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Enzyme Nomenclature
Information on EC 1.13.11.4 - gentisate 1,2-dioxygenase
for references in articles please use BRENDA:EC1.13.11.4
Word Map on EC 1.13.11.4
- 1.13.11.4
- maleylpyruvate
- protocatechuate
- 3-hydroxybenzoate
- alcaligenes
-
pseudaminobacter
- salicylatoxidans
- 1-hydroxy-2-naphthoate
-
3,4-dioxygenase
-
monohydroxylated
- fumarylpyruvate
-
5-hydroxylase
-
isofunctional
-
ncimb
-
ring-fission
-
extradiol
-
bicupins
-
ring-cleaving
- acidovorans
- nocardioides
- 5-aminosalicylate
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The expected taxonomic range for this enzyme is: Bacteria, Archaea
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EC NUMBER 
COMMENTARY 
1.13.11.4
-
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RECOMMENDED NAME
GeneOntology No.
gentisate 1,2-dioxygenase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2,5-dihydroxybenzoate + O2 = maleylpyruvate
-
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
oxidation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
gentisate:oxygen 1,2-oxidoreductase (decyclizing)
Requires Fe2+.
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CAS REGISTRY NUMBER
COMMENTARY
9029-48-5
-
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
three nagl genes, nagI1, nagI2, and nagI3, the latter belongs to the third cluster
-
-
three nagl genes, nagI1, nagI2, and nagI3, the latter belongs to the third cluster
-
-
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
physiological function
additional information
metabolism
the gene genH belongs to the group involved in naphthalene and salicylate degradation, by the nar and gen gene clusters, respectively, overview
metabolism
narI is involved in salicylate, i.e. 3-hydroxybenzoate, and gentisate catabolism, organization of the 3HBA-gentisate catabolic cluster, overview
metabolism
-
strain CJ2 metabolizes naphthalene via the gentisate pathway using gentisate 1,2-dioxygenase, patterns in regulation, transcription and enzyme activity, overview. The nagR regulator controls the third catabolic gene cluster
metabolism
-
strain CJ2 metabolizes naphthalene via the gentisate pathway using gentisate 1,2-dioxygenase, patterns in regulation, transcription and enzyme activity, overview. The nagR regulator controls the third catabolic gene cluster
-
metabolism
-
the gene genH belongs to the group involved in naphthalene and salicylate degradation, by the nar and gen gene clusters, respectively, overview
-
metabolism
-
narI is involved in salicylate, i.e. 3-hydroxybenzoate, and gentisate catabolism, organization of the 3HBA-gentisate catabolic cluster, overview
-
physiological function
-
although all three nagI genes in strain CJ2 influence naphthalene degradation, the nagI3 gene plays the most significant role. NagI3 may prevent toxic intracellular levels of gentisate from accumulating in CJ2 cells
physiological function
the enzyme is involved in the 3-phenylpropionic acid degradation pathway
physiological function
-
although all three nagI genes in strain CJ2 influence naphthalene degradation, the nagI3 gene plays the most significant role. NagI3 may prevent toxic intracellular levels of gentisate from accumulating in CJ2 cells
-
additional information
strain NCIMB 12038 utilizes naphthalene as a sole source of carbon and energy, and degrades naphthalene via salicylate and gentisate. The strain can also use salicylate, i.e. 3-hydroxybenzoate, as sole source of energy and carbon
additional information
-
strain NCIMB 12038 utilizes naphthalene as a sole source of carbon and energy, and degrades naphthalene via salicylate and gentisate. The strain can also use salicylate, i.e. 3-hydroxybenzoate, as sole source of energy and carbon
additional information
-
binding modes for salicylate and gentisate
additional information
-
binding modes for salicylate and gentisate
-
additional information
-
strain NCIMB 12038 utilizes naphthalene as a sole source of carbon and energy, and degrades naphthalene via salicylate and gentisate. The strain can also use salicylate, i.e. 3-hydroxybenzoate, as sole source of energy and carbon
-
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
3-bromosalicylate + O2
?
-
kcat/KM is less than 1% of the kcat/Km for gentisate
-
-
?
3-chlorogentisate + O2
3-chloro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-chlorosalicylate + O2
?
-
kcat/KM is less than 1% of the kcat/Km for gentisate
-
-
?
