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

•Hydroquinol 1,2-dioxygenase (HQDO) is a Fe-dependent ring cleaving dioxygenase.•HQDO is a heterotetramer α2β2 formed by two different subunits which fold as a cupin.•The crystal structures of the native enzyme and of three HQDO complexes were solved.•In the wt-HQDO the iron ion is coordinated to His258, Glu264, His305 and a water.•HQDO shows a different coordination at the Fe(II) center than previously reported.

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 38 kDa, 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.