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Information on EC 1.13.11.57 - gallate dioxygenase
for references in articles please use BRENDA:EC1.13.11.57
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EC Tree 1 Oxidoreductases
1.13 Acting on single donors with incorporation of molecular oxygen (oxygenases)
1.13.11 With incorporation of two atoms of oxygen
1.13.11.57 gallate dioxygenase
IUBMB Comments
Contains non-heme Fe2+. The enzyme is a ring-cleavage dioxygenase that acts specifically on 3,4,5-trihydroxybenzoate to produce the keto-tautomer of 4-oxalomesaconate [1,2].
The enzyme appears in viruses and cellular organisms
- 1.13.11.57
-
4,5-dioxygenase
- protocatechuate
-
sphingomonas
- paucimobilis
- syringate
- ligab
- 3-o-methylgallate
- vanillate
-
4,5-cleavage
-
tetrahydrofolate-dependent
- o-demethylase
- tetrahydrofolate
-
extradiol
- 4-oxalomesaconate
-
h4folate
-
20-oxidases
- gibberellin
- sphingobium
showSynonyms
gallate dioxygenase, ga dioxygenase, more
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
DesB
GA dioxygenase
GALA
GALA
-
-
-
-
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
3,4,5-trihydroxybenzoate + O2 = (1E)-4-oxobut-1-ene-1,2,4-tricarboxylate
-
-
-
-
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PATHWAY SOURCE
PATHWAYS
BRENDA
MetaCyc
gallate degradation I
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SYSTEMATIC NAME
IUBMB Comments
gallate:oxygen oxidoreductase
Contains non-heme Fe2+. The enzyme is a ring-cleavage dioxygenase that acts specifically on 3,4,5-trihydroxybenzoate to produce the keto-tautomer of 4-oxalomesaconate [1,2].
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
3,4,5-trihydroxybenzoate + O2
(1E)-4-oxobut-1-ene-1,2,4-tricarboxylate
G2IKE5
Substrates: DesB has strict substrate specificity for 3,4,5-trihydroxybenzoate (gallate). Biochemical and structural study show the substrate recognition and catalytic mechanisms of extradiol dioxygenase DesB. Mutational analysis reveals that His124 and His192 in the active site are essential to the catalytic reaction of the extradiol dioxygenase DesB. His124, which interacts with OH(4) of the bound gallate, seems to contribute to proper positioning of the substrate in the active site. His192, which is located close to OH (3) of the gallate, is likely to serve as the catalytic base. Glu377' interacts with OH(5) of the gallate and seems to play a critical role in the substrate specificity
Products: -
Products: -
?
gallate + O2
(1E)-4-oxobut-1-ene-1,2,4-tricarboxylate
-
Substrates: gallate is also namend gallic acid or 3,4,5-trihydroxybenzoic acid
Products: -
Products: -
?
gallate + O2
(1E)-4-oxobut-1-ene-1,2,4-tricarboxylate
-
Substrates: gallate is also namend gallic acid or 3,4,5-trihydroxybenzoic acid
Products: -
Products: -
?
gallate + O2
(2E,4E)-4-(carboxymethylidene)-2-hydroxypent-2-enedioate
-
Substrates: -
Products: -
Products: -
?
gallate + O2
(2E,4E)-4-(carboxymethylidene)-2-hydroxypent-2-enedioate
G2IKE5
Substrates: -
Products: -
Products: -
?
gallate + O2
4-oxalomesaconate
-
Substrates: the substrate specificity is very restricted toward gallate
Products: -
Products: -
?
gallate + O2
4-oxalomesaconate
-
Substrates: the substrate specificity is very restricted toward gallate
Products: -
Products: -
?
gallate + O2
4-oxalomesaconate
Substrates: -
Products: -
Products: -
?
additional information
?
-
-
Substrates: no activity with protocatechuate, catechol, resorcinolate, resorcinol, gentisate, hydroquinone, pyrogallol, methylgallate, or syringate
Products: -
Products: -
?
additional information
?
-
-
Substrates: no activity with protocatechuate, catechol, resorcinolate, resorcinol, gentisate, hydroquinone, pyrogallol, methylgallate, or syringate
Products: -
Products: -
?
additional information
?
-
Substrates: no activity with protocatechuate, 3-O-methylgallate, gentisate, 2,3-dihydroxybiphenyl, 4-methylcatechol, 2,3-dihydroxybenzoate, and methylgallate
Products: -
Products: -
?
additional information
?
-
Substrates: no activity with protocatechuate, 3-O-methylgallate, gentisate, 2,3-dihydroxybiphenyl, 4-methylcatechol, 2,3-dihydroxybenzoate, and methylgallate
Products: -
Products: -
?
additional information
?