3-hydroxysalicylate + O2
?
-
kcat/KM is less than 1% of the kcat/Km for gentisate
-
-
?
3-methylgentisate + O2
3-methyl-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
Vmax is 10.1% of Vmax for gentisate
-
-
?
3-methylsalicylate + O2
?
-
kcat/KM is less than 1% of the kcat/Km for gentisate
-
-
?
4-bromosalicylate + O2
?
-
kcat/KM is less than 1% of the kcat/Km for gentisate
-
-
?
4-chlorosalicylate + O2
?
-
kcat/KM is less than 1% of the kcat/Km for gentisate
-
-
?
4-hydroxysalicylate + O2
?
-
kcat/KM is less than 1% of the kcat/Km for gentisate
-
-
?
4-methylgentisate + O2
4-hydroxy-2-isopropyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
4-methylsalicylate + O2
?
-
kcat/KM is less than 1% of the kcat/Km for gentisate
-
-
?
5-bromosalicylate + O2
?
-
kcat/KM is less than 1% of the kcat/Km for gentisate
-
-
?
5-chlorosalicylate + O2
?
-
kcat/KM is less than 1% of the kcat/Km for gentisate
-
-
?
1-hydroxy-2-naphthoate + O2
?
weak activity
-
-
?
2,5-dihydroxybenzoate + O2
maleylpyruvate
the enzyme is highly specific for 2,5-dihydroxybenzoate
-
-
?
2,5-dihydroxybenzoate + O2
maleylpyruvate
the enzyme is highly specific for 2,5-dihydroxybenzoate
-
-
?
2,5-dihydroxybenzoate + O2
maleylpyruvate
the enzyme is involbved in the 3-phenylpropionic acid deg´radation pathway
-
-
?
2,5-dihydroxybenzoate + O2
maleylpyruvate
-
-
-
-
?
2,5-dihydroxybenzoate + O2
maleylpyruvate
-
i.e. gentisate
-
-
?
2,5-dihydroxybenzoate + O2
maleylpyruvate
-
-
-
-
?
2,5-dihydroxybenzoate + O2
maleylpyruvate
-
-
-
?
3,4-dichlorosalicylate + O2
?
-
kcat/KM is less than 1% of the kcat/Km for gentisate
-
-
?
3,4-dichlorosalicylate + O2
?
-
kcat/KM is less than 1% of the kcat/Km for gentisate
-
-
?
3,5-dibromosalicylate + O2
?
-
kcat/KM is less than 1% of the kcat/Km for gentisate
-
-
?
3,5-dibromosalicylate + O2
?
-
kcat/KM is less than 1% of the kcat/Km for gentisate
-
-
?
3-aminosalicylate + O2
?
-
kcat/KM is less than 1% of the kcat/Km for gentisate
-
-
?
3-aminosalicylate + O2
?
-
kcat/KM is less than 1% of the kcat/Km for gentisate
-
-
?
3-bromogentisate + O2
3-bromo-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-bromogentisate + O2
3-bromo-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-bromogentisate + O2
3-bromo-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-bromogentisate + O2
3-bromo-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-bromogentisate + O2
3-bromo-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
Vmax is 48.5% of Vmax for gentisate
-
-
?
3-bromogentisate + O2
3-bromo-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-bromogentisate + O2
3-bromo-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-bromogentisate + O2
3-bromo-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-bromogentisate + O2
3-bromo-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-ethylgentisate + O2
3-ethyl-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-ethylgentisate + O2
3-ethyl-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-ethylgentisate + O2
3-ethyl-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-ethylgentisate + O2
3-ethyl-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
Vmax is 39.7% of Vmax for gentisate
-
-
?
3-ethylgentisate + O2
3-ethyl-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
Vmax is 39.7% of Vmax for gentisate
-
-
?
3-fluorogentisate + O2
3-fluoro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-fluorogentisate + O2
3-fluoro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-fluorogentisate + O2
3-fluoro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-fluorogentisate + O2
3-fluoro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-fluorogentisate + O2
3-fluoro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
Vmax of recombinant enzyme is 20.5% higher compared to gentisate
-
-
?
3-fluorogentisate + O2
3-fluoro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-fluorogentisate + O2
3-fluoro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
Vmax of recombinant enzyme is 20.5% higher compared to gentisate
-
-
?
