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Information on EC 2.3.1.253 - phloroglucinol synthase
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2.3.1.253 phloroglucinol synthaseIUBMB Comments
The enzyme, characterized from the bacterium Pseudomonas protegens Pf-5, is a type III polyketide synthase. The mechanism involves the cyclization of an activated 3,5-dioxoheptanedioate intermediate. The enzyme exhibits broad substrate specificity, and can accept C4-C12 aliphatic acyl-CoAs and phenylacetyl-CoA as the starter molecules, forming 6-(polyoxoalkyl)-alpha-pyrones by sequential condensation with malonyl-CoA.
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The expected taxonomic range for this enzyme is: Pseudomonas fluorescens group
Synonyms
phloroglucinol synthase, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
PhlD
phloroglucinol synthase
type III polyketide synthase
PhlD
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
3 malonyl-CoA = phloroglucinol + 3 CO2 + 3 CoA
-
-
-
-
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SYSTEMATIC NAME
IUBMB Comments
malonyl-CoA:malonyl-CoA malonyltransferase (decarboxylating, phloroglucinol-forming)
The enzyme, characterized from the bacterium Pseudomonas protegens Pf-5, is a type III polyketide synthase. The mechanism involves the cyclization of an activated 3,5-dioxoheptanedioate intermediate. The enzyme exhibits broad substrate specificity, and can accept C4-C12 aliphatic acyl-CoAs and phenylacetyl-CoA as the starter molecules, forming 6-(polyoxoalkyl)-alpha-pyrones by sequential condensation with malonyl-CoA.
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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
decanoyl-CoA
4-hydroxy-6-octyl-2H-pyran-2-one + 4-hydroxy-6-(2-oxoundecyl)-2H-pyran-2-one + 4-hydroxyl-6-(2',4',6'-trioxopentadecyl)-2-pyrone + CO2 + CoA
hexanoyl-CoA
4-hydroxy-6-pentyl-2H-pyran-2-one + 4-hydroxy-6-(2-oxoheptyl)-2H-pyran-2-one + CO2 + CoA
8% activity compared to malonyl-CoA
-
-
?
lauroyl-CoA
6-decyl-4-hydroxy-2H-pyran-2-one + 4-hydroxy-6-(2-oxotridecyl)-2H-pyran-2-one + CO2 + CoA
7.6% activity compared to malonyl-CoA
-
-
?
octanoyl-CoA
6-heptyl-4-hydroxy-2H-pyran-2-one + 4-hydroxy-6-(2-oxononyl)-2H-pyran-2-one + 4-hydroxyl-6-(2',4',6'-trioxotridecyl)-2-pyrone + 4-hydroxyl-6-(2',4',6',8'-tetraoxopentadecyl)-2-pyrone + CO2 + CoA
7% activity compared to malonyl-CoA
-
-
?
phenylacetyl-CoA
6-(cyclohepta-1,3,6-trien-1-yl)-4-hydroxy-2H-pyran-2-one + 6-[2-(cyclohepta-1,3,6-trien-1-yl)-2-oxoethyl]-4-hydroxy-2H-pyran-2-one + CO2 + CoA
3.3% activity compared to malonyl-CoA
-
-
?
3 malonyl-CoA
phloroglucinol + 3 CO2 + 3 CoA
-
-
-
-
?
3 malonyl-CoA
phloroglucinol + 3 CO2 + 3 CoA
-
-
-
?
3 malonyl-CoA
phloroglucinol + 3 CO2 + 3 CoA
-
-
phloroglucinol is 1,3,5-trihydroxylbenzene
-
?
3 malonyl-CoA
phloroglucinol + 3 CO2 + 3 CoA
preferred substrate
-
-
?
3 malonyl-CoA
phloroglucinol + 3 CO2 + 3 CoA
-
-
-
?
3 malonyl-CoA
phloroglucinol + 3 CO2 + 3 CoA
-
-
-
?
3 malonyl-CoA
phloroglucinol + 3 CO2 + 3 CoA
-
-
phloroglucinol is 1,3,5-trihydroxylbenzene
-
?
3 malonyl-CoA
phloroglucinol + 3 CO2 + 3 CoA
preferred substrate
-
-
?
