani, F.S.
Functional expression in Escherichia coli of the tyrosine-inducible tyrosine ammonia-lyase enzyme from yeast Trichosporon cutaneum for production of p-hydroxycinnamic acid
Enzyme Microb. Technol.
41
413-422
2007
Cutaneotrichosporon cutaneum
-
brenda
Xue, Z.; McCluskey, M.; Cantera, K.; Ben-Bassat, A.; Sariaslani, F.S.; Huang, L.
Improved production of p-hydroxycinnamic acid from tyrosine using a novel thermostable phenylalanine/tyrosine ammonia lyase enzyme
Enzyme Microb. Technol.
42
58-64
2007
Phanerochaete chrysosporium, Rhodotorula glutinis
-
brenda
Wall, M.J.; Quinn, A.J.; DCunha, G.B.
Manganese (Mn2+)-dependent storage stabilization of Rhodotorula glutinis phenylalanine ammonia-lyase activity
J. Agric. Food Chem.
56
894-902
2008
Rhodotorula glutinis
brenda
Verhoef, S.; Ballerstedt, H.; Volkers, R.J.; de Winde, J.H.; Ruijssenaars, H.J.
Comparative transcriptomics and proteomics of p-hydroxybenzoate producing Pseudomonas putida S12: novel responses and implications for strain improvement
Appl. Microbiol. Biotechnol.
87
679-690
2010
Pseudomonas putida, Pseudomonas putida S12
brenda
Hsieh, L.S.; Ma, G.J.; Yang, C.C.; Lee, P.D.
Cloning, expression, site-directed mutagenesis and immunolocalization of phenylalanine ammonia-lyase in Bambusa oldhamii
Phytochemistry
71
1999-2009
2010
Bambusa oldhamii (D5KS97)
brenda
MacDonald, M.C.; Arivalagan, P.; Barre, D.E.; MacInnis, J.A.; DCunha, G.B.
Rhodotorula glutinis phenylalanine/tyrosine ammonia lyase enzyme catalyzed synthesis of the methyl ester of para-hydroxycinnamic acid and its potential antibacterial activity
Front. Microbiol.
7
281
2016
Rhodotorula glutinis
brenda
Dressen, A.; Hilberath, T.; Mackfeld, U.; Billmeier, A.; Rudat, J.; Pohl, M.
Phenylalanine ammonia lyase from Arabidopsis thaliana (AtPAL2) A potent MIO-enzyme for the synthesis of non-canonical aromatic alpha-amino acids Part I Comparative characterization to the enzymes from Petroselinum crispum (PcPAL1) and Rhodosporidium to the enzymes from Petroselinum crispum (PcPAL1) and Rhodosporidium toruloides (RtPAL)
J. Biotechnol.
258
148-157
2017
Rhodotorula toruloides (P11544)
brenda
Castaneda, M.T.; Adachi, O.; Hours, R.A.
Reduction of L-phenylalanine in protein hydrolysates using L-phenylalanine ammonia-lyase from Rhodosporidium toruloides
J. Ind. Microbiol. Biotechnol.
42
1299-1307
2015
Rhodotorula toruloides (P11544), Rhodotorula toruloides NBRC 0559 (P11544)
brenda
Jun, S.Y.; Sattler, S.A.; Cortez, G.S.; Vermerris, W.; Sattler, S.E.; Kang, C.
Biochemical and structural analysis of substrate specificity of a phenylalanine ammonia-lyase
Plant Physiol.
176
1452-1468
2018
Sorghum bicolor (C5XXT8), Sorghum bicolor (C5YCD6)
brenda
Kong, J.
Phenylalanine ammonia-lyase, a key component used for phenylpropanoids production by metabolic engineering
RSC Adv.
5
62587-62603
2015
Rhodotorula toruloides (P11544)
-
brenda
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