3-hydroxybenzoate + O2
3,4-dihydroxy-6-oxo-hepta-2,4-dienedioic acid
-
minor pathway
-
-
?
3-hydroxybenzoate + O2
3,4-dihydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-hydroxybenzoate + O2
3,4-dihydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-hydroxybenzoate + O2
3,4-dihydroxy-6-oxo-hepta-2,4-dienedioic acid
-
main pathway
-
-
?
3-isopropyl-gentisate + O2
4-hydroxy-3-isopropyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-isopropyl-gentisate + O2
4-hydroxy-3-isopropyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-isopropyl-gentisate + O2
4-hydroxy-3-isopropyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-isopropyl-gentisate + O2
4-hydroxy-3-isopropyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-isopropylgentisate + O2
4-hydroxy-3-isopropyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-isopropylgentisate + O2
4-hydroxy-3-isopropyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-isopropylgentisate + O2
4-hydroxy-3-isopropyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-isopropylgentisate + O2
4-hydroxy-3-isopropyl-6-oxo-hepta-2,4-dienedioic acid
-
Vmax is 57.1% of Vmax for gentisate
-
-
?
3-methylgentisate + O2
4-hydroxy-3-methyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-methylgentisate + O2
4-hydroxy-3-methyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-methylgentisate + O2
4-hydroxy-3-methyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-methylgentisate + O2
4-hydroxy-3-methyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-methylgentisate + O2
4-hydroxy-3-methyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-methylgentisate + O2
4-hydroxy-3-methyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-methylgentisate + O2
4-hydroxy-3-methyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
3-methylgentisate + O2
4-hydroxy-3-methyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
4-chlorogentisate + O2
2-chloro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
4-chlorogentisate + O2
2-chloro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
4-chlorogentisate + O2
2-chloro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
4-chlorogentisate + O2
2-chloro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
4-chlorogentisate + O2
2-chloro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
4-fluorogentisate + O2
2-fluoro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
4-fluorogentisate + O2
2-fluoro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
4-fluorogentisate + O2
2-fluoro-4-hydroxy-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
4-isopropylgentisate + O2
4-hydroxy-2-isopropyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
4-isopropylgentisate + O2
4-hydroxy-2-isopropyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
4-methylgentisate + O2
4-hydroxy-2-methyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
4-methylgentisate + O2
4-hydroxy-2-methyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
4-methylgentisate + O2
4-hydroxy-2-methyl-6-oxo-hepta-2,4-dienedioic acid
-
-
-
-
?
5-aminosalicylate + O2
?
-
a gentisate 1,2-dioxygenase with an extremely relaxed substrate specificity is responsible for the unusual oxidation of salicylate by Pseudoaminobacter salicylatoxidans BN12. Relative activities with salicylate, 5-aminosalicylate, 1-hydroxy-2-naphthoate, and gentisate with both preparations are about 1:10:40:120
-
-
?
5-aminosalicylate + O2
?
-
kcat/KM is less than 1% of the kcat/Km for gentisate
-
-
?
5-aminosalicylate + O2
?
-
a gentisate 1,2-dioxygenase with an extremely relaxed substrate specificity is responsible for the unusual oxidation of salicylate by Pseudoaminobacter salicylatoxidans BN12. Relative activities with salicylate, 5-aminosalicylate, 1-hydroxy-2-naphthoate, and gentisate with both preparations are about 1:10:40:120
-
-
?
5-aminosalicylate + O2
?
-
kcat/KM is less than 1% of the kcat/Km for gentisate
-
-
?
5-aminosalicylate + O2
?
partly preferred substrate
-
-
?
5-aminosalicylate + O2
?
partly preferred substrate
-
-
?
5-fluorosalicylate + O2
?
-
kcat/KM is 1.4% of the kcat/Km for gentisate
-
-
?
5-methylsalicylate + O2
?
