Abstract
Carbazole 1,9a-dioxygenase (CARDO), which consists of an oxygenase component and the electron-transport components ferredoxin (CARDO-F) and ferredoxin reductase (CARDO-R), is a Rieske nonheme iron oxygenase (RO). ROs are classified into five subclasses (IA, IB, IIA, IIB and III) based on their number of constituents and the nature of their redox centres. In this study, two types of crystal structure (type I and type II) were resolved of the class III CARDO-R from Janthinobacterium sp. J3 (CARDO-RJ3). Superimposition of the type I and type II structures revealed the absence of flavin adenine dinucleotide (FAD) in the type II structure along with significant conformational changes to the FAD-binding domain and the C-terminus, including movements to fill the space in which FAD had been located. Docking simulation of NADH into the FAD-bound form of CARDO-RJ3 suggested that shifts of the residues at the C-terminus caused the nicotinamide moiety to approach the N5 atom of FAD, which might facilitate electron transfer between the redox centres. Differences in domain arrangement were found compared with RO reductases from the ferredoxin-NADP reductase family, suggesting that these differences correspond to differences in the structures of their redox partners ferredoxin and terminal oxygenase. The results of docking simulations with the redox partner class III CARDO-F from Pseudomonas resinovorans CA10 suggested that complex formation suitable for efficient electron transfer is stabilized by electrostatic attraction and complementary shapes of the interacting regions.
Highlights
Rieske nonheme iron oxygenases (ROs) are the initial catalysts in the degradation pathways of numerous environmentally hazardous aromatic compounds and components of crude oil (Mason & Cammack, 1992; Nojiri & Omori, 2002; Nojiri, 2012)
The three molecules in the asymmetric unit of each structure were connected by a noncrystallographic threefold axis, CARDO-RJ3 was a monomer in solution
The type I structure contained the [2Fe-2S] cluster and flavin adenine dinucleotide (FAD), while the type II structure lacked FAD, which is essential for the physiological function of CARDO-RJ3
Summary
Rieske nonheme iron oxygenases (ROs) are the initial catalysts in the degradation pathways of numerous environmentally hazardous aromatic compounds and components of crude oil (Mason & Cammack, 1992; Nojiri & Omori, 2002; Nojiri, 2012). ROs generally consist of two or three discrete components that form an electron-transfer chain from NAD(P)H via flavin and [2Fe–2S] redox centres to the site of dioxygen activation (Bugg & Ramaswamy, 2008). Class I ROs consist of reductase and oxygenase components, with their reductase components containing both flavin [flavin mononucleotide (FMN) in class IA and flavin adenine dinucleotide (FAD) in class IB] and a chloroplast-type [2Fe–2