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

Biochim Biophys Acta Proteins Proteom. 2017 May;1865(5):520-530. doi: 10.1016/j.bbapap.2017.02.013. Epub 2017 Feb 20.

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.

Keywords: Crystallography; Cupin superfamily; Dioxygenase; Metal binding motif; Ring cleaving.

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Catalytic Domain
  • Crystallography, X-Ray
  • Dioxygenases / chemistry*
  • Dioxygenases / genetics
  • Dioxygenases / metabolism
  • Hydroquinones / chemistry*
  • Iron / chemistry*
  • Nitrophenols / chemistry
  • Parabens / chemistry
  • Protein Conformation
  • Sequence Homology, Amino Acid
  • Sphingomonas / enzymology*

Substances

  • Hydroquinones
  • Nitrophenols
  • Parabens
  • Iron
  • Dioxygenases
  • 4-hydroxybenzoic acid
  • hydroquinone
  • 4-nitrophenol