-
kcat/KM is 1.5% of the kcat/Km for gentisate
-
-
?
gentisate + O2
maleylpyruvate
-
gentisate 1,2-dioxygenase with an extraordinary substrate range. Relative activities with salicylate, 5-aminosalicylate, 1-hydroxy-2-naphthoate, and gentisate with both preparations are about 1:10:40:120
-
-
?
gentisate + O2
maleylpyruvate
-
gentisate 1,2-dioxygenase with an extraordinary substrate range. Relative activities with salicylate, 5-aminosalicylate, 1-hydroxy-2-naphthoate, and gentisate with both preparations are about 1:10:40:120
-
-
?
gentisate + O2
maleylpyruvate
-
preferred substrate
-
-
?
salicylate + O2
2-oxohepta-3,5-dienedioic acid
-
a gentisate 1,2-dioxygenase with an extremely relaxed substrate specificity is responsible for the unusual oxidation of salicylate by Pseudoaminobacter salicylatoxidans BN12. Relative activities with salicylate, 5-aminosalicylate, 1-hydroxy-2-naphthoate, and gentisate with both preparations are about 1:10:40:120
-
-
?
salicylate + O2
2-oxohepta-3,5-dienedioic acid
-
kcat/KM is 6.6% of the kcat/Km for gentisate
-
-
?
salicylate + O2
2-oxohepta-3,5-dienedioic acid
-
a gentisate 1,2-dioxygenase with an extremely relaxed substrate specificity is responsible for the unusual oxidation of salicylate by Pseudoaminobacter salicylatoxidans BN12. Relative activities with salicylate, 5-aminosalicylate, 1-hydroxy-2-naphthoate, and gentisate with both preparations are about 1:10:40:120
-
-
?
salicylate + O2
2-oxohepta-3,5-dienedioic acid
-
-
-
-
?
additional information
?
-
no activity with salicylate, 3-methylsalicylate, 4-methylsalicylate, 5-methylsalicylate, 3-bromosalicylate, 4-bromosalicylate, 5-iodosalicylate, and 1-hydroxy-2-naphthoate
-
-
-
additional information
?
-
no activity with salicylate, 3-methylsalicylate, 4-methylsalicylate, 5-methylsalicylate, 3-bromosalicylate, 4-bromosalicylate, 5-iodosalicylate, and 1-hydroxy-2-naphthoate
-
-
-
additional information
?
-
methyl 2,5-dihydroxybenzoate, 1,4-benzoquinone, 2,5-dihydroxybenzaldehyde, 4,5-dihydroxy-1,3-benzene-disulphonic acid and 2,3,5,6-tetrachloro-1,4-benzenediol give no substrate activity
-
-
-
additional information
?
-
-
no activity with: 6-methylgentisate, 3,4-dimethylgentisate
-
-
-
additional information
?
-
-
the salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans strain BN12 is a versatile gentisate 1,2-dioxygenase that converts both gentisate (2,5-dihydroxybenzoate) and various monohydroxylated substrates
-
-
-
additional information
?
-
-
the salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans strain BN12 is a versatile gentisate 1,2-dioxygenase that converts both gentisate (2,5-dihydroxybenzoate) and various monohydroxylated substrates
-
-
-
additional information
?
-
-
GDO-II is strictly inducible by aromatic substrates such as 3-hydroxybenzoate and gentisate
-
-
-
additional information
?
-
-
GDO-II is unable to utilize gentisate that is substituted at the carbon-4 position (i.e., 4-chloro- and 4-methylgentisate)
-
-
-
additional information
?
-
-
GDO-II is strictly inducible by aromatic substrates such as 3-hydroxybenzoate and gentisate
-
-
-
additional information
?
-
-
GDO-II is unable to utilize gentisate that is substituted at the carbon-4 position (i.e., 4-chloro- and 4-methylgentisate)
-
-
-
additional information
?
-
no activity against catechol, benzoate, 5-methylsalicylate, 5-chlorosalicylate, and homogentisate
-
-
-
additional information
?
-
no activity against catechol, benzoate, 5-methylsalicylate, 5-chlorosalicylate, and homogentisate
-
-
-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
2,5-dihydroxybenzoate + O2
maleylpyruvate
Q8NLB9
the enzyme is highly specific for 2,5-dihydroxybenzoate
-
-
?
2,5-dihydroxybenzoate + O2
maleylpyruvate
Q8NLB9
the enzyme is highly specific for 2,5-dihydroxybenzoate
-
-
?
2,5-dihydroxybenzoate + O2
maleylpyruvate
Q330M9
the enzyme is involbved in the 3-phenylpropionic acid deg´radation pathway
-
-
?
additional information
?
