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3,4-dihydroxybenzoate + O2
4-carboxy-2-hydroxymuconate semialdehyde
3,4-dihydroxyphenyl sulfonate + O2
2-hydroxy-6-oxo-4-sulfohexa-2,4-dienoate
3-O-methylgallate + O2
4-carboxy-2-hydroxy-6-methoxy-6-oxohexa-2,4-dienoate + 2-pyrone-4,6-dicarboxylate
3-O-methylgallate + O2
?
-
-
-
?
5-methoxygallic acid + O2
?
-
-
-
-
?
5-methylprotocatechuate + O2
4-carboxy-2-hydroxy-3-methylmuconate semialdehyde
gallic acid + O2
2-pyrone-4,6-dicarboxylic acid + H2O
-
-
major product formed
-
?
gallic acid + O2
?
-
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
additional information
?
-
3,4-dihydroxybenzoate + O2
4-carboxy-2-hydroxymuconate semialdehyde
-
-
-
?
3,4-dihydroxybenzoate + O2
4-carboxy-2-hydroxymuconate semialdehyde
-
-
-
?
3,4-dihydroxyphenyl sulfonate + O2
2-hydroxy-6-oxo-4-sulfohexa-2,4-dienoate
-
-
-
-
?
3,4-dihydroxyphenyl sulfonate + O2
2-hydroxy-6-oxo-4-sulfohexa-2,4-dienoate
-
-
-
-
?
3-O-methylgallate + O2
4-carboxy-2-hydroxy-6-methoxy-6-oxohexa-2,4-dienoate + 2-pyrone-4,6-dicarboxylate
-
-
-
-
?
3-O-methylgallate + O2
4-carboxy-2-hydroxy-6-methoxy-6-oxohexa-2,4-dienoate + 2-pyrone-4,6-dicarboxylate
-
-
-
-
?
5-methylprotocatechuate + O2
4-carboxy-2-hydroxy-3-methylmuconate semialdehyde
-
-
-
-
?
5-methylprotocatechuate + O2
4-carboxy-2-hydroxy-3-methylmuconate semialdehyde
-
-
-
-
?
gallate + O2
?
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
-
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
-
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
-
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
-
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
-
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
-
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
-
-
-
-
?
sulfonylcatechol + O2
?
-
-
-
-
?
sulfonylcatechol + O2
?
-
-
-
-
?
additional information
?
-
-
no activity on 3-O-methylgallate
-
-
?
additional information
?
-
LigAB has the broadest substrate utilization profile
-
-
?
additional information
?
-
-
LigAB has the broadest substrate utilization profile
-
-
?
additional information
?
-
protocatechuate 4,5-dioxygenase (LigAB) catalyzes dioxygenation of multiple lignin derived aromatic compounds with decreasing efficiency as the molecule size increases. Residue F103 of the alpha-subunit controls substrate specificity through interaction with the C5-funtionality of bound substrates. In silico docking of substrates to the enzyme mutants, overview
-
-
?
