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Information on EC 5.4.3.11 - phenylalanine aminomutase (D-beta-phenylalanine forming)
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EC Tree
5.4.3.11 phenylalanine aminomutase (D-beta-phenylalanine forming)IUBMB Comments
The enzyme from the bacterium Pantoea agglomerans produces D-beta-phenylalanine, an intermediate in the biosynthesis of the polyketide non-ribosomal antibiotic andrimid. The enzyme contains the cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO), which is formed autocatalytically by cyclization and dehydration of the three amino-acid residues alanine, serine and glycine. cf. EC 5.4.3.10, phenylalanine aminomutase (L-beta-phenylalanine forming).
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Word Map
- 5.4.3.11
- pantoea
- synthesis
- agglomerans
-
unnatural
- taxus
-
stereochemistry
-
isomerizes
-
isomerization
- drug development
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
Synonyms
papam, phenylalanine 2,3-aminomutase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
HitA
PAM
phenylalanine aminomutase
phenylalanine-2,3-aminomutase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
L-phenylalanine = D-beta-phenylalanine
-
-
-
-
L-phenylalanine = D-beta-phenylalanine
reaction mechanism, detailed overview. Proposed elimination mechanisms for the displacement of the NH2-MIO adduct. The final reaction sequence of the MIO-dependent aminomutases involves an alpha,beta-addition reaction, where the NH2-MIO and a proton add across the double bond of the acrylate intermediate. Alternatively, PaPAM can use a stepwise addition sequence where the nucleophile (NH2-MIO) couples to form a 1,4-Michael adduct. This conjugate addition route benefits from an electropositive (delta+) Cbeta by delocalizing the Pi-electrons toward the carboxylate of the substrate
L-phenylalanine = D-beta-phenylalanine
the proposed mechanism of action of PaPAM: starting from either direction with the cooperation of two catalytically essential tyrosine residues (Tyr1 and Tyr2) and the MIO prosthetic group, N-MIO intermediates of alpha- or beta-phenylalanine are formed which interconvert by a alpha - beta migration of the amino group involving a postulated (E)-cinnamate intermediate. PaPAM-catalysed kinetic resolutions starting from racemic alpha-arylalanines or racemic beta-arylalanines result in the opposite enantiomers as products vs. unreacted enantiomers. Mechanism, overview. Formation of significant amounts of (E)-arylacrylates is observed with many substrates indicating substantial lyase-activity of enzyme PaPAM
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SYSTEMATIC NAME
IUBMB Comments
L-phenylalanine 2,3-aminomutase [(S)-3-amino-3-phenylpropanoate]
The enzyme from the bacterium Pantoea agglomerans produces D-beta-phenylalanine, an intermediate in the biosynthesis of the polyketide non-ribosomal antibiotic andrimid. The enzyme contains the cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO), which is formed autocatalytically by cyclization and dehydration of the three amino-acid residues alanine, serine and glycine. cf. EC 5.4.3.10, phenylalanine aminomutase (L-beta-phenylalanine forming).
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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'-methyl-(2S)-alpha-phenylalanine
2'-methyl-beta-phenylalanine
-
plus about 2% of 2'-methyl-(E)-cinnamate
-
?
2-fluoro-L-phenylalanine
(S)-3-amino-3-(2-fluorophenyl)propanoic acid
-
-
-
?
2-methoxy-L-phenylalanine
(S)-3-amino-3-(2-methoxyphenyl)propanoic acid
-
-
-
?
2-methyl-L-phenylalanine
(S)-3-amino-3-(o-tolyl)propanoic acid
-
-
-
?
3-bromo-L-phenylalanine
(S)-3-amino-3-(3-bromophenyl)propanoic acid
-
-
-
?
3-chloro-L-phenylalanine
(S)-3-amino-3-(3-chlorophenyl)propanoic acid
-
-
-
?
