Information on EC 1.13.11.38 - 1-hydroxy-2-naphthoate 1,2-dioxygenase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
1.13.11.38
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RECOMMENDED NAME
GeneOntology No.
1-hydroxy-2-naphthoate 1,2-dioxygenase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
1-hydroxy-2-naphthoate + O2 = (3Z)-4-(2-carboxyphenyl)-2-oxobut-3-enoate
show the reaction diagram
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
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redox reaction
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reduction
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Microbial metabolism in diverse environments
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Polycyclic aromatic hydrocarbon degradation
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SYSTEMATIC NAME
IUBMB Comments
1-hydroxy-2-naphthoate:oxygen 1,2-oxidoreductase (decyclizing)
Requires Fe2+. Involved, with EC 4.1.2.34 4-(2-carboxyphenyl)-2-oxobut-3-enoate aldolase, in the metabolism of phenanthrene in bacteria.
CAS REGISTRY NUMBER
COMMENTARY hide
85941-64-6
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Gram-negative coccus
strain B156 isolated from soil and able to grow on phenanthrene as sole source of carbon and energy
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Manually annotated by BRENDA team
Gram-negative coccus B156
strain B156 isolated from soil and able to grow on phenanthrene as sole source of carbon and energy
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Manually annotated by BRENDA team
strain PPD
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Manually annotated by BRENDA team
strain PPD
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
metabolism
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
1-hydroxy-2-naphthoate + O2
(3E)-4-(2-carboxyphenyl)-2-oxobut-3-enoate
show the reaction diagram
1-hydroxy-2-naphthoate + O2
(3Z)-4-(2-carboxyphenyl)-2-oxobut-3-enoate
show the reaction diagram
1-hydroxy-2-naphthoate + O2
?
show the reaction diagram
1-hydroxy-2-naphthoic acid + O2
2-carboxybenzylpyruvic acid
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
1-hydroxy-2-naphthoate + O2
(3E)-4-(2-carboxyphenyl)-2-oxobut-3-enoate
show the reaction diagram
1-hydroxy-2-naphthoate + O2
(3Z)-4-(2-carboxyphenyl)-2-oxobut-3-enoate
show the reaction diagram
1-hydroxy-2-naphthoic acid + O2
2-carboxybenzylpyruvic acid
show the reaction diagram
additional information
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Iron
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contains 1.15 mol of iron per mol of enzyme
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,10-phenanthroline
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1-hydroxy-2-naphthoic acid
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substrate inhibition
3-hydroxy-2-naphthoate
3-Hydroxy-2-naphthoic acid
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competitive inhibition
Fe3+
Gram-negative coccus
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o-phenanthroline
additional information
no inhibition when the concentration of the substrate 1-hydroxy-2-napthoate is 0.01 mM and that of the tested compounds is 0.1 or 1 mM: gentisate, 3-hydroxyanthranilate, 2-hydroxy-1-naphthoate, salicylate, m-hydroxybenzoate, p-hydroxybenzoate, and protocatechuate
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.01 - 0.144
1-hydroxy-2-naphthoate
0.0135
2-Hydroxy-1-naphthoic acid
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additional information
additional information
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.2 - 114
1-hydroxy-2-naphthoate
70.4
2-Hydroxy-1-naphthoic acid
Pseudomonas sp.
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
27.5 - 369.6
1-hydroxy-2-naphthoate
2064
5185
2-Hydroxy-1-naphthoic acid
Pseudomonas sp.
