Literature summary for 1.13.11.66 extracted from

Ferraroni, M.; Da Vela, S.; Kolvenbach, B.A.; Corvini, P.F.; Scozzafava, A.
The crystal structures of native hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 and of substrate and inhibitor complexes (2017), Biochim. Biophys. Acta, 1865, 520-530 .

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Crystallization (Commentary)

Crystallization (Comment)	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.

Crystallization (Comment)

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	Comment	Organism	Structure
4-hydroxybenzoate	binding structure, overview	Sphingomonas sp.
4-nitrophenol	binding structure, overview	Sphingomonas sp.

Metals/Ions

Metals/Ions	Comment	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	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
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	Comment	Textmining
Sphingomonas sp.	F8TW82 AND F8TW83	alpha and beta subunits	-
Sphingomonas sp. TTNP3	F8TW82 AND F8TW83	alpha and beta subunits	-

Reaction

Reaction	Comment	Organism	Reaction ID
benzene-1,4-diol + O2 = (2Z,4E)-4-hydroxy-6-oxohexa-2,4-dienoate	catalytic mechanism, overview	Sphingomonas sp.	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
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	-	?
methylhydroquinone + O2	substrate binding structure, overview	Sphingomonas sp.	?	-	?
methylhydroquinone + O2	substrate binding structure, overview	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	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	Sphingomonas sp. TTNP3	?	-	?

Subunits

Subunits	Comment	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	Comment	Organism
HQDO	-	Sphingomonas sp.
type II HQDO	-	Sphingomonas sp.

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
25	-	assay at	Sphingomonas sp.

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7	-	assay at	Sphingomonas sp.

General Information

General Information	Comment	Organism
additional information	active site structure analysis, apo or with bound substrate methylhydroquinone, overview	Sphingomonas sp.