Information on EC 1.13.11.8 - protocatechuate 4,5-dioxygenase

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The expected taxonomic range for this enzyme is: Bacteria

EC NUMBER
COMMENTARY
1.13.11.8
-
RECOMMENDED NAME
GeneOntology No.
protocatechuate 4,5-dioxygenase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
protocatechuate + O2 = 4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
involvement of sulfhydryl groups at the active site, 2 free sulfhydryl groups per enzyme molecule
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
extradiol cleavage
-
-
-
-
oxidation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
3,4-dichlorobenzoate degradation
-
-
3-chlorobenzoate degradation II (via protocatechuate)
-
-
Aminobenzoate degradation
-
-
Benzoate degradation
-
-
Microbial metabolism in diverse environments
-
-
Polycyclic aromatic hydrocarbon degradation
-
-
protocatechuate degradation I (meta-cleavage pathway)
-
-
SYSTEMATIC NAME
IUBMB Comments
protocatechuate:oxygen 4,5-oxidoreductase (decyclizing)
Requires Fe2+.
SYNONYMS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
protocatechuate 4,5-oxygenase
-
-
-
-
protocatechuic 4,5-dioxygenase
-
-
-
-
protocatechuic 4,5-oxygenase
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
9029-56-5
-
ORGANISM
COMMENTARY
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
-
-
Manually annotated by BRENDA team
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
-
-
Manually annotated by BRENDA team
alpha-subunit; T-2
SwissProt
Manually annotated by BRENDA team
beta-subunit; T-2
Swissprot
Manually annotated by BRENDA team
grown on 4-hydroxybenzoate containing medium; strain Pt-L5, ATCC 49249
-
-
Manually annotated by BRENDA team
grown on p-hydroxybenzoate-containing medium
-
-
Manually annotated by BRENDA team
grown on p-hydroxybenzoate-containing medium; strain Pt-L5, ATCC 49249
-
-
Manually annotated by BRENDA team
strain Pt-L5, ATCC 49249
-
-
Manually annotated by BRENDA team
Comamonas testosteroni Pt-L5
strain Pt-L5, ATCC 49249
-
-
Manually annotated by BRENDA team
Comamonas testosteroni T-2
alpha-subunit; T-2
SwissProt
Manually annotated by BRENDA team
Comamonas testosteroni T-2
beta-subunit; T-2
Swissprot
Manually annotated by BRENDA team
no activity in Stenotrophomonas maltophilia
-
-
-
Manually annotated by BRENDA team
no activity in Stenotrophomonas maltophilia KB2
-
-
-
Manually annotated by BRENDA team
protocatechuate 4,5-dioxygenase alpha subunit; strain K82
SwissProt
Manually annotated by BRENDA team
protocatechuate 4,5-dioxygenase beta subunit; strain K82
SwissProt
Manually annotated by BRENDA team
biovar viceae, strain USDA 2370, grown on 4-hydroxybenzoate-containing medium
-
-
Manually annotated by BRENDA team
Sphingomonas paucimobilis SYK-6
strain SYK-6
-
-
Manually annotated by BRENDA team
Sphingomonas paucimobilis SYK-6
SYK-6
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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
-
catabolic pathway for protocatechuate in strain E6 and gene organization of the PCA45 pathway genes, 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
-
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
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
Comamonas testosteroni, Comamonas testosteroni Pt-L5
-
-
-
-
?
3-O-methylgallate + O2
4-carboxy-2-hydroxy-6-methoxy-6-oxohexa-2,4-dienoate + 2-pyrone-4,6-dicarboxylate
show the reaction diagram
Sphingomonas paucimobilis, Sphingomonas paucimobilis SYK-6
-
-
-
-
?
5-methoxygallic acid + O2
?
show the reaction diagram
-
-
-
-
?
5-methylprotocatechuate + O2
4-carboxy-2-hydroxy-3-methylmuconate semialdehyde
show the reaction diagram
Comamonas testosteroni, Comamonas testosteroni Pt-L5
-
-
-
-
?
gallate + O2
?
show the reaction diagram
Q8RNX9, Q8RNY0
-
-
-
?
gallate + O2
?
show the reaction diagram
Comamonas testosteroni T-2
Q8RNX9, Q8RNY0
-
-
-
?
gallic acid + O2
?
show the reaction diagram
-
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
-
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
-
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
-
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
-
-
-
-
-
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
Q8RNX9, Q8RNY0
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
-
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
Sphingomonas paucimobilis SYK-6
-
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
Comamonas testosteroni T-2
Q8RNX9, Q8RNY0
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
Comamonas testosteroni Pt-L5
-
-
-
-
?
sulfonylcatechol + O2
?
show the reaction diagram
Comamonas testosteroni, Comamonas testosteroni Pt-L5
-
-
-
-
?
gallic acid + O2
2-pyrone-4,6-dicarboxylic acid + H2O
show the reaction diagram
-
-
major product formed
-
?
additional information
?