3-fluoro-L-phenylalanine
(S)-3-amino-3-(3-fluorophenyl)propanoic acid
-
-
-
?
3-furan-2-yl-L-phenylalanine
(S)-3-amino-3-(furan-2-yl)propanoic acid
-
-
-
?
3-methoxy-L-phenylalanine
(S)-3-amino-3-(3-methoxyphenyl)propanoic acid
-
-
-
?
3-methyl-L-phenylalanine
(S)-3-amino-3-(3-methylphenyl)propanoic acid
-
-
-
?
3-nitro-L-phenylalanine
(S)-3-amino-3-(3-nitrophenyl)propanoic acid
-
-
-
?
3-thiophen-2-yl-L-phenylalanine
(S)-3-amino-3-(thiophen-2-yl)propanoic acid
-
-
-
?
3-thiophen-3-yl-L-phenylalanine
(S)-3-amino-3-(thiophen-3-yl)propanoic acid
-
-
-
?
4-bromo-L-phenylalanine
(S)-3-amino-3-(4-bromophenyl)propanoic acid
-
-
-
?
4-chloro-L-phenylalanine
(S)-3-amino-3-(4-chlorophenyl)propanoic acid
-
-
-
?
4-fluoro-L-phenylalanine
(S)-3-amino-3-(4-fluorophenyl)propanoic acid
-
-
-
?
4-methoxy-L-phenylalanine
(S)-3-amino-3-(4-methoxyphenyl)propanoic acid
-
-
-
?
4-methyl-L-phenylalanine
(S)-3-amino-3-(4-methylphenyl)propanoic acid
-
-
-
?
4-nitro-L-phenylalanine
(S)-3-amino-3-(4-nitrophenyl)propanoic acid
-
-
-
?
D-alpha-phenylalanine
D-beta-phenylalanine
(S)-alpha-phenylalanine
-
-
?
L-phenylalanine
L-beta-phenylalanine
-
when L-Phe enters the active site, the carboxylate group forms a bidentate salt bridge with residue R325. The carboxylate group further interacts with residue Q319. The amine group and the pro-3S hydrogen atom are oriented in an anti-periplanar geometry suitable for the elimination step. A nucleophilic attack of the amine group of the substrate on the 4-methylideneimidazole-5-one cofactor group preceeds abstraction of the proton by the general base Y80, possibly assisted by another basic group, and elimination of 4-methylideneimidazole-5-one-NH2. This leads to formation of trans-cinnamic acid, with the carboxylate group still bound to residue R325. The next step is the readdition of 4-methylideneimidazole-5-one-NH2 to the beta-position and of the proton to the alpha-position. This step requires exposure of the Re face of Cbeta to the 4-methylideneimidazole-5-one-NH2 and the carboxylate group to function as a good electron sink
-
r
rac-2-chloro-phenylalanine
2-chloro-D-beta-phenylalanine + 2-chloro-L-beta-phenylalanine
-
-
-
?
rac-2-fluoro-phenylalanine
2-fluoro-D-beta-phenylalanine + 2-fluoro-L-beta-phenylalanine
-
-
-
?
rac-2-nitro-phenylalanine
2-nitro-D-beta-phenylalanine + 2-nitro-L-beta-phenylalanine
-
-
-
?
rac-3-chloro-phenylalanine
3-chloro-D-beta-phenylalanine + 3-chloro-L-beta-phenylalanine
-
-
-
?
rac-3-fluoro-phenylalanine
3-fluoro-D-beta-phenylalanine + 3-fluoro-L-beta-phenylalanine
-
-
-
?
rac-3-nitro-phenylalanine
3-nitro-D-beta-phenylalanine + 3-nitro-L-beta-phenylalanine
-
-
-
?
rac-4-bromo-phenylalanine
4-bromo-D-beta-phenylalanine + 4-bromo-L-beta-phenylalanine
-
-
-
?
rac-4-chloro-phenylalanine
4-chloro-D-beta-phenylalanine + 4-chloro-L-beta-phenylalanine
-
-
-
?
rac-4-fluoro-phenylalanine
4-fluoro-D-beta-phenylalanine + 4-fluoro-L-beta-phenylalanine
-
-
-
?
rac-4-nitro-phenylalanine
4-nitro-D-beta-phenylalanine + 4-nitro-L-beta-phenylalanine
-
-
-
?
rac-thiophen-2-ylalanine
D-beta-thiophen-2-ylalanine + L-beta-thiophen-2-ylalanine
-
-
-
?