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-
the salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans strain BN12 is a versatile gentisate 1,2-dioxygenase that converts both gentisate (2,5-dihydroxybenzoate) and various monohydroxylated substrates
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-
-
additional information
?
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the salicylate 1,2-dioxygenase from Pseudaminobacter salicylatoxidans strain BN12 is a versatile gentisate 1,2-dioxygenase that converts both gentisate (2,5-dihydroxybenzoate) and various monohydroxylated substrates
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-
-
additional information
?
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-
GDO-II is strictly inducible by aromatic substrates such as 3-hydroxybenzoate and gentisate
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-
-
additional information
?
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GDO-II is strictly inducible by aromatic substrates such as 3-hydroxybenzoate and gentisate
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-
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe2+
Iron
additional information
Fe2+
contains 1 mol iron per subunit, in the presence of 2 mM Fe2+ activity is increased by 115%
Fe2+
-
purified GDO proteins NagI2 and NagI3 are highly unstable in phosphate buffer without ferrous ions
Fe2+
-
the catalytic center contains a mononuclear iron(II) ion coordinated to three histidine residues (His119, His121, and His160), located within the N-terminal domain in a solvent-accessible pocket
Fe2+
-
two ferrous centers are located in its two homologous cupin domains, respectively. The N-terminal Fe2+-binding site is essential for the enzyme activity but dispensable for the protein overall tertiary structure
Iron
ferrous ion specifically functions in the formation of the active tetramer structure, the enzyme contains 0.98 mol iron per mol subunit
additional information
Ca2+, Ni2+, Mg2+, and Zn2+ have no impact on enzyme activity
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1-hydroxy 2 naphthoate
0.33 mM, 19% of wild type enzyme activity remaining
Co2+
the addition of 0.005 mM Co2+ does inhibit enzyme activity to 53%
salicylate
0.33 mM, 38% of wild type enzyme activity remaining
additional information
-
K+, Na+, Mg2+, and Ca2+ do not inhibit the activity
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.14
1-hydroxynaphthalene-2-carboxylic acid
-
wild-type enzyme, pH and temperature not specified in the publication
0.06843
2,5-Dihydroxybenzoate
-
mutant enzyme Y181F, in 0.1 M KH2PO4 buffer (pH 7.4) at 23°C
0.0862
2,5-Dihydroxybenzoate
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wild type enzyme, in 0.1 M KH2PO4 buffer (pH 7.4) at 23°C
0.04591
3-Bromogentisate
-
wild type enzyme, in 0.1 M KH2PO4 buffer (pH 7.4) at 23°C
0.07826
3-Bromogentisate
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mutant enzyme Y181F, in 0.1 M KH2PO4 buffer (pH 7.4) at 23°C
0.07669
3-Fluorogentisate
-
wild type enzyme, in 0.1 M KH2PO4 buffer (pH 7.4) at 23°C
0.08962
3-Fluorogentisate
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mutant enzyme Y181F, in 0.1 M KH2PO4 buffer (pH 7.4) at 23°C
0.053
3-Isopropylgentisate
-
in 0.1 M phosphate buffer, pH 7.4, at 23°C
0.06769
3-Isopropylgentisate
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mutant enzyme Y181F, in 0.1 M KH2PO4 buffer (pH 7.4) at 23°C
0.07937
3-Isopropylgentisate
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wild type enzyme, in 0.1 M KH2PO4 buffer (pH 7.4) at 23°C
0.06234
3-Methylgentisate
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wild type enzyme, in 0.1 M KH2PO4 buffer (pH 7.4) at 23°C
0.08734
3-Methylgentisate
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mutant enzyme Y181F, in 0.1 M KH2PO4 buffer (pH 7.4) at 23°C
0.02326
4-Chlorogentisate
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wild type enzyme, in 0.1 M KH2PO4 buffer (pH 7.4) at 23°C
0.06069
4-Chlorogentisate
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mutant enzyme Y181F, in 0.1 M KH2PO4 buffer (pH 7.4) at 23°C
0.07258
4-Methylgentisate
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mutant enzyme Y181F, in 0.1 M KH2PO4 buffer (pH 7.4) at 23°C
0.07426
4-Methylgentisate
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wild type enzyme, in 0.1 M KH2PO4 buffer (pH 7.4) at 23°C
0.216
5-Aminosalicylate
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wild-type enzyme, pH and temperature not specified in the publication
0.047
5-Fluorosalicylate
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wild-type enzyme, pH and temperature not specified in the publication
0.788
5-Methylsalicylate
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wild-type enzyme, pH and temperature not specified in the publication
0.167
gentisate
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wild-type enzyme, pH and temperature not specified in the publication