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0.021
3,4-dihydroxybenzoate
pH 9.5, 20°C, recombinant enzyme
0.39 - 4
3-O-methylgallate
0.125
5-methoxygallic acid
-
-
0.02 - 1.6
protocatechuate
additional information
additional information
-
0.39
3-O-methylgallate
pH 7.5, 25°C, recombinant mutant F103T
0.93
3-O-methylgallate
pH 7.5, 25°C, recombinant mutant F103H
1
3-O-methylgallate
pH 7.5, 25°C, recombinant mutant F103V
2.3
3-O-methylgallate
pH 7.5, 25°C, recombinant wild-type enzyme
4
3-O-methylgallate
pH 7.5, 25°C, recombinant mutant F103L
0.19
gallate
pH 7.5, 25°C, recombinant mutant F103H
0.21
gallate
pH 7.5, 25°C, recombinant mutant F103T
0.44
gallate
pH 7.5, 25°C, recombinant wild-type enzyme
0.9
gallate
pH 7.5, 25°C, recombinant mutant F103V
7
gallate
pH 7.5, 25°C, recombinant mutant F103L
0.02
protocatechuate
-
-
0.046
protocatechuate
-
-
0.051
protocatechuate
pH 7.5, 25°C, recombinant wild-type enzyme
0.055
protocatechuate
30°C, pH 7.5
0.066
protocatechuate
pH 7.5, 25°C, recombinant mutant A18W
0.081
protocatechuate
pH 7.5, 25°C, recombinant wild-type enzyme
0.108
protocatechuate
pH 7.5, 25°C, recombinant mutant F103H
0.13
protocatechuate
pH 7.5, 25°C, recombinant wild-type enzyme, with vanillin
0.21
protocatechuate
pH 7.5, 25°C, recombinant mutant F103T
0.26
protocatechuate
pH 7.5, 25°C, recombinant mutant F103V
1.6
protocatechuate
pH 7.5, 25°C, recombinant mutant F103L
additional information
additional information
Michaelis-Menten steady-state kinetics measuring O2 consumption
-
additional information
additional information
-
Michaelis-Menten steady-state kinetics measuring O2 consumption
-
additional information
additional information
Michaelis-Menten steady-state kinetics of wild-type and mutant enzymes
-
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7
3-O-methylgallate
pH 7.5, 25°C, recombinant mutant F103L
7.3
3-O-methylgallate
pH 7.5, 25°C, recombinant wild-type enzyme
15.1
3-O-methylgallate
pH 7.5, 25°C, recombinant mutant F103T
49
3-O-methylgallate
pH 7.5, 25°C, recombinant mutant F103V
91
3-O-methylgallate
pH 7.5, 25°C, recombinant mutant F103H
5
gallate
pH 7.5, 25°C, recombinant mutant F103L
22.7
gallate
pH 7.5, 25°C, recombinant mutant F103T
24
gallate
pH 7.5, 25°C, recombinant mutant F103V
41
gallate
pH 7.5, 25°C, recombinant mutant F103H
53
gallate
pH 7.5, 25°C, recombinant wild-type enzyme
33
protocatechuate
pH 7.5, 25°C, recombinant mutant F103L
89
protocatechuate
pH 7.5, 25°C, recombinant mutant F103V
110
protocatechuate
pH 7.5, 25°C, recombinant mutant F103H
112
protocatechuate
pH 7.5, 25°C, recombinant mutant F103T
122
protocatechuate
pH 7.5, 25°C, recombinant mutant A18W
178
protocatechuate
pH 7.5, 25°C, recombinant wild-type enzyme
216
protocatechuate
pH 7.5, 25°C, recombinant wild-type enzyme
230
protocatechuate
pH 7.5, 25°C, recombinant wild-type enzyme, with vanillin
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evolution
protocatechuate 4,5-dioxygenase (LigAB) from Sphingobium sp. strain SYK-6 is the defining member of the type II extradiol dioxygenase superfamily, a.k.a. PCA dioxygenase superfamily or PCADSF, computational docking and sequence comparisons of the enzyme with PCA dioxygenase superfamily LigAB enzymes
metabolism
-
catabolic pathway for protocatechuate in strain E6 and gene organization of the PCA45 pathway genes, overview
metabolism
-
the enzyme is involved in the catabolic degradation pathway of protocatechuate, 2-pyrone-4,6-dicarboxylate is a normal intermediate in the meta fission degradative pathway of protocatechuate
metabolism
-
the enzyme takes part in the protocatechuate (PCA) 4,5-cleavage pathway, one of the key metabolic routes for degradation of various aromatic compounds, e.g lignin-derived low-molecular-weight aromatic compounds, phthalate isomers, and fluorene
metabolism
-
the enzyme takes part in the protocatechuate (PCA) 4,5-cleavage pathway, one of the key metabolic routes for degradation of various aromatic compounds, e.g lignin-derived low-molecular-weight aromatic compounds, phthalate isomers, and fluorene
metabolism
-
catabolic pathway for protocatechuate in strain E6 and gene organization of the PCA45 pathway genes, overview
-
physiological function
the enzyme plays a key aromatic ring-opening role in the metabolism of several lignin derived aromatic compounds
physiological function
-
transcriptional regulation of the Comamonas-type enzyme, overview
physiological function
-
transcriptional regulation of the Sphingobium-type enzyme, overview
additional information
-
