Crystal structure of the hydroxyquinol 1,2-dioxygenase from Nocardioides simplex 3E, a key enzyme involved in polychlorinated aromatics biodegradation

J Biol Chem. 2005 Jun 3;280(22):21144-54. doi: 10.1074/jbc.M500666200. Epub 2005 Mar 16.

Abstract

Hydroxyquinol 1,2-dioxygenase (1,2-HQD) catalyzes the ring cleavage of hydroxyquinol (1,2,4-trihydroxybenzene), a central intermediate in the degradation of aromatic compounds including a variety of particularly recalcitrant polychloro- and nitroaromatic pollutants. We report here the primary sequence determination and the analysis of the crystal structure of the 1,2-HQD from Nocardioides simplex 3E solved at 1.75 A resolution using the multiple wavelength anomalous dispersion of the two catalytic irons (1 Fe/293 amino acids). The catalytic Fe(III) coordination polyhedron composed by the side chains of Tyr164, Tyr197, His221, and His223 resembles that of the other known intradiol-cleaving dioxygenases, but several of the tertiary structure features are notably different. One of the most distinctive characteristics of the present structure is the extensive openings and consequent exposure to solvent of the upper part of the catalytic cavity arranged to favor the binding of hydroxyquinols but not catechols. A co-crystallized benzoate-like molecule is also found bound to the metal center forming a distinctive hydrogen bond network as observed previously also in 4-chlorocatechol 1,2-dioxygenase from Rhodococcus opacus 1CP. This is the first structure of an intradiol dioxygenase specialized in hydroxyquinol ring cleavage to be investigated in detail.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Actinomycetales / metabolism*
  • Algorithms
  • Amino Acid Sequence
  • Binding Sites
  • Catalysis
  • Catalytic Domain
  • Catechols / chemistry
  • Cloning, Molecular
  • Crystallography, X-Ray
  • Dioxygenases / chemistry*
  • Histidine / chemistry
  • Hydrogen Bonding
  • Ions
  • Kinetics
  • Metals / chemistry
  • Models, Chemical
  • Models, Molecular
  • Molecular Sequence Data
  • Polymerase Chain Reaction
  • Protein Conformation
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Sequence Homology, Amino Acid
  • Substrate Specificity
  • Sulfates / chemistry
  • Temperature
  • Tyrosine / chemistry

Substances

  • Catechols
  • Ions
  • Metals
  • Sulfates
  • Tyrosine
  • Histidine
  • Dioxygenases
  • hydroxyquinol 1,2-dioxygenase

Associated data

  • PDB/1TMX