3 malonyl-CoA
phloroglucinol + 3 CO2 + 3 CoA
-
-
-
?
acetoacetyl-CoA
phloroglucinol + 4-hydroxy-6-methyl-2H-pyran-2-one + CO2 + CoA
1.6% activity compared to malonyl-CoA
-
-
?
acetoacetyl-CoA
phloroglucinol + 4-hydroxy-6-methyl-2H-pyran-2-one + CO2 + CoA
1.6% activity compared to malonyl-CoA
-
-
?
butyryl-CoA
phloroglucinol + 4-hydroxy-6-propyl-2H-pyran-2-one + CO2 + CoA
0.2% activity compared to malonyl-CoA
-
-
?
butyryl-CoA
phloroglucinol + 4-hydroxy-6-propyl-2H-pyran-2-one + CO2 + CoA
0.2% activity compared to malonyl-CoA
-
-
?
decanoyl-CoA
4-hydroxy-6-octyl-2H-pyran-2-one + 4-hydroxy-6-(2-oxoundecyl)-2H-pyran-2-one + 4-hydroxyl-6-(2',4',6'-trioxopentadecyl)-2-pyrone + CO2 + CoA
18% activity compared to malonyl-CoA
-
-
?
decanoyl-CoA
4-hydroxy-6-octyl-2H-pyran-2-one + 4-hydroxy-6-(2-oxoundecyl)-2H-pyran-2-one + 4-hydroxyl-6-(2',4',6'-trioxopentadecyl)-2-pyrone + CO2 + CoA
18% activity compared to malonyl-CoA
-
-
?
additional information
?
-
the enzyme shows barely detectable activity toward acetyl-CoA, isobutyryl-CoA, benzoyl-CoA, and crotonyl-CoA. No activity with myristoyl-CoA and palmitoyl-CoA
-
-
?
additional information
?
-
acetate is successfully transformed into phloroglucinol by the combined activity of recombinant acetyl-CoA carboxylase (ACC) from Acinetobacter calcoaceticus strain CGMCC 1.6186 and recombinant phloroglucinol synthase (PhlD) from Pseudomonas fluorescens strain Pf-5 in an in vitro system, synthetic pathway of phloroglucinol and in vitro synthesis of phloroglucinol from acetate, method optimization, overview
-
-
-
additional information
?
-
acetate is successfully transformed into phloroglucinol by the combined activity of recombinant acetyl-CoA carboxylase (ACC) from Acinetobacter calcoaceticus strain CGMCC 1.6186 and recombinant phloroglucinol synthase (PhlD) from Pseudomonas fluorescens strain Pf-5 in an in vitro system, synthetic pathway of phloroglucinol and in vitro synthesis of phloroglucinol from acetate, method optimization, overview
-
-
-
additional information
?
-
acetate is successfully transformed into phloroglucinol by the combined activity of recombinant acetyl-CoA carboxylase (ACC) from Acinetobacter calcoaceticus strain CGMCC 1.6186 and recombinant phloroglucinol synthase (PhlD) from Pseudomonas fluorescens strain Pf-5 in an in vitro system, synthetic pathway of phloroglucinol and in vitro synthesis of phloroglucinol from acetate, method optimization, overview
-
-
-
additional information
?
-
the enzyme shows barely detectable activity toward acetyl-CoA, isobutyryl-CoA, benzoyl-CoA, and crotonyl-CoA. No activity with myristoyl-CoA and palmitoyl-CoA
-
-
?
additional information
?
-
acetate is successfully transformed into phloroglucinol by the combined activity of recombinant acetyl-CoA carboxylase (ACC) from Acinetobacter calcoaceticus strain CGMCC 1.6186 and recombinant phloroglucinol synthase (PhlD) from Pseudomonas fluorescens strain Pf-5 in an in vitro system, synthetic pathway of phloroglucinol and in vitro synthesis of phloroglucinol from acetate, method optimization, overview
-
-
-
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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
3 malonyl-CoA
phloroglucinol + 3 CO2 + 3 CoA
-
-
-
-
?
3 malonyl-CoA
phloroglucinol + 3 CO2 + 3 CoA
-
-
-
?
3 malonyl-CoA
phloroglucinol + 3 CO2 + 3 CoA
-
-
phloroglucinol is 1,3,5-trihydroxylbenzene
-
?
3 malonyl-CoA
phloroglucinol + 3 CO2 + 3 CoA
preferred substrate
-
-
?
3 malonyl-CoA
phloroglucinol + 3 CO2 + 3 CoA
-
-
-
?
3 malonyl-CoA
phloroglucinol + 3 CO2 + 3 CoA
-
-
-
?
3 malonyl-CoA
phloroglucinol + 3 CO2 + 3 CoA
-
-
phloroglucinol is 1,3,5-trihydroxylbenzene
-
?
3 malonyl-CoA
phloroglucinol + 3 CO2 + 3 CoA
preferred substrate
-
-
?