0.017
salicylate
-
wild-type enzyme, pH and temperature not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
24
1-hydroxynaphthalene-2-carboxylic acid
-
wild-type enzyme, pH and temperature not specified in the publication
2.8
5-Aminosalicylate
-
wild-type enzyme, pH and temperature not specified in the publication
2.4
5-Fluorosalicylate
-
wild-type enzyme, pH and temperature not specified in the publication
2.1
5-Methylsalicylate
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wild-type enzyme, pH and temperature not specified in the publication
133
gentisate
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wild-type enzyme, pH and temperature not specified in the publication
0.9
salicylate
-
wild-type enzyme, pH and temperature not specified in the publication
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
the protein shows gentisate 1,2-dioxygenase specific activity of 0.17 U/mg of protein
additional information
activity is not detectable in pyruvate-grown cells
additional information
the specific activity of the purified recombinant enzyme is 102 units/mg at pH 7.5
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7 - 9
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
30
40
50
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25 - 50
-
isozyme Nagl2, 74.1% activity at 25°C, maximum activity at 50°C
25 - 65
-
isozyme Nagl4, 72.4% activity at 25°C, maximum activity at 65°C
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4.6 - 4.8
5.4
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
additional information
additional information
-
growth rate of wild-type strain CJ2 and three nagI knockout mutants on six different agar media, overview
additional information
-
growth rate of wild-type strain CJ2 and three nagI knockout mutants on six different agar media, overview
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additional information
strain R7 is able to grow on naphthalene as well as on o-xylene
additional information
-
strain R7 is able to grow on naphthalene as well as on o-xylene
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additional information
strain NCIMB 12038 utilizes naphthalene as a sole source of carbon and energy
additional information
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strain NCIMB 12038 utilizes naphthalene as a sole source of carbon and energy
additional information
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strain NCIMB 12038 utilizes naphthalene as a sole source of carbon and energy
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additional information
the strain nov.127W is capable of degrading a wide range of cyclic aromatic compounds such as dibenzothiophene, biphenyl, naphthalene, anthracene, and phenanthrene even under extremely low oxygen
additional information
-
the strain nov.127W is capable of degrading a wide range of cyclic aromatic compounds such as dibenzothiophene, biphenyl, naphthalene, anthracene, and phenanthrene even under extremely low oxygen
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
35000
38000
38500
40000
45000
154000
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
hexamer
homodimer
homotetramer
tetramer
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging drop vapour diffusion method using 0.1 M BisTris pH 6.5 and 20% polyethylene glycol 5000 monomethylether
diffraction-quality crystals of salicylate 1,2-dioxygenase are obtained using the sitting-drop vapour-diffusion method at 4°C from a solution containing 10%(w/v) ethanol, 6%(w/v) PEG 400, 0.1 M sodium acetate pH 4.6. Crystals belong to the primitive tetragonal space group P4(3)2(1)2 or P4(1)2(1)2, with unit-cell parameters a = 133.3, c = 191.51 A
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purified G106A enzyme mutant free and complexes with gentisate and salicylate, crystallization under anaerobic conditions, sitting drop vapor diffusion method, mixing of 0.001 ml of protein solution with 0.0008 ml of 8% poly(ethylene glycol)10000 and 0.1 M Tris/HCl pH 8.0, and 0.0002 ml of 0.1 M calcium chloride, crystal quality is improved using the seeding technique, X-ray diffraction structure determination and analysis at 2.0-2.58 A resolution
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crystal structure at 2.8 A resolution, hanging drop vapor diffusion crystallization at 16°C. The crystal form belongs to the R32 space group, with two protein molecules (named as A and B) per asymmetric unit and 45% solvent content
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6 - 8
6.5
GDO loses its activity after being kept in buffer below pH 6.5 for 12 h in the absence of ferrous iron and cysteine
672692
7 - 9
7.4
8
GDO loses its activity after being kept in buffer above pH 8.0 for 12 h in the absence of ferrous iron and cysteine
672692
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
50
50
the enzyme loses almost all its activity after incubation at 50°C for 15 min
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