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15493
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.116
1-hydroxy-2-naphthoic acid
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substrate inhibition
0.022
3-hydroxy-2-naphthoate
0.024
3-Hydroxy-2-naphthoic acid
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competitive inhibition
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.9
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cell-free extract
8.4
enzyme in extract of strain KP7
11.2
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heat treatment (60°C)
29
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anion-exchange chromatography
53
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3-H2NA-affinity chromatography
61.5
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after all purification steps from Pseudomonas sp. PPD cells grown on phenanthrene
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
39000
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SDS-PAGE under denaturing conditions, 4 * 39000
42000
x * 42000, recombinant Diox1, x * 45000, native enzyme, SDS-PAGE; x * 42000, recombinant Diox2, x * 45000, native enzyme, SDS-PAGE
160000
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Sephacryl S-200-HR gel-filtration chromatography; SDS-PAGE under denaturing conditions, homotetramer, subunit molecular mass of about 39000
180000
gel filtration; gel filtration
185000
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gel filtration
270000
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexamer
tetramer
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
mutant A85H and W104Y variants and mutant W104Y with gentiate, sitting drop vapor diffusion method, 4°C, mixing of 0.001 ml of protein solution with 0.0008 ml of crystallization solution containing 8% PEG10000 and 0.1 M Tris-HCl pH 8.0, with 0.0002 ml of a 0.1 M calcium chloride solution, crystals quality is also improved using seeding techniques, X-ray diffraction structure determination and analysis at 2.5-2.7 A resolution
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0
Gram-negative coccus
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24 h, 90% loss of activity
60
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heat stability for 20 min at 60°C
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
no stabilization by ethanol, acetone or glycerol up to 10% v/v
Gram-negative coccus
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the enzyme is very unstable in the cell-free extract and requires Fe(II) (0.1 mM), DTT (2 mM) and ethanol (10%) for stability
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C, purified enzyme, 1 mM DTT, 48 h, stable
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
native enzyme by anion exchange and hydrophobic interaction chromatography, and gel filtration; native enzyme by anion exchange and hydrophobic interaction chromatography, and gel filtration
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21 (DE3) by nickel affinity chromatography
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strain B156, isolated from soil and able to grow on phenanthrene as sole source of carbon and energy, partial purification
Gram-negative coccus
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to homogeneity using a 3-hydroxy-2-naphthoic acid (3-H2NA)-affinity matrix, DEAE-anion-exchange chromatography
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21 (DE3)
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gene diox1, gene diox1 is found on an indigenous Sphe3 plasmid, DNA and amino acid sequence determination and analysis, genetic organization, sequence comparisons and phylogenetic tree. The relative RNA transcription level of the chromosomal (diox2) gene is significantly higher than that of its plasmid (diox1) homol, overexpression in Escherichia coli; gene diox2, diox2 is located on the chromosome, DNA and amino acid sequence determination and analysis, genetic organization, sequence comparisons and phylogenetic tree. The relative RNA transcription level of the chromosomal (diox2) gene is significantly higher than that of its plasmid (diox1) homol, overexpression in Escherichia coli
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
gene diox1 is induced by the presence of phenanthrene used as a sole carbon and energy source; gene diox2 is induced by the presence of phenanthrene used as a sole carbon and energy source
gene diox1 is subject to carbon catabolite repression; gene diox2 is subject to carbon catabolite repression
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
A85H
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site-directed mutagenesis, the salicylate 1,2-dioxygenase variant shows higher catalytic efficiencies toward 1-hydroxy-2-naphthoate than the wild-type enzyme and no more activity with gentisate. substitution of Ala85 with a histidine residue caused significant changes in the orientation of the loop containing this residue which is involved in the active site closing upon substrate binding. In SDO A85H this specific loop shifts away from the active site and thus opens the cavity favoring the binding of bulkier substrates. Since this loop also interacts with the N-terminal residues of the vicinal subunit, the structure and packing of the holoenzyme might be also affected.
L38Q
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site-directed mutagenesis, the salicylate 1,2-dioxygenase variant shows higher catalytic efficiencies toward 1-hydroxy-2-naphthoate compared to gentisate than the wild-type enzyme
W104Y
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site-directed mutagenesis, the salicylate 1,2-dioxygenase variant shows increased catalytic efficiencies toward 1-hydroxy-2-naphthoate compared to gentisate and to the wild-type enzyme. W104Y SDO mutant exhibits reduced reaction rates for all substrates
A85H
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site-directed mutagenesis, the salicylate 1,2-dioxygenase variant shows higher catalytic efficiencies toward 1-hydroxy-2-naphthoate than the wild-type enzyme and no more activity with gentisate. substitution of Ala85 with a histidine residue caused significant changes in the orientation of the loop containing this residue which is involved in the active site closing upon substrate binding. In SDO A85H this specific loop shifts away from the active site and thus opens the cavity favoring the binding of bulkier substrates. Since this loop also interacts with the N-terminal residues of the vicinal subunit, the structure and packing of the holoenzyme might be also affected.
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L38Q
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site-directed mutagenesis, the salicylate 1,2-dioxygenase variant shows higher catalytic efficiencies toward 1-hydroxy-2-naphthoate compared to gentisate than the wild-type enzyme
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W104Y
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site-directed mutagenesis, the salicylate 1,2-dioxygenase variant shows increased catalytic efficiencies toward 1-hydroxy-2-naphthoate compared to gentisate and to the wild-type enzyme. W104Y SDO mutant exhibits reduced reaction rates for all substrates
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additional information