5M26

Crystal structure of hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 in complex with methylhydroquinone

Summary for 5M26

• Entry DOI: 10.2210/pdb5m26/pdb
• Descriptor: Hydroquinone dioxygenase small subunit, Hydroquinone dioxygenase large subunit, FE (III) ION, ... (5 entities in total)
• Functional Keywords: dioxygenase, cupin, oxidoreductase
• Biological source: Sphingomonas sp. TTNP3; More
• Total number of polymer chains: 8
• Total formula weight: 227962.32

Authors

Ferraroni, M.,Da Vela, S.,Scozzafava, A.,Kolvenbach, B.,Corvini, P.F.X. (deposition date: 2016-10-12, release date: 2017-09-27, Last modification date: 2024-01-17)

Primary citation

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.
Biochim. Biophys. Acta, 1865:520-530, 2017

PubMed Abstract: The crystal structure of hydroquinone 1,2-dioxygenase, a Fe(II) ring cleaving dioxygenase from Sphingomonas sp. strain TTNP3, which oxidizes a wide range of hydroquinones to the corresponding 4-hydroxymuconic semialdehydes, has been solved by Molecular Replacement, using the coordinates of PnpCD from Pseudomonas sp. strain WBC-3. The enzyme is a heterotetramer, constituted of two subunits α and two β of 19 and 38kDa, respectively. Both the two subunits fold as a cupin, but that of the small α subunit lacks a competent metal binding pocket. Two tetramers are present in the asymmetric unit. Each of the four β subunits in the asymmetric unit binds one Fe(II) ion. The iron ion in each β subunit is coordinated to three protein residues, His258, Glu264, and His305 and a water molecule. The crystal structures of the complexes with the substrate methylhydroquinone, obtained under anaerobic conditions, and with the inhibitors 4-hydroxybenzoate and 4-nitrophenol were also solved. The structures of the native enzyme and of the complexes present significant differences in the active site region compared to PnpCD, the other hydroquinone 1,2-dioxygenase of known structure, and in particular they show a different coordination at the metal center.

PubMed: 28232026
DOI: 10.1016/j.bbapap.2017.02.013

Experimental method

X-RAY DIFFRACTION (1.9 Å)