L-phenylalanine
D-beta-phenylalanine
-
plus trans-cinnamate. At steady state, enzyme converts (S)-alpha-phenylalanine to (S)-beta-phenylalanine/transcinnamate in a 90:10 ratio
-
?
L-phenylalanine
D-beta-phenylalanine
the NH2 and pro-(3S) hydrogen groups at Calpha and Cbeta, respectively, of the substrate are removed and interchanged completely intramolecularly with inversion of configuration at the migration centers to form beta-phenylalanine
-
-
?
additional information
?
-
enzyme additionally displays ammonia lyase activity, EC. 4.3.1.24, catalyzing the elimination of ammonia from L-phenylalanine to give trans-cinnamate. No trans-cinnamate is produced upon incubation with L-phenylalanine at 25°C, whilst very low lyase activity can be observed at 30°C
-
-
?
additional information
?
-
enzyme reacts by an alkylamine elimination pathway, which involves covalent attachment between the amino group of the substrate and the product as well as the 4-methylidene-1H-imidazol-5(4H)-one cofactor
-
-
?
additional information
?
-
in nature, phenylalanine 2,3-aminonutase from Pantoea agglomerans is an (S)-selective enzyme, transforming the (S)-alpha-phenylalanine in (S)-beta-phenylalanine
-
-
?
additional information
?
-
enzyme substrate specificity, detailed overview. Interactions the most significant are between the substrates and residues Phe428, Val108, Leu421, Leu104, Gln456, and Tyr. Electronic effects of ortho-, para-, and meta-substituents. The enzyme produces a different amount of cinnamate as side-product dependent on the substrate, e.g. the product pool catalyzed by PaPAM from 13 contains more cinnamate analogue (21.7%) compared to that made from other m-substituted substrates 3-bromo-L-phenylalanine, 3-chloro-L-phenylalanine, 3-nitro-L-phenylalanine, and 3-methoxy-L-phenylalanine that contain between 1.0% and 7.4%. Relationship between PaPAM-substrate interaction energies, flexibility, and Km. Compounds 2-bromo-L-phenylalanine, 2-chloro-L-phenylalanine, and 2-nitro-L-phenylalanine are no substrates
-
-
?
additional information
?
-
PaPAM converts (S)-alpha-amino acids to (S)-beta-amino acids
-
-
?
additional information
?
-
the enzyme performs enantiomer-selective isomerization of various racemic alpha- and beta-arylalanines, both alpha- and beta-arylalanines are accepted as substrates when the aryl moiety is relatively small, like phenyl, 2-, 3-, 4-fluorophenyl or thiophen-2-yl. While 2-substituted alpha-phenylalanines bearing bulky electron withdrawing substituents do not react, the corresponding substituted beta-aryl analogues are converted rapidly. Conversion of 3- and 4-substituted alpha-arylalanines happens smoothly, while conversion of the corresponding beta-arylalanines is poor or non-existent. The high enantiomeric excess (ee) values of the products indicate excellent enantiomer selectivity and stereospecificity of the isomerization except for (S)-2-nitro-a-phenylalanine (ee 92%) from the beta-isomer. Computational modelling reveals that one of the main factors controlling biocatalytic activity is the energy difference between the covalent regioisomeric enzyme-substrate complexes. Formation of significant amounts of (E)-arylacrylates is observed with many substrates indicating substantial lyase-activity of enzyme PaPAM. Differences of conversions of the PaPAM-catalysed isomerizations from alpha- and beta-arylalanines racemates, substrate categories and relative energy differences of the regioisomeric N-MIO intermediates, substrate specificity and reaction products, overview
-
-
?
additional information
?