3 malonyl-CoA
phloroglucinol + 3 CO2 + 3 CoA
-
-
-
?
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0056
malonyl-CoA
-
pH and temperature not specified in the publication
0.0101
malonyl-CoA
mutant enzyme A289R, pH and temperature not specified in the publication
0.0103
malonyl-CoA
mutant enzyme Y256R/A289R, pH and temperature not specified in the publication
0.0112
malonyl-CoA
mutant enzyme Y256R, pH and temperature not specified in the publication
0.0119
malonyl-CoA
mutant enzyme K210L, pH and temperature not specified in the publication
0.0131
malonyl-CoA
wild type enzyme, pH and temperature not specified in the publication
0.0135
malonyl-CoA
mutant enzyme K210L/Y256R, pH and temperature not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.08
malonyl-CoA
mutant enzyme Y256R/A289R, pH and temperature not specified in the publication
0.11
malonyl-CoA
mutant enzyme K210L/Y256R, pH and temperature not specified in the publication
0.12
malonyl-CoA
wild type enzyme, pH and temperature not specified in the publication
0.13
malonyl-CoA
mutant enzyme A289R, pH and temperature not specified in the publication
0.17
malonyl-CoA
-
pH and temperature not specified in the publication
0.2
malonyl-CoA
mutant enzyme Y256R, pH and temperature not specified in the publication
0.21
malonyl-CoA
mutant enzyme K210L, pH and temperature not specified in the publication
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
7.5
malonyl-CoA
mutant enzyme Y256R/A289R, pH and temperature not specified in the publication
8.3
malonyl-CoA
mutant enzyme K210L/Y256R, pH and temperature not specified in the publication
9.3
malonyl-CoA
wild type enzyme, pH and temperature not specified in the publication
12.8
malonyl-CoA
mutant enzyme A289R, pH and temperature not specified in the publication
17.5
malonyl-CoA
mutant enzyme K210L, pH and temperature not specified in the publication
17.7
malonyl-CoA
mutant enzyme Y256R, pH and temperature not specified in the publication
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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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). PHLD_PSEF5
Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5)
349
0
38617
Swiss-Prot
-
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homodimer
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
A289R
the mutant shows 1.4fold improved catalytic efficiency compared to the wild type enzyme
A60L
the mutant still retains the wild type activity to react with lauroyl-CoA
H24L
the mutant shows reduced reactivity toward lauroyl-CoA and has lost the ability to produce phloroglucinol
H24V
the mutation significantly reduces the reactivity of the enzyme with lauroyl-CoA while still retaining its physiological activity to synthesize phloroglucinol
K210L
the mutant shows 1.9fold improved catalytic efficiency compared to the wild type enzyme
K210L/Y256R
the mutant shows 0.9fold improved catalytic efficiency compared to the wild type enzyme
L59M
the mutation significantly reduces the reactivity of the enzyme with lauroyl-CoA while still retaining its physiological activity to synthesize phloroglucinol
M21I
the mutation significantly reduces the reactivity of the enzyme with lauroyl-CoA while still retaining its physiological activity to synthesize phloroglucinol
M21T
M21T/L54V/A82T/S96R/A181S
-
the mutant shows 110% of wild type specific activity
M21T/N27D/A82T/A181S
-
the mutant shows 90% of wild type specific activity
M21T/N27D/L54V/A82T/A181S/S243T
-
the mutant shows wild type specific activity
M21T/N27D/L54V/A82T/L136M/A181S/S243T
-
the mutant shows 110% of wild type specific activity
Y256R
the mutant shows 1.9fold improved catalytic efficiency compared to the wild type enzyme
Y256R/A289R
the mutant shows 0.8fold improved catalytic efficiency compared to the wild type enzyme
A289R
-
the mutant shows 1.4fold improved catalytic efficiency compared to the wild type enzyme
-
H24L
-
the mutant shows reduced reactivity toward lauroyl-CoA and has lost the ability to produce phloroglucinol
-
H24V
-
the mutation significantly reduces the reactivity of the enzyme with lauroyl-CoA while still retaining its physiological activity to synthesize phloroglucinol
-
K210L
-
the mutant shows 1.9fold improved catalytic efficiency compared to the wild type enzyme
-
K210L/Y256R
-
the mutant shows 0.9fold improved catalytic efficiency compared to the wild type enzyme
-
L59M
-
the mutation significantly reduces the reactivity of the enzyme with lauroyl-CoA while still retaining its physiological activity to synthesize phloroglucinol
-
M21I
-
the mutation significantly reduces the reactivity of the enzyme with lauroyl-CoA while still retaining its physiological activity to synthesize phloroglucinol
-
M21T
-
the mutant still retains the wild type activity to react with lauroyl-CoA
-
Y256R
-
the mutant shows 1.9fold improved catalytic efficiency compared to the wild type enzyme
-
Y256R/A289R
-
the mutant shows 0.8fold improved catalytic efficiency compared to the wild type enzyme
-
M21T
the mutant still retains the wild type activity to react with lauroyl-CoA
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25 - 37
the times required to reduce the activity of the enzyme by 50% at 25, 30, and 37°C are 128, 74, and 7.2 min, respectively
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and ultrafiltration
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
codon-optimized gene phlD, functional recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3), method optimization
expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli BL21(DE3) cells
-
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
synthesis
synthesis
the enzyme can be used for production of important industrial chemicals from acetate in in vitro systems
synthesis
-
the enzyme can be used for production of important industrial chemicals from acetate in in vitro systems
-
synthesis
-
the enzyme can be used for production of important industrial chemicals from acetate in in vitro systems
-
synthesis
-
the enzyme can be used for production of important industrial chemicals from acetate in in vitro systems
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Cao, Y.; Jiang, X.; Zhang, R.; Xian, M.
