BRENDA - Enzyme Database
show all sequences of 1.13.11.66

The crystal structures of native hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 and of substrate and inhibitor complexes

Ferraroni, M.; Da Vela, S.; Kolvenbach, B.A.; Corvini, P.F.; Scozzafava, A.; Biochim. Biophys. Acta 1865, 520-530 (2017)

Data extracted from this reference:

Crystallization (Commentary)
Crystallization (Commentary)
Organism
purified enzyme free or in complex with substrate methylhydroquinone under anaerobic conditions, or with inhibitors 4-hydroxybenzoate and 4-nitrophenol, sitting drop vapor diffusion method, mixing of 0.001 ml of 8 mg/ml protein in 25 mM Tris, pH 7.0, 5 mM NaCl, and 0.5 mM ligand, with 0.001 ml of reservoir solution containing 14% PEG 3350, 0.35 M MgCl2, and 0.1 M MES, pH 6.5, 4°C, 1 day, the structure of the free enzyme is obtained by soaking the crystals in a stabilizing solution containing 16% PEG 3350, 0.35 M MgCl2, and 0.1 M MES, pH 6.5, for two days, changing the solution three times, in order to remove the ligands, X-ray diffraction structure determination and analysis at 1.90-2.40 resolution, molecular replacement using the coordinates of PnpCD structure from Pseudomonas sp. strain WBC-3, PDB ID 4ZXA as template, modeling
Sphingomonas sp.
Inhibitors
Inhibitors
Commentary
Organism
Structure
4-hydroxybenzoate
binding structure, overview
Sphingomonas sp.
4-nitrophenol
binding structure, overview
Sphingomonas sp.
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Fe2+
required for catalysis, each of the four beta subunits in the asymmetric unit of the enzyme crystal binds one Fe(II) ion. The iron ion in each beta subunit is coordinated to three protein residues, His258, Glu264, and His305 and a water molecule
Sphingomonas sp.
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
benzene-1,4-diol + O2
Sphingomonas sp.
-
(2Z,4E)-4-hydroxy-6-oxohexa-2,4-dienoate
-
-
?
benzene-1,4-diol + O2
Sphingomonas sp. TTNP3
-
(2Z,4E)-4-hydroxy-6-oxohexa-2,4-dienoate
-
-
?
Organism
Organism
UniProt
Commentary
Textmining
Sphingomonas sp.
F8TW82 AND F8TW83
alpha and beta subunits
-
Sphingomonas sp. TTNP3
F8TW82 AND F8TW83
alpha and beta subunits
-
Reaction
Reaction
Commentary
Organism
Reaction ID
benzene-1,4-diol + O2 = (2Z,4E)-4-hydroxy-6-oxohexa-2,4-dienoate
catalytic mechanism, overview
Sphingomonas sp.
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
Substrate Product ID
benzene-1,4-diol + O2
-
744430
Sphingomonas sp.
(2Z,4E)-4-hydroxy-6-oxohexa-2,4-dienoate
-
-
-
?
benzene-1,4-diol + O2
-
744430
Sphingomonas sp. TTNP3
(2Z,4E)-4-hydroxy-6-oxohexa-2,4-dienoate
-
-
-
?
methylhydroquinone + O2
substrate binding structure, overview
744430
Sphingomonas sp.
?
-
-
-
?
methylhydroquinone + O2
substrate binding structure, overview
744430
Sphingomonas sp. TTNP3
?
-
-
-
?
additional information
hydroquinone 1,2-dioxygenase, a Fe(II) ring cleaving dioxygenase from Sphingomonas sp. strain TTNP3, oxidizes a wide range of hydroquinones to the corresponding 4-hydroxymuconic semialdehydes
744430
Sphingomonas sp.
?
-
-
-
-
additional information
hydroquinone 1,2-dioxygenase, a Fe(II) ring cleaving dioxygenase from Sphingomonas sp. strain TTNP3, oxidizes a wide range of hydroquinones to the corresponding 4-hydroxymuconic semialdehydes
744430
Sphingomonas sp. TTNP3
?
-
-
-
-
Subunits
Subunits
Commentary
Organism
heterotetramer
2 * 19000, subunit alpha, + 2 * 38000, subunit beta
Sphingomonas sp.
More
both subunits alpha and beta fold as a cupin, but that of the small alpha subunit lacks a competent metal binding pocket. Two tetramers are present in the asymmetric unit of the enzyme crystals
Sphingomonas sp.
Synonyms
Synonyms
Commentary
Organism
HQDO
-
Sphingomonas sp.
type II HQDO
-
Sphingomonas sp.
Temperature Optimum [°C]
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
25
-
assay at
Sphingomonas sp.
pH Optimum
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7
-
assay at
Sphingomonas sp.