-
enzyme additionally displays ammonia lyase activity, EC. 4.3.1.24, catalyzing the elimination of ammonia from L-phenylalanine to give trans-cinnamate. No trans-cinnamate is produced upon incubation with L-phenylalanine at 25°C, whilst very low lyase activity can be observed at 30°C
-
-
?
additional information
?
-
-
the recombinant enzyme displays a broad substrate spectrum
-
-
?
additional information
?
-
enzyme additionally displays ammonia lyase activity, EC. 4.3.1.24, catalyzing the elimination of ammonia from L-phenylalanine to give trans-cinnamate
-
-
?
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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
D-alpha-phenylalanine
D-beta-phenylalanine
(S)-alpha-phenylalanine
-
-
?
additional information
?
-
in nature, phenylalanine 2,3-aminonutase from Pantoea agglomerans is an (S)-selective enzyme, transforming the (S)-alpha-phenylalanine in (S)-beta-phenylalanine
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
4-methylidene-1H-imidazol-5(4H)-one
MIO, a protein-derived cofactor, which is generated autocatalytically from three active site residues, Ala-Ser-Gly (Thr-Ser-Gly in PaPAM), forming a MIO signature motif
4-methylidene-1H-imidazol-5(4H)-one
MIO, prosthetic group, dependent on
4-methylidene-1H-imidazol-5(4H)-one
MIO, prosthetic group, dependent on, proposed elimination mechanisms for the displacement of the NH2-MIO adduct. Formation of an NH2-MIO adduct, where the amino group of the substrate is covalently attached to the enzyme during alpha/beta-isomerization
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
NH4+
changing the (NH4)2CO3 concentration in the range of 50-1000 mM at pH 8.0 significantly influences the product compositions
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
4-methylidene-1H-imidazol-5(4H)-one
cofactor is formed autocatalytically from a Thr-Ser-Gly tandem
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.415
3-furan-2-yl-L-phenylalanine
pH 8.0, 31°C, recombinant enzyme
0.132
3-thiophen-2-yl-L-phenylalanine
pH 8.0, 31°C, recombinant enzyme
0.337
3-thiophen-3-yl-L-phenylalanine
pH 8.0, 31°C, recombinant enzyme
additional information
additional information
Michaelis-Menten kinetics
-
0.027
D-beta-phenylalanine
25°C, pH not specified in the publication
0.04
D-beta-phenylalanine
25°C, pH not specified in the publication
0.022
L-phenylalanine
25°C, pH not specified in the publication
0.05
L-phenylalanine
pH not specified in the publication, temperature not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.236
3-furan-2-yl-L-phenylalanine
pH 8.0, 31°C, recombinant enzyme
0.026
3-thiophen-2-yl-L-phenylalanine
pH 8.0, 31°C, recombinant enzyme
0.143
3-thiophen-3-yl-L-phenylalanine
pH 8.0, 31°C, recombinant enzyme
0.059
D-beta-phenylalanine
25°C, pH not specified in the publication
0.22
D-beta-phenylalanine
25°C, pH not specified in the publication
0.061
L-phenylalanine
pH not specified in the publication, temperature not specified in the publication
0.159
L-phenylalanine
25°C, pH not specified in the publication
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.588
3-furan-2-yl-L-phenylalanine
pH 8.0, 31°C, recombinant enzyme
0.19
3-thiophen-2-yl-L-phenylalanine
pH 8.0, 31°C, recombinant enzyme
0.428
3-thiophen-3-yl-L-phenylalanine
pH 8.0, 31°C, recombinant enzyme
2.2
D-beta-phenylalanine
25°C, pH not specified in the publication
5.53
D-beta-phenylalanine
25°C, pH not specified in the publication
1.2
L-phenylalanine
pH not specified in the publication, temperature not specified in the publication
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7 - 9
alteration of pH of the buffer solution in the range of pH 7-9 (at 100 mM (NH4)2CO3) is indifferent to enzymatic conversion
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