Improved phloroglucinol production by metabolically engineered Escherichia coli
Appl. Microbiol. Biotechnol.
91
1545-1552
2011
Pseudomonas fluorescens, Pseudomonas fluorescens Pf-5
brenda
Rao, G.; Lee, J.K.; Zhao, H.
Directed evolution of phloroglucinol synthase PhlD with increased stability for phloroglucinol production
Appl. Microbiol. Biotechnol.
97
5861-5867
2013
Pseudomonas fluorescens, Pseudomonas fluorescens Pf-5
brenda
Achkar, J.; Xian, M.; Zhao, H.; Frost, J.W.
Biosynthesis of phloroglucinol
J. Am. Chem. Soc.
127
5332-5333
2005
Pseudomonas fluorescens, Pseudomonas fluorescens Pf-5
brenda
Bangera, M.G.; Thomashow, L.S.
Identification and characterization of a gene cluster for synthesis of the polyketide antibiotic 2,4-diacetylphloroglucinol from Pseudomonas fluorescens Q2-87
J. Bacteriol.
181
3155-3163
1999
Pseudomonas fluorescens, Pseudomonas fluorescens Q2-87
brenda
Zha, W.; Rubin-Pitel, S.B.; Zhao, H.
Characterization of the substrate specificity of PhlD, a type III polyketide synthase from Pseudomonas fluorescens
J. Biol. Chem.
281
32036-32047
2006
Pseudomonas fluorescens (Q4K418), Pseudomonas fluorescens Pf-5 (Q4K418)
brenda
Zha, W.; Rubin-Pitel, S.B.; Zhao, H.
Exploiting genetic diversity by directed evolution: molecular breeding of type III polyketide synthases improves productivity
Mol. Biosyst.
4
246-248
2008
Pseudomonas fluorescens (Q4K418), Pseudomonas fluorescens Pf-5 (Q4K418)
brenda
Ramette, A.; Moenne-Loccoz, Y.; Defago, G.
Polymorphism of the polyketide synthase gene phID in biocontrol fluorescent pseudomonads producing 2,4-diacetylphloroglucinol and comparison of PhID with plant polyketide synthases
Mol. Plant Microbe Interact.
14
639-652
2001
Pseudomonas fluorescens (Q9REL4), Pseudomonas fluorescens (Q9REL5), Pseudomonas fluorescens (Q9REM4), Pseudomonas fluorescens (Q9REZ8), Pseudomonas fluorescens (Q9REZ9), Pseudomonas fluorescens Pf-5 (Q9REL4), Pseudomonas fluorescens UP61 (Q9REM4), Pseudomonas fluorescens Q8r1-96 (Q9REZ8), Pseudomonas fluorescens M1-96 (Q9REZ9), Pseudomonas fluorescens CHA0 (Q9REL5)
brenda
Zhang, R.; Liu, W.; Cao, Y.; Xu, X.; Xian, M.; Liu, H.
An in vitro synthetic biosystem based on acetate for production of phloroglucinol
BMC Biotechnol.
17
66
2017
Pseudomonas fluorescens (Q4K418), Pseudomonas fluorescens Pf-5 (Q4K418), Pseudomonas fluorescens ATCC BAA-477 (Q4K418), Pseudomonas fluorescens NRRL B-23932 (Q4K418)
brenda
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