Crystallization (Commentary) (protein specific)
Crystallization
Organism
purified enzyme free or in complex with substrate methylhydroquinone under anaerobic conditions, or with inhibitors 4-hydroxybenzoate and 4-nitrophenol, sitting drop vapor diffusion method, mixing of 0.001 ml of 8 mg/ml protein in 25 mM Tris, pH 7.0, 5 mM NaCl, and 0.5 mM ligand, with 0.001 ml of reservoir solution containing 14% PEG 3350, 0.35 M MgCl2, and 0.1 M MES, pH 6.5, 4°C, 1 day, the structure of the free enzyme is obtained by soaking the crystals in a stabilizing solution containing 16% PEG 3350, 0.35 M MgCl2, and 0.1 M MES, pH 6.5, for two days, changing the solution three times, in order to remove the ligands, X-ray diffraction structure determination and analysis at 1.90-2.40 resolution, molecular replacement using the coordinates of PnpCD structure from Pseudomonas sp. strain WBC-3, PDB ID 4ZXA as template, modeling
Sphingomonas sp.
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
4-hydroxybenzoate
binding structure, overview
Sphingomonas sp.
4-nitrophenol
binding structure, overview
Sphingomonas sp.
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Fe2+
required for catalysis, each of the four beta subunits in the asymmetric unit of the enzyme crystal binds one Fe(II) ion. The iron ion in each beta subunit is coordinated to three protein residues, His258, Glu264, and His305 and a water molecule
Sphingomonas sp.
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
ID
benzene-1,4-diol + O2
Sphingomonas sp.
-
(2Z,4E)-4-hydroxy-6-oxohexa-2,4-dienoate
-
-
?
benzene-1,4-diol + O2
Sphingomonas sp. TTNP3
-
(2Z,4E)-4-hydroxy-6-oxohexa-2,4-dienoate
-
-
?
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
ID
benzene-1,4-diol + O2
-
744430
Sphingomonas sp.
(2Z,4E)-4-hydroxy-6-oxohexa-2,4-dienoate
-
-
-
?
benzene-1,4-diol + O2
-
744430
Sphingomonas sp. TTNP3
(2Z,4E)-4-hydroxy-6-oxohexa-2,4-dienoate
-
-
-
?
methylhydroquinone + O2
substrate binding structure, overview
744430
Sphingomonas sp.
?
-
-
-
?
methylhydroquinone + O2
substrate binding structure, overview
744430
Sphingomonas sp. TTNP3
?
-
-
-
?
additional information
hydroquinone 1,2-dioxygenase, a Fe(II) ring cleaving dioxygenase from Sphingomonas sp. strain TTNP3, oxidizes a wide range of hydroquinones to the corresponding 4-hydroxymuconic semialdehydes
744430
Sphingomonas sp.
?
-
-
-
-
additional information
hydroquinone 1,2-dioxygenase, a Fe(II) ring cleaving dioxygenase from Sphingomonas sp. strain TTNP3, oxidizes a wide range of hydroquinones to the corresponding 4-hydroxymuconic semialdehydes
744430
Sphingomonas sp. TTNP3
?
-
-
-
-
Subunits (protein specific)
Subunits
Commentary
Organism
heterotetramer
2 * 19000, subunit alpha, + 2 * 38000, subunit beta
Sphingomonas sp.
More
both subunits alpha and beta fold as a cupin, but that of the small alpha subunit lacks a competent metal binding pocket. Two tetramers are present in the asymmetric unit of the enzyme crystals
Sphingomonas sp.
Temperature Optimum [°C] (protein specific)
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
25
-
assay at
Sphingomonas sp.
pH Optimum (protein specific)
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
7
-
assay at
Sphingomonas sp.
General Information
General Information
Commentary
Organism
additional information
active site structure analysis, apo or with bound substrate methylhydroquinone, overview
Sphingomonas sp.
General Information (protein specific)
General Information
Commentary
Organism
additional information
active site structure analysis, apo or with bound substrate methylhydroquinone, overview
Sphingomonas sp.
Other publictions for EC 1.13.11.66
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Synonyms
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
744430
Ferraroni
The crystal structures of nat ...
Sphingomonas sp., Sphingomonas sp. TTNP3
Biochim. Biophys. Acta
1865
520-530
2017
-
-
-
1
-
-
2
-
-
1
-
2
-
5
-
-
-
1
-
-
-
-
6
2
2
1
-
-
-
1
-
-
-
-
-
-
-
-
-
-
1
-
-
-
2
-
-
-
1
-
2
-
-
-
-
-
-
-
-
6
2
1
-
-
-
1
-
-
-
-
1
1
-
-
-
745331
Liu
Crystal structure of PnpCD, a ...
Pseudomonas sp.
J. Biol. Chem.
290
24547-24560
2015
-
-
1
1
9
-
-
-
-
3
-
2
-
1
-
-
1
-
-
-
-
-
2
2
2
1
-
-
-
1
-
-
-
-
-
-
-
-
1
-
1
9
-
-
-
-
-
-
3
-
2
-
-
-
1
-
-
-
-
2
2
1
-
-
-
1
-
-
-
-
3
3
-
-
-
745802
Mancini
A copper-induced quinone degr ...