the ammonia lyase activity shows a temperature maximum at 70°C
additional information
the ammonia lyase activity shows a temperature maximum at about 75°C
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
i.e. Enterobacter agglomerans or Erwinia herbicola
UniProt
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
metabolism
physiological function
PaPAM makes the (3S)-beta-phenylalanine antipode on the biosynthetic pathway to the antibiotic andrimid starting from (S)-beta-phenylalanine via (S)-alpha-phenylalanine
additional information
evolution
phenylalanine 2,3-mutases, PAMs, belong to the class I lyase-like family that includes tyrosine 2,3-aminomutases (TAMs), tyrosine ammonia-lyases (TALs), and histidine ammonia-lyases (HALs). All these enzymes rely on a protein-derived cofactor, 4-methylideneimidazol-5-one (MIO), which is generated autocatalytically from three active site residues, Ala-Ser-Gly (Thr-Ser-Gly in PaPAM), forming a MIO signature motif
evolution
the enzyme belongs to a class I lyase-like superfamily of catalysts, along with other MIO-dependent aminomutases
malfunction
a hitA knockout mutant shows no hitachimycin production, but antibiotic production is restored by feeding with (S)-beta-Phe
malfunction
Embleya scabrispora JCM 11712 / DSM 41855
-
a hitA knockout mutant shows no hitachimycin production, but antibiotic production is restored by feeding with (S)-beta-Phe
-
metabolism
the enzyme is important in the hitachimycin biosynthetic pathway. A plausible biosynthetic pathway for hitachimycin, including a unique polyketide skeletal transformation mechanism, is proposed
metabolism
Embleya scabrispora JCM 11712 / DSM 41855
-
the enzyme is important in the hitachimycin biosynthetic pathway. A plausible biosynthetic pathway for hitachimycin, including a unique polyketide skeletal transformation mechanism, is proposed
-
additional information
enzyme structure-activity analysis and modeling of substrate-PaPAM structural interactions, overview
additional information
molecular modelling of the covalent enzyme-substrate N-MIO complexes in PaPAM
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). A0A7W2J416_9PSED
527
0
57169
TrEMBL
-
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
to 1.7 A resolution with cinnamate included in the crystallization buffer. The monomer consists of mostly alphahelices that run parallel to one another and form a four-helix bundle at the center. The catalytically relevant species is a dimer of dimers, in which the two monomers in the asymmetric unit are related by a crystallographic twofold axis to the other two monomers that comprise the catalytically functional tetramer, and each subunit contains an active site. During the reaction, the phenylpropanoid carbon backbone remains mostly stationary above the amino group that is attached to the cofactor moiety
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
F455A
reaction proceeds at approximately 2% of the rate of wild-type, in a 40:60 ratio of products D-beta-phenylalanine and trans-cinnamate, where trans-cinnamate prevails
F455N
reaction proceeds at approximately 2% of the rate of wild-type, in a 40:60 ratio of products D-beta-phenylalanine and trans-cinnamate, where trans-cinnamate prevails
additional information
additional information
construction of a hitA knockout mutant strain
additional information
Embleya scabrispora JCM 11712 / DSM 41855
-
construction of a hitA knockout mutant strain
-
additional information
-
evaluation of recombinant enzyme production in Escherichia coli strain BL21 and synthesis of beta-arylalanines. Maximal enzyme activity of 2.5 U/mg at pH 9.0, 30°C. Synthesis of beta-arylalanines with different groups at the benzene ring, 93% yield of 2-nitro-beta-phenylalanine
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