Burkholderia cepacia (bacteria)
The microbial degradation of aromatic compounds provides the potential to destroy widespread, toxic and persistent environmental pollutants and could, therefore, be a tool among bioremediation strategies. The aerobic degradation of aromatic compounds such as toluene, naphthalene, and biphenyl generally proceeds via a catecholic catabolite with hydroxyl substituents on two adjacent carbon atoms. This catecholic compound is cleaved by a dioxygenase from one of two distinct classes. Intradiol dioxygenases cleave the bond located between the two hydroxyl groups and typically depend on mononuclear non-heme Fe(III). In contrast, extradiol dioxygenases cleave a bond adjacent to the two hydroxyl groups and typically require mononuclear non-heme Fe(II). 2,3-Dihydroxybiphenyl 1,2-dioxygenase (DHBD) is a component of the aerobic biphenyl degradation pathway of a number of microorganisms and cleaves 2,3-dihydroxybiphenyl (DHB) in an extradiol fashion.
The crystal structure of DHBD from a polychlorinated biphenyl-degrading strain of Pseudomonas capeasia is shown. DHBD is a homo-octamer and each subunit consists of amino- and carboxyl-terminal domains. The iron atom of the active site has five ligands in square pyramidal geometry: one glutamate and two histidine side chains, and two water molecules. At the general primary steps of extradiol oxygenases catecholic substrates displace water ligands and bind to the iron atom through both hydroxyl groups. The active site structure of DHBD is consistent with the initial steps.
Protein Data Bank (PDB)
author: Aki Nagata