-
-
Substrates: no activity with protocatechuate, 3-O-methylgallate, gentisate, 2,3-dihydroxybiphenyl, 4-methylcatechol, 2,3-dihydroxybenzoate, and methylgallate
Products: -
Products: -
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Fe2+
Fe2+
G2IKE5
the catalytic reaction of the extradiol dioxygenase DesB requires the shift of the Fe(II) ion, leading to the bidentate coordination of the substrate to the Fe(II) ion
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
2,2'-dipyridyl
-
2 mM 2,2'-dipyridyl, a specific Fe2+-chelator, abolishes the gallate dioxygenase activity completely
H2O2
-
hydrogen peroxide at 1 mM reduces the gallate dioxygenase activity to 15%, and the activity can be partially restored (50% activity of the untreated enzyme) upon addition of 10 mM ascorbate
protocatechuate
G2IKE5
most potent inhibitor with mixed (competitive and non-competitive) inhibition profile, 49% inhibition at 5 mM
4-nitrocatechol
-
36.6% inhibition when the inhibitor is present in 5fold excess over substrate
EDTA
-
complete inhibition at 1 mM, the activity is only fully recovered with Fe2+
EDTA
complete inhibition at 0.5 mM, the oxygen consumption activity after EDTA treatment is completely recovered by addition of Fe2+ (119%)
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.045
gallate
-
at pH 7.5, temperature not specified in the publication
0.0669
gallate
in 50 mM GTA buffer (pH 8.5) consisting of 50 mM 3,3-dimethylglutarate, 50 mM Tris, and 50 mM 2-amino-2-methyl-1,3-propanediol, at 30°C
0.123
gallate
G2IKE5
at pH 7.5, temperature not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
316
gallate
G2IKE5
at pH 7.5, 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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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
5.48
protocatechuate
G2IKE5
at pH 7.5, temperature not specified in the publication
8.13
vanilliate
G2IKE5
at pH 7.5, temperature not specified in the publication
-
2.3
4-nitrocatechol
-
at pH 7.5, temperature not specified in the publication
13.3
4-nitrocatechol
G2IKE5
at pH 7.5, temperature not specified in the publication
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6 - 9
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
physiological function
the enzyme is involved in syringate catabolism, the pathway involving DesB plays an especially important role in the growth of Sphingomonas paucimobilis SYK-6 on syringate, and DesB is involved in gallate degradation
physiological function
-
the GalA protein is the only dioxygenase involved in gallate cleavage in Pseudomonas putida KT2440
physiological function
-
the GalA protein is the only dioxygenase involved in gallate cleavage in Pseudomonas putida KT2440
-
physiological function
-
the enzyme is involved in syringate catabolism, the pathway involving DesB plays an especially important role in the growth of Sphingomonas paucimobilis SYK-6 on syringate, and DesB is involved in gallate degradation
-
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UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). GALA_PSEPK
Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
340
0
38459
Swiss-Prot
-
Q5NTE5_SPHPI
418
0
46896
TrEMBL
other Location (Reliability: 2)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homodimer
homotrimer
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CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
hanging drop vapor diffusion method, using 25% (w/v) PEG 8000, 0.1 M sodium acetate trihydrate, 0.1 M HEPES-NaOH pH 7.8, at 4°C
-
crystallographic analyses of DesB shows that gallate is recognized by several hydrogen bonds. Three groups of the hydrogen bonds recognize a substrate and place the substrate in a productive arrangement
G2IKE5
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
the expression of the galA gene is specifically induced by gallate
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Sugimoto, K.; Yamamoto, Y.; Antoni, S.; Senda, M.; Kasai, D.; Masai, E.; Fukuda, M.; Senda, T.
Crystallization and preliminary crystallographic analysis of gallate dioxygenase DesB from Sphingobium sp. SYK-6
Acta Crystallogr. Sect. F
F65
1171-1174
2009
Sphingobium sp.
brenda
Kasai, D.; Masai, E.; Miyauchi, K.; Katayama, Y.; Fukuda, M.
Characterization of the gallate dioxygenase gene: three distinct ring cleavage dioxygenases are involved in syringate degradation by Sphingomonas paucimobilis SYK-6
J. Bacteriol.
187
5067-5074
2005
Sphingomonas paucimobilis (Q5NTE5), Sphingomonas paucimobilis SYK-6 (Q5NTE5), Sphingomonas paucimobilis SYK-6
brenda
Nogales, J.; Canales, A.; Jimenez-Barbero, J.; Garcia, J.L.; Diaz, E.
Molecular characterization of the gallate dioxygenase from Pseudomonas putida KT2440. The prototype of a new subgroup of extradiol dioxygenases
J. Biol. Chem.
280
35382-35390
2005
Pseudomonas putida, Pseudomonas putida KT 2240
brenda
Nogales, J.; Canales, A.; Jimenez-Barbero, J.; Serra, B.; Pingarron, J.M.; Garcia, J.L.; Diaz, E.
Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida
Mol. Microbiol.
79
359-374
2011
Pseudomonas putida, Pseudomonas putida KT 2240
brenda
Sugimoto, K.; Senda, M.; Kasai, D.; Fukuda, M.; Masai, E.; Senda, T.
Molecular mechanism of strict substrate specificity of an extradiol dioxygenase, DesB, derived from Sphingobium sp. SYK-6
PLoS ONE
9
e92249
2014
Sphingobium sp. SYK-6 (G2IKE5)
brenda
Uchendu, S.N.; Rafalowski, A.; Cohn, E.F.; Davoren, L.W.; Taylor, E.A.
Anaerobic protein purification and kinetic analysis via oxygen electrode for studying DesB dioxygenase activity and inhibition
J. Vis. Exp.
140
58307
2018
Sphingobium sp. SYK-6
brenda
Uchendu, S.; Rafalowski, A.; Schick, D.; Cohn, E.; Hassan, B.; Taylor, E.
Identifying metabolic pathway intermediates that modulate the gallate dioxygenase (DesB) from Sphingobium sp. strain SYK-6
Process Biochem.
102
408-416
2021
Sphingobium sp. SYK-6 (G2IKE5)
-
brenda
EXTERNAL LINKS (specific for EC-Number 1.13.11.57)
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