Initiating the biodegradation of PCBs: Structural analysis of the biphenyl dioxygenase system
Abstract
The first step in the aerobic microbial degradation of biphenyl and polychlorinated biphenyls (PCBs) utilizes a short electron transfer chain to facilitate dioxygenase-catalyzed formation of a cis-dihydrodiol from the aromatic substrate. The electron transfer chain includes a ferredoxin reductase (BphG), a Rieske-type ferredoxin (BphF), and the ring-hydroxylating dioxygenase (BphA1A2). This work will present the X-ray crystal structures of the ferredoxin from Burkholderia cepacia to 1.6 Å resolution and the biphenyl dioxygenase from Comomonas testosteroni to 1.5 Å resolution. The intrinsic Fe atoms provided MAD phasing information in both cases. The structure of BphF is the first for a dioxygenase ferredoxin (Fd) and affords an opportunity for comparisons with Rieske subunits from other systems. The redox properties of dioxygenase Fds differ significantly from those of the Rieske proteins of the bc1 (mitochondria) and b6f (chloroplast) complexes: the midpoint potentials of the former are ∼450mV lower and are relatively independent of ionic strength and pH. It has previously been proposed that differences in the accessibility of the clusters are the cause of these variations, and that the Fe2S2 cluster of the dioxygenase Fd was likely to be sequestered. Despite low sequence identity and variations in key segments of the cluster binding domain, BphF clearly shows a remarkable overall similarity to the bc1 and b 6f structures, and its Fe2S2 cluster has equivalent solvent accessibility. Therefore, the differences in redox properties must arise from other factors. The BphF system enables a detailed study of the subtleties of protein control of redox potential. BphA1A2 is an α3β3 hexamer. Each α-subunit binds one Rieske Fe2S2 cluster and catalyzes ring-hydroxylation at a mono-nuclear, non-heme Fe(II) active site. A structural comparison of BphA1A2 with that of naphthalene dioxygenase provides insight into key aspects of structure and catalysis. Additionally, this structure provides information to the debate surrounding the coordination geometry of the mononuclear Fe site that arose from contrasting results between the spectroscopically characterized phthalate dioxygenase and the structure of naphthalene dioxygenase. Moreover, the structure of BphA1A2 can be used in conjunction with that of BphF to potentially identify features involved in protein-protein association and electron transfer.
Degree
Ph.D.
Advisors
Bolin, Purdue University.
Subject Area
Biophysics|Biochemistry
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