Lactococcus lactis, Lactococcus lactis IL1403
Mol. Microbiol.
95
645-659
2015
-
-
1
-
-
1
1
1
-
2
-
6
-
13
-
-
1
-
-
-
-
-
11
1
3
1
-
-
-
1
-
-
-
-
-
-
-
-
1
-
-
-
1
-
1
-
1
-
2
-
6
-
-
-
1
-
-
-
-
11
1
1
-
-
-
1
-
-
-
1
1
1
1
-
-
719179
Zhang
Identification of the para-nit ...
Pseudomonas sp.
BMC Microbiol.
12
27
2012
-
-
1
-
-
-
-
-
-
-
1
-
-
7
-
-
1
-
-
-
-
-
2
-
2
1
1
1
-
1
1
2
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
1
-
-
-
-
2
-
1
1
1
-
1
1
2
-
-
-
-
-
-
-
718555
Kolvenbach
Purification and characterizat ...
Sphingomonas sp., Sphingomonas sp. TTNP3
AMB Express
1
08
2011
-
-
-
-
-
-
9
1
-
1
3
-
-
7
-
-
1
-
-
-
1
-
32
1
-
-
-
-
1
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
18
-
2
-
1
6
-
-
-
-
2
-
-
2
-
32
2
-
-
-
2
-
2
-
-
-
-
-
-
1
2
718916
Machonkin
Substrate specificity of Sphin ...
Sphingobium chlorophenolicum
Biochemistry
50
8899-8913
2011
-
-
-
-
-
-
3
12
-
-
-
-
-
1
-
-
-
-
-
-
-
-
8
-
-
-
-
-
9
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
3
-
12
-
-
-
-
-
-
-
-
-
-
-
-
8
-
-
-
-
9
-
-
-
-
-
-
-
-
9
9
719104
Shen
Cloning and characterization o ...
Pseudomonas putida, Pseudomonas putida DLL-E4
Biores. Technol.
101
7516-7522
2010
-
-
-
-
1
-
-
-
-
-
2
-
-
6
-
-
-
-
-
-
-
-
4
1
2
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-
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-
-
2
-
-
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2
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-
-
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-
-
-
4
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
719327
Yin
Characterization of MnpC, a hy ...
Cupriavidus necator, Cupriavidus necator JMP 134-1
Curr. Microbiol.
61
471-476
2010
-
-
1
-
-
-
-
1
-
2
1
-
-
27
-
-
-
-
-
-
1
3
4
1
1
-
-
-
-
1
1
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
1
-
2
1
-
-
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-
1
3
4
1
-
-
-
-
1
1
-
-
-
-
-
-
-
-
720066
Machonkin
Determination of the active si ...
Sphingobium chlorophenolicum
J. Biol. Inorg. Chem.
15
291-301
2010
-
-
1
1
5
-
-
-
-
1
-
-
-
1
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
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-
1
-
1
5
-
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-
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-
1
-
-
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-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
719714
Moonen
Hydroquinone dioxygenase from ...
Pseudomonas fluorescens, Pseudomonas fluorescens ACB
J. Bacteriol.
190
5199-5209
2008
1
-
-
-
-
-
12
1
-
1
3
-
-
11
-
-
1
-
-
-
1
-
14
1
-
-
-
-
1
1
-
-
-
1
-
-
1
-
-
-
-
-
-
-
12
1
1
-
1
3
-
-
-
-
1
-
-
1
-
14
1
-
-
-
1
1
-
-
-
-
-
-
-
-
-
718727
Xun
Characterization of 2,6-dichlo ...
Sphingobium chlorophenolicum
Biochem. Biophys. Res. Commun.
266
322-325
1999
-
-
1
-
-
-
-
1
-
1
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1
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-
2
-
1
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1
1
1
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1
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1
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1
-
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-
-
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-
-
2
-
-
-
-
1
1
1
-
-
-
-
-
-
-
-
718831
Xu
Evidence that pcpA encodes 2,6 ...
Sphingobium chlorophenolicum
Biochemistry
38
7659-7669
1999
-
-
-
-
-
-
-
-
-
2
1
-
-
1
-
-
1
-
-
-
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-
1
1
-
-
-
-
-
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-
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-
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-
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-
-
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2
1
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1
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-
1
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
719693
Miyauchi
Cloning and sequencing of a no ...
Sphingomonas paucimobilis
J. Bacteriol.
181
6712-6719
1999
-
-
1
-
3
-
-
-
-
1
1
-
-
1
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-
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-
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2
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3
1
1
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-
-
-
-
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-
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1
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-
3
-
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-
1
1
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-
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-
-
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2
-
3
1
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