-
-
no activity on 3-O-methylgallate
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
gallic acid + O2
2-pyrone-4,6-dicarboxylic acid + H2O
show the reaction diagram
-
-
major product formed
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
-
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
-
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
-
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
Q8RNX9, Q8RNY0
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
-
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
Sphingomonas paucimobilis SYK-6
-
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
Comamonas testosteroni T-2
Q8RNX9, Q8RNY0
-
-
-
?
protocatechuate + O2
4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
Comamonas testosteroni Pt-L5
-
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe2+
-
iron is present in active enzyme in the high-spin ferrous state; present at a significant mol fraction, metal-free enzyme is inactive, iron can be removed by treatment with tiron
Fe2+
-
four iron atoms per molecule
Fe2+
-
characterization of Fe2+ environment with EPR and Mössbauer studies; iron is present in active enzyme in the high-spin ferrous state
Fe2+
-
1 mol iron per mol of holoenzyme
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3-Amino-4-hydroxybenzoic acid
-
-
3-Chloro-4-hydroxybenzoic acid
-
-
3-Fluoro-4-hydroxybenzoic acid
-
-
3-Hydroxy-4-aminobenzoic acid
-
-
3-Hydroxybenzoate
-
-
3-Iodo-4-hydroxybenzoic acid
-
-
3-methoxy-4-hydroxybenzoic acid
-
-
3-Nitro-4-hydroxybenzoic acid
-
-
4-hydroxybenzoate
-
-
4-nitrocatechol
-
competitive inhibitor
iodoacetamide
-
competitive inhibitor
p-chloromercuribenzoic acid
-
excellent competitive inhibitor
Protocatechualdehyde
-
competitive inhibitor
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.125
5-methoxygallic acid
-
-
0.0735
gallic acid
-
-
0.02
protocatechuate
-
-
0.046
protocatechuate
-
-
0.055
protocatechuate
Q8RNX9, Q8RNY0
30°C, pH 7.5
0.08
protocatechuate
-
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
350
protocatechuate
-
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
3.3
3-Hydroxybenzoate
-
-
1
4-hydroxybenzoate
-
-
0.56
4-nitrocatechol
-
-
0.96
Protocatechualdehyde
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.1
Q8RNX9, Q8RNY0
-
50
-
purified enzyme, pH 7.0, temperature not specified in the publication
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
8.5
-
assay at
9.5 - 9.8
-
CAPS
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
-
enzyme assay
30
-
assay at
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5 - 35
-
approx. 85% of maximal activity at 5°C, approx. 20% of maximal activity at 35°C
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
54000
-
gel filtration
659688
120000
-
gel filtration
439362
140000
-
-
439358
142000
-
gel filtration
439357, 439361
180000
Q8RNX9, Q8RNY0
gel filtration
657697
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
?
-
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
?
Sphingomonas paucimobilis SYK-6
-
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
-
dimer
-
1 * 17000, + 1 * 34000, SDS-PAGE
homodimer
-
2 * 62000, SDS-PAGE
octamer
Q8RNX9, Q8RNY0
alpha,beta, 4 * 18000 + 4 * 31000, SDS-PAGE
octamer
Comamonas testosteroni T-2
-
alpha,beta, 4 * 18000 + 4 * 31000, 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
Sphingomonas paucimobilis SYK-6
-
2 * alpha + 2 * beta, loose dimer of two tightly bound alpha-beta heterodimers, gel filtration, crystallographic results
-
tetramer
Comamonas testosteroni Pt-L5
-
alpha2, beta2. 2 * 17700 + 2 * 33800, dimer of a heterodimer, SDS-PAGE
-
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
under strictly anaerobic conditions
-
under aerobic conditions
-
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
dialysis can be performed only at temperatures at or below 4°C
-
rapid loss of activity during purification due to the oxidation of an active-site ferrous iron group
-
OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
rapidly inactivated by oxidizing agents such as H2O2 or ferricyanide, partial reactivation by ascorbate
-
439357
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-196°C, in liquid nitrogen, without significant loss of activity for several years
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
heat treatment, DEAE-Sepharose, superdex 200, Resource Q
Q8RNX9, Q8RNY0
ammonium sulfate, Q-Sepharose
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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
-
;
Q1WCM6, Q1WCM7
expression in Escherichia coli
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
the enzyme is induced by protocatechuate
-
the enzyme is induced by protocatechuate
-
-