cysteine stabilizes
Fe2+ stabilizes
highly unstable in 50 mM MOPS buffer with no additives
purified GDO proteins NagI2 and NagI3 are highly unstable in phosphate buffer without ferrous ions
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OXIDATION STABILITY
ORGANISM
UNIPROT
LITERATURE
exposure of enzyme to oxidants, e.g. H2O2 or K3Fe(CN)6, at 1 mM concentrations results in complete loss of activity, even under anaerobic conditions
under turnover conditions enzyme is rapidly inactivated at O2 concentrations above 0.8 mM
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389987
exposure of enzyme to oxidants, e.g. H2O2 or K3Fe(CN)6, at 1 mM concentrations results in complete loss of activity, even under anaerobic conditions
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389985
exposure of enzyme to oxidants, e.g. H2O2 or K3Fe(CN)6, at 1 mM concentrations results in complete loss of activity, even under anaerobic conditions
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389985, 389987
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, addition of glycerol and beta-mercaptoethanol, 96 h, 25% of activity remains
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-20°C, MOPS buffer with 0.1 mM Fe2+, 2 mM L-cysteine, and 10% (v/v) glycerol, 12 months, 3.5% residual activity
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-20°C, MOPS buffer with 0.1 mM Fe2+, 2 mM L-cysteine, and 10% (v/v) glycerol, 12 months, 42.9% residual activity
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-20°C, MOPS buffer with 0.1 mM Fe2+, 2 mM L-cysteine, and 10% (v/v) glycerol, 3 months, 42.5% residual activity
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-20°C, MOPS buffer with 0.1 mM Fe2+, 2 mM L-cysteine, and 10% (v/v) glycerol, 3 months, 86.5% residual activity
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-20°C, MOPS buffer with 0.1 mM Fe2+, 2 mM L-cysteine, and 10% (v/v) glycerol, 6 months, 23.1% residual activity
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-20°C, MOPS buffer with 0.1 mM Fe2+, 2 mM L-cysteine, and 10% (v/v) glycerol, 6 months, 70.9% residual activity
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-80°C, storage following rapid freezing in liquid N2, protein concentration above 10 mg/ml, about 15% loss of activity after 1 year
4°C, MOPS buffer with no additives, 96 h, complete loss of activity
cell free extracts adsorbed on polyester filters, stable
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-80°C, storage following rapid freezing in liquid N2, protein concentration above 10 mg/ml, about 15% loss of activity after 1 year
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-80°C, storage following rapid freezing in liquid N2, protein concentration above 10 mg/ml, about 15% loss of activity after 1 year
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4°C, MOPS buffer with no additives, 96 h, complete loss of activity
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
; ammonium sulfate fractionation, DEAE-Sepharose fast flow column chromatography
recombinant enzyme
recombinant Nagl2 and Nagl3 isozymes from Escherichia coli strain BL21(DE3) by gel filtration and sequential anion exchange chromatography
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; ammonium sulfate fractionation, DEAE-Sepharose fast flow column chromatography
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; ammonium sulfate fractionation, DEAE-Sepharose fast flow column chromatography
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
deduced amino acid sequence contains 4 novel histidine clusters and a possible extradiol fingerprint region
-
expressed in Escherichia coli
expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli Rosetta cells
expression in Escherichia coli
gene dbdB, DNA and amino acid sequence determination and analysis, genetic organization, phylogenetic analysis, overview
gene genH, DNA and amino acid sequence determination and analysis, gene genH belongs to the gen gene cluster, RT-PCR expression and genomic analysis, overview
gene narI, DNA and amino acid sequence determination and analysis of the gentisate catabolic gene cluster. Among the 13 complete open reading frames deduced from this fragment, three narIKL encode the enzymes involved in the reactions of gentisate catabolism, of these, NarI is gentisate 1,2-dioxygenase which converts gentisate to maleylpyruvate. Genes narI, narK, and narL genes are transcribed as a single operon only in the presence of naphthalene. Sequence comparisons, overview. Expression in Escherichia coli strain Rosetta (DE3) pLysS
genes nagI1, nagI2, and nagI3, the latter encoded in the third cluster, nagl3 is polycistronic and is expressed at a relatively high level, genetic organization, DNA and amino acid sequence determination and analysis, real-time RT-PCR for gene expression analysis of genes nagI1, nagI2 and nagI3 and the third catabolic gene cluster, overview. Overexpression of all three genes in Escherichia coli strain BL21(DE3). The transformation efficiency of the pET21bnagI1 ligation product is very low compared with that of the nagI2 and nagI3 genes