PCA 4,5-dioxygenase is essential for growth of strain E6 on protocatechuate, disruption of pmdB in E6, which code for the beta-subunit of PCA 4,5-dioxygenase results in a growth defect on protocatechuate, while inactivation of pmdBII does not affect the growth
additional information
-
PCA 4,5-dioxygenase is essential for growth of strain E6 on protocatechuate, disruption of pmdB in E6, which code for the beta-subunit of PCA 4,5-dioxygenase results in a growth defect on protocatechuate, while inactivation of pmdBII does not affect the growth
-
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16000
-
x * 16000, A-subunit, x * 30000, B-subunit, SDS-PAGE of His-tagged recombinant proteins. x * 18049, A-subunit, x * 33254, B-subunit, calculated for His-tagged recombinant proteins
17000
-
1 * 17000, + 1 * 34000, SDS-PAGE
17700
-
alpha2, beta2. 2 * 17700 + 2 * 33800, dimer of a heterodimer, SDS-PAGE
18000
alpha,beta, 4 * 18000 + 4 * 31000, SDS-PAGE
18049
-
x * 16000, A-subunit, x * 30000, B-subunit, SDS-PAGE of His-tagged recombinant proteins. x * 18049, A-subunit, x * 33254, B-subunit, calculated for His-tagged recombinant proteins
30000
-
x * 16000, A-subunit, x * 30000, B-subunit, SDS-PAGE of His-tagged recombinant proteins. x * 18049, A-subunit, x * 33254, B-subunit, calculated for His-tagged recombinant proteins
31000
alpha,beta, 4 * 18000 + 4 * 31000, SDS-PAGE
33254
-
x * 16000, A-subunit, x * 30000, B-subunit, SDS-PAGE of His-tagged recombinant proteins. x * 18049, A-subunit, x * 33254, B-subunit, calculated for His-tagged recombinant proteins
33800
-
alpha2, beta2. 2 * 17700 + 2 * 33800, dimer of a heterodimer, SDS-PAGE
34000
-
1 * 17000, + 1 * 34000, SDS-PAGE
62000
-
2 * 62000, SDS-PAGE
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dimer
-
1 * 17000, + 1 * 34000, SDS-PAGE
homodimer
-
2 * 62000, SDS-PAGE
?
-
x * 16000, A-subunit, x * 30000, B-subunit, SDS-PAGE of His-tagged recombinant proteins. x * 18049, A-subunit, x * 33254, B-subunit, calculated for His-tagged recombinant proteins
?
-
x * 16000, A-subunit, x * 30000, B-subunit, SDS-PAGE of His-tagged recombinant proteins. x * 18049, A-subunit, x * 33254, B-subunit, calculated for His-tagged recombinant proteins
-
monomer
1 * 45000, SDS-PAGE
monomer
-
1 * 45000, SDS-PAGE
-
octamer
alpha,beta, 4 * 18000 + 4 * 31000, SDS-PAGE
octamer
-
alpha,beta, 4 * 18000 + 4 * 31000, SDS-PAGE
-
tetramer
-
alpha2, beta2. 2 * 17700 + 2 * 33800, dimer of a heterodimer, SDS-PAGE
tetramer
-
alpha2, beta2. 2 * 17700 + 2 * 33800, dimer of a heterodimer, SDS-PAGE
-
tetramer
-
2 * alpha + 2 * beta, loose dimer of two tightly bound alpha-beta heterodimers, gel filtration, crystallographic results
tetramer
-
2 * alpha + 2 * beta, loose dimer of two tightly bound alpha-beta heterodimers, gel filtration, crystallographic results
-
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A18W
site-directed mutagenesis, mutation in the betaa-subunit, residue Ala18b is located opening of the putative allosteric pocket, the mutant displays reduced activity and altered rate enhancement by vanillin compared to the wild-type enzyme
F103H
site-directed mutagenesis, mutation in the alpha-subunit, residue Phe103a is located in the putative allosteric pocket, the mutant displays reduced activity and altered rate enhancement by vanillin compared to the wild-type enzyme
F103L
site-directed mutagenesis, mutation in the alpha-subunit, residue Phe103a is located in the putative allosteric pocket, the mutant displays reduced activity and altered rate enhancement by vanillin compared to the wild-type enzyme
additional information
in silico docking of substrates to the enzyme mutants, and impact of Phe103alpha mutations on allosteric activation of alternate substrate dioxygenation, overview
F103T
site-directed mutagenesis, mutation in the alpha-subunit, residue Phe103a is located in the putative allosteric pocket, the mutant displays reduced activity and altered rate enhancement by vanillin compared to the wild-type enzyme
F103T
site-directed mutagenesis, mutation in the alpha-subunit, the mutant shows enhanced utilization of substrates gallate and 3-O-methylgallate, but not of protocatechuate, compared to the wild-type enzyme
F103V
site-directed mutagenesis, mutation in the alpha-subunit, residue Phe103a is located in the putative allosteric pocket, the mutant displays reduced activity and altered rate enhancement by vanillin compared to the wild-type enzyme
F103V
site-directed mutagenesis, mutation in the alpha-subunit, the mutant shows enhanced utilization of substrates gallate and 3-O-methylgallate, but not of protocatechuate, compared to the wild-type enzyme
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Trippett, S.; Dagley, S.; Stopher, D.A.
Bacterial oxidation of protocatechuic acid
Biochem. J.
76
9P
1960
Pseudomonas sp.
-
brenda
Arciero, D.M.; Orville, A.M.; Lipscomb, J.D.
Protocatechuate 4,5-dioxygenase from Pseudomonas testosteroni
Methods Enzymol.
188
89-95
1990
Comamonas testosteroni, Comamonas testosteroni Pt-L5 / ATCC 49249
brenda
Zabinski, R.; Munck, E.; Champion, P.M.; Wood, J.M.
Kinetic and Mossbauer studies on the mechanism of protocatechuic acid 4,5-oxygenase
Biochemistry
11
3212-3219
1972
Comamonas testosteroni
brenda
Arciero, D.M.; Lipscomb, J.D.
Binding of 17O-labeled substrate and inhibitors to protocatechuate 4,5-dioxygenase-nitrosyl complex. Evidence for direct substrate binding to the active site Fe2+ of extradiol dioxygenases
J. Biol. Chem.
261
2170-2178
1986
Comamonas testosteroni, Comamonas testosteroni Pt-L5 / ATCC 49249
brenda
Arciero, D.M.; Orville, A.M.; Lipscomb, J.D.
Water and nitric oxide binding by protocatechuate 4,5-dioxygenase and catechol 2,3-dioxygenase. Evidence for binding of exogenous ligands to the active site Fe2+ of extradiol dioxygenases
J. Biol. Chem.
260
14035-14044
1985
Comamonas testosteroni, Comamonas testosteroni Pt-L5 / ATCC 49249
brenda
Arciero, D.M.; Lipscomb, J.D.; Huynh, B.H.; Kent, T.A.; Munck, E.
EPR and Mossbauer studies of protocatechuate 4,5-dioxygenase. Characterization of a new Fe2+ environment
J. Biol. Chem.
258
14981-14991
1983
Comamonas testosteroni
brenda
Chen, Y.P.; Lovell, C.R.
Purification and properties of a homodimeric protocatechuate 4,5-dioxygenase from Rhizobium leguminosarum
Arch. Microbiol.
161
191-195
1994
Rhizobium leguminosarum
-
brenda
Sugimoto, K.; Senda, T.; Aoshima, H.; Masai, E.; Fukuda, M.; Mitsui, Y.
Crystal structure of an aromatic ring opening dioxygenase LigAB, a protocatechuate 4,5-dioxygenase, under aerobic conditions
Structure
7
953-965
1999
Sphingomonas paucimobilis, Sphingomonas paucimobilis SYK-6
brenda
Mampel, J.; Providenti, M.A.; Cook, A.M.
Protocatechuate 4,5-dioxygenase from Comamonas testosteroni T-2: biochemical and molecular properties of a new subgroup within class III of extradiol dioxygenases
Arch. Microbiol.
183
130-139
2005
Comamonas testosteroni (Q8RNX9), Comamonas testosteroni (Q8RNY0), Comamonas testosteroni, Comamonas testosteroni T-2 (Q8RNX9), Comamonas testosteroni T-2 (Q8RNY0), Comamonas testosteroni T-2
brenda
Yun, S.H.; Yun, C.Y.; Kim, S.I.
Characterization of protocatechuate 4,5-dioxygenase induced from p-hydroxybenzoate-cultured Pseudomonas sp. K82
J. Microbiol.
42
152-155
2004
Pseudomonas sp. K82
brenda
Yoon, Y.; Park, S.; Leem, S.; Kim, S.I.
Cloning of p-hydroxybenzoate degradation genes and the overexpression of protocatechuate 4,5-dioxygenase from Pseudomonas sp. K82
J. Microbiol. Biotechnol.
16
1995-1999
2006
Pseudomonas sp. (Q1WCM6), Pseudomonas sp. (Q1WCM7)
-
brenda
Kasai, D.; Masai, E.; Katayama, Y.; Fukuda, M.
Degradation of 3-O-methylgallate in Sphingomonas paucimobilis SYK-6 by pathways involving protocatechuate 4,5-dioxygenase
FEMS Microbiol. Lett.
274
323-328
2007
Sphingomonas paucimobilis, Sphingomonas paucimobilis SYK-6
brenda
Kamimura, N.; Aoyama, T.; Yoshida, R.; Takahashi, K.; Kasai, D.; Abe, T.; Mase, K.; Katayama, Y.; Fukuda, M.; Masai, E.
Characterization of the protocatechuate 4,5-cleavage pathway operon in Comamonas sp. strain E6 and discovery of a novel pathway gene
Appl. Environ. Microbiol.
76
8093-8101
2010
Comamonas sp., Comamonas sp. E6
brenda
Kersten, P.J.; Dagley, S.; Whittaker, J.W.; Arciero, D.M.; Lipscomb, J.D.
2-pyrone-4,6-dicarboxylic acid, a catabolite of gallic acids in Pseudomonas species
J. Bacteriol.
152
1154-1162
1982
Brevibacterium fuscum
brenda
Wojcieszynska, D.; Guzik, U.; Gren, I.; Perkosz, M.; Hupert-Kocurek, K.
Induction of aromatic ring: cleavage dioxygenases in Stenotrophomonas maltophilia strain KB2 in cometabolic systems
World J. Microbiol. Biotechnol.
27
805-811
2011
no activity in Stenotrophomonas maltophilia, no activity in Stenotrophomonas maltophilia KB2
brenda
Barry, K.P.; Ngu, A.; Cohn, E.F.; Cote, J.M.; Burroughs, A.M.; Gerbino, J.P.; Taylor, E.A.
Exploring allosteric activation of LigAB from Sphingobium sp. strain SYK-6 through kinetics, mutagenesis and computational studies
Arch. Biochem. Biophys.
567
35-45
2015
Sphingobium sp. (G2IQQ4 AND G2IQQ3), Sphingobium sp.
brenda
Kamimura, N.; Masai, E.
The protocatechuate 4,5-cleavage pathway overview and new findings
Biodegr. Bacteria
2014
207-226
2014
Comamonas sp., Sphingobium sp.
-
brenda
Barry, K.; Cohn, E.; Ngu, A.; Taylor, E.
Improving alternate lignin catabolite utilization of LigAB from Sphingobium sp. strain SYK-6 through site directed mutagenesis
Process Biochem.
50
1634-1639
2015
Sphingobium sp. (G2IQQ4 AND G2IQQ3)
-
brenda
Tsagogiannis, E.; Vandera, E.; Primikyri, A.; Asimakoula, S.; Tzakos, A.G.; Gerothanassis, I.P.; Koukkou, A.I.
Characterization of protocatechuate 4,5-dioxygenase from Pseudarthrobacter phenanthrenivorans Sphe3 and in situ reaction monitoring in the NMR tube
Int. J. Mol. Sci.
22
9647
2021
Pseudarthrobacter phenanthrenivorans (F0MCP7), Pseudarthrobacter phenanthrenivorans Sphe3 (F0MCP7), Pseudarthrobacter phenanthrenivorans Sphe3
brenda