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 ACCESSION NO.
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
-
protocatechuate + O2 = 4-carboxy-2-hydroxymuconate semialdehyde
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
extradiol cleavage
-
-
-
-
oxidation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
-
PATHWAY
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 ACCESSION NO.
COMMENTARY
LITERATURE
LigAB
Sphingomonas paucimobilis SYK-6
-
-
-
PCA 4,5-dioxygenase
-
-
PCA 4,5-dioxygenase
-
-
-
PCD4,5
Q1WCM6, Q1WCM7
-
PmdAB
Comamonas testosteroni T-2
Q8RNX9
-
-
protocatechuate 4,5-oxygenase
-
-
-
-
protocatechuic 4,5-dioxygenase
-
-
-
-
protocatechuic 4,5-oxygenase
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
9029-56-5
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
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 ACCESSION NO.
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 ACCESSION NO.
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 ACCESSION NO.
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 ACCESSION NO.
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 ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
3-Amino-4-hydroxybenzoic acid
-
-
3-Chloro-4-hydroxybenzoic acid
-
-
3-Fluoro-4-hydroxybenzoic acid
-
-
3-Hydroxy-4-aminobenzoic acid
-
-
3-Iodo-4-hydroxybenzoic acid
-
-
3-Methoxy-4-hydroxybenzoic acid
-
-
3-Nitro-4-hydroxybenzoic acid
-
-
4-nitrocatechol
-
competitive inhibitor
iodoacetamide
-
competitive inhibitor
p-chloromercuribenzoic acid
-
excellent competitive inhibitor
Protocatechualdehyde
-
competitive inhibitor
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
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]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
350
-
protocatechuate
-
-
Ki VALUE [mM]
Ki VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
3.3
-
3-Hydroxybenzoate
-
-
1
-
4-hydroxybenzoate
-
-
0.56
-
4-nitrocatechol
-
-
0.96
-
Protocatechualdehyde
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
0.1
-
-, Q8RNX9, Q8RNY0
-
50
-
-
purified enzyme, pH 7.0, temperature not specified in the publication
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7
-
-
assay at
8.5
-
-
assay at
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
30
-
-
enzyme assay
30
-
-
assay at
TEMPERATURE RANGE
TEMPERATURE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
5
35
-
approx. 85% of maximal activity at 5°C, approx. 20% of maximal activity at 35°C
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
54000
-
-
gel filtration
120000
-
-
gel filtration
142000
-
-
gel filtration
180000
-
-, Q8RNX9, Q8RNY0
gel filtration
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
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
Comamonas testosteroni Pt-L5
-
alpha2, beta2. 2 * 17700 + 2 * 33800, dimer of a heterodimer, SDS-PAGE
-
tetramer
Sphingomonas paucimobilis SYK-6
-
2 * alpha + 2 * beta, loose dimer of two tightly bound alpha-beta heterodimers, gel filtration, crystallographic results
-
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
under strictly anaerobic conditions
-
under aerobic conditions
-
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
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 ACCESSION NO.
LITERATURE
rapidly inactivated by oxidizing agents such as H2O2 or ferricyanide, partial reactivation by ascorbate
-
439357
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
-196°C, in liquid nitrogen, without significant loss of activity for several years
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
heat treatment, DEAE-Sepharose, superdex 200, Resource Q
-, Q8RNX9, Q8RNY0
ammonium sulfate, Q-Sepharose
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
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 ACCESSION NO.
LITERATURE
the enzyme is induced by protocatechuate
-
the enzyme is induced by protocatechuate
-
-