Information on EC 1.13.11.8 - protocatechuate 4,5-dioxygenase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
1.13.11.8
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RECOMMENDED NAME
GeneOntology No.
protocatechuate 4,5-dioxygenase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
protocatechuate + O2 = 4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
extradiol cleavage
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oxidation
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redox reaction
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reduction
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
3,4-dichlorobenzoate degradation
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3-chlorobenzoate degradation II (via protocatechuate)
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protocatechuate degradation I (meta-cleavage pathway)
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Benzoate degradation
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Polycyclic aromatic hydrocarbon degradation
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Aminobenzoate degradation
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Microbial metabolism in diverse environments
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SYSTEMATIC NAME
IUBMB Comments
protocatechuate:oxygen 4,5-oxidoreductase (decyclizing)
Requires Fe2+.
CAS REGISTRY NUMBER
COMMENTARY hide
9029-56-5
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
a phthalate-degrading bacterium, gene pmdB encodes for the beta-subunit of PCA 4,5-dioxygenase, and harboring of another PCA 4,5-dioxygenase gene, pmdAIIBII
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Manually annotated by BRENDA team
no activity in Stenotrophomonas maltophilia
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Manually annotated by BRENDA team
no activity in Stenotrophomonas maltophilia KB2
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Manually annotated by BRENDA team
biovar viceae, strain USDA 2370, grown on 4-hydroxybenzoate-containing medium
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
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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
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
3,4-dihydroxyphenyl sulfonate + O2
2-hydroxy-6-oxo-4-sulfohexa-2,4-dienoate
show the reaction diagram
3-O-methylgallate + O2
4-carboxy-2-hydroxy-6-methoxy-6-oxohexa-2,4-dienoate + 2-pyrone-4,6-dicarboxylate
show the reaction diagram
3-O-methylgallate + O2
?
show the reaction diagram
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-
-
-
?
5-methoxygallic acid + O2
?
show the reaction diagram
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-
-
-
?
5-methylprotocatechuate + O2
4-carboxy-2-hydroxy-3-methylmuconate semialdehyde
show the reaction diagram
gallate + O2
?
show the reaction diagram
gallic acid + O2
2-pyrone-4,6-dicarboxylic acid + H2O
show the reaction diagram
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major product formed
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?
gallic acid + O2
?
show the reaction diagram
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?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
sulfonylcatechol + O2
?
show the reaction diagram
additional information
?
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
gallic acid + O2
2-pyrone-4,6-dicarboxylic acid + H2O
show the reaction diagram
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major product formed
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?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3-Amino-4-hydroxybenzoic acid
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3-Chloro-4-hydroxybenzoic acid
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3-Fluoro-4-hydroxybenzoic acid
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3-Hydroxy-4-aminobenzoic acid
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3-hydroxybenzoate
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3-Iodo-4-hydroxybenzoic acid
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3-methoxy-4-hydroxybenzoic acid
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3-Nitro-4-hydroxybenzoic acid
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4-hydroxybenzoate
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4-nitrocatechol
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competitive inhibitor
iodoacetamide
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competitive inhibitor
p-chloromercuribenzoic acid
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excellent competitive inhibitor
Protocatechualdehyde
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competitive inhibitor
protocatechuate
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substrate inhibition
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Vanillin
additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.39 - 4
3-O-methylgallate
0.125
5-methoxygallic acid
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0.19 - 7
gallate
0.0735
gallic acid
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0.02 - 1.6
protocatechuate
additional information
additional information
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
7 - 91
3-O-methylgallate
5 - 53
gallate
33 - 350
protocatechuate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
21 - 2200
protocatechuate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3.3
3-hydroxybenzoate
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1
4-hydroxybenzoate
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0.56
4-nitrocatechol
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0.96
Protocatechualdehyde
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17 - 18
protocatechuate
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
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purified enzyme, pH 7.0, temperature not specified in the publication
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.5
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assay at
8.5
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assay at
9.5 - 9.8
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CAPS
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25
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assay at
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 35
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approx. 85% of maximal activity at 5C, approx. 20% of maximal activity at 35C
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
16000
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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
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1 * 17000, + 1 * 34000, SDS-PAGE
17700
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alpha2, beta2. 2 * 17700 + 2 * 33800, dimer of a heterodimer, SDS-PAGE
18000
alpha,beta, 4 * 18000 + 4 * 31000, SDS-PAGE
18049
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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
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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
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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
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alpha2, beta2. 2 * 17700 + 2 * 33800, dimer of a heterodimer, SDS-PAGE
34000
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1 * 17000, + 1 * 34000, SDS-PAGE
54000
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gel filtration
62000
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2 * 62000, SDS-PAGE
120000
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gel filtration
142000
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gel filtration
180000
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
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1 * 17000, + 1 * 34000, SDS-PAGE
homodimer
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2 * 62000, SDS-PAGE
octamer
tetramer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
under strictly anaerobic conditions
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under aerobic conditions
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
dialysis can be performed only at temperatures at or below 4C
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rapid loss of activity during purification due to the oxidation of an active-site ferrous iron group
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
rapidly inactivated by oxidizing agents such as H2O2 or ferricyanide, partial reactivation by ascorbate
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439357
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-196C, in liquid nitrogen, without significant loss of activity for several years
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate, Q-Sepharose
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heat treatment, DEAE-Sepharose, superdex 200, Resource Q
recombinant His6-tagged wild-type and mutant enzymes anaerobically from Escherichia coli strain DH5alpha by nickel affinity chromatography, tag cleavage anaerobically by thrombin cleavage
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
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gene organization of the PCA45 pathway genes in strain E6, overview. Identification of the pmd promoter region, the transcription start site of the pmd operon is a thymine 167 nt upstream of the pmdU start codon, overview
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genetic organization Comamonas-type with a single operon
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genetic organization Sphingobium-type with several transcriptional units
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recombinant expression of His6-tagged wild-type and mutant enzymes in Escherichia coli strain DH5alpha
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
the enzyme is induced by protocatechuate
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
A18W
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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
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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
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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
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in silico docking of substrates to the enzyme mutants, and impact of Phe103alpha mutations on allosteric activation of alternate substrate dioxygenation, overview
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
biofuel production
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enhanced utilization of substrates by enzyme mutants F103T and F103V makes them potentially useful for efforts to develop engineered organisms that catabolize lignin into biofuels or fine chemicals
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