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overexpressed as a hexahistidine fusion protein from Escherichia coli
-
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
nagl3 gene expression is induced by salicylate in wild-type strain CJ2 but not in the nagR knockout mutant strain CJN110
nagl3 gene expression is induced by salicylate in wild-type strain CJ2 but not in the nagR knockout mutant strain CJN110
-
nagl3 gene expression is induced by salicylate in wild-type strain CJ2 but not in the nagR knockout mutant strain CJN110
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
A112D
the mutant gains the ability to oxidize salicylate and several other monohydroxylated substrates
A112G
the mutant gains the ability to oxidize salicylate and several other monohydroxylated substrates
A112I
the mutant gains the ability to oxidize salicylate and several other monohydroxylated substrates
A112S
the mutant gains the ability to oxidize salicylate and several other monohydroxylated substrates
A112D
-
the mutant gains the ability to oxidize salicylate and several other monohydroxylated substrates
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A112G
-
the mutant gains the ability to oxidize salicylate and several other monohydroxylated substrates
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A112I
-
the mutant gains the ability to oxidize salicylate and several other monohydroxylated substrates
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A112S
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the mutant gains the ability to oxidize salicylate and several other monohydroxylated substrates
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G106A
-
site-directed mutagenesis, in contrast to the wild-type enzyme, mutant G106A oxidizes only gentisate, while 1-hydroxy-2-naphthoate and salicylate are not converted. The mutant shows slightly decreased activity with salicylate, but shows a higher affinity to this substratecompared to the wild-type. Salicylate is coordinated in the G106A variant with the catalytically active Fe(II) ion in an unusual and unproductive manner because of the inability of salicylate to displace a hydrogen bond that is formed between Trp104 and Asp174 in the G106A variant
G106A
-
site-directed mutagenesis, in contrast to the wild-type enzyme, mutant G106A oxidizes only gentisate, while 1-hydroxy-2-naphthoate and salicylate are not converted. The mutant shows slightly decreased activity with salicylate, but shows a higher affinity to this substratecompared to the wild-type. Salicylate is coordinated in the G106A variant with the catalytically active Fe(II) ion in an unusual and unproductive manner because of the inability of salicylate to displace a hydrogen bond that is formed between Trp104 and Asp174 in the G106A variant
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Y181F
-
mutant demonstrates 4-, 3-, 6-, and 16fold increase in relative activity towards 2,5-dihydroxybenzoate, 3-fluoro-, 4-methyl-, and 3-methylgentisate, respectively, and shows 464% relative activity compared to the wild type enzyme for 2,5-dihydroxybenzoate
Y181F
-
mutant demonstrates 4-, 3-, 6-, and 16fold increase in relative activity towards 2,5-dihydroxybenzoate, 3-fluoro-, 4-methyl-, and 3-methylgentisate, respectively, and shows 464% relative activity compared to the wild type enzyme for 2,5-dihydroxybenzoate
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H119A/H121A
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despite its wild-type like structural propertie, the mutant shows extremely low gentisate 1,2-dioxygenase activity
additional information
additional information
-
construction of individual knockout mutants of all three nagI genes via 2 bp unmarked gene deletion mutagenesis, all three nagI knockout mutants still contain stop codons within their nagI genes. Mutant CJ2DELTAnagI3 shows severely diminished GDO activity and grows slowest on aromatic substrates
additional information
-
construction of individual knockout mutants of all three nagI genes via 2 bp unmarked gene deletion mutagenesis, all three nagI knockout mutants still contain stop codons within their nagI genes. Mutant CJ2DELTAnagI3 shows severely diminished GDO activity and grows slowest on aromatic substrates
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additional information
-
double mutant Phe3Leu, Val334Ala, doubled enzymatic activity, mutants in conserved core regions with less activity
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Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cell free extracts adsorbed on polyester filters, reactivation using ferrous iron and ascorbate
-
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LINKS TO OTHER DATABASES (specific for EC-Number 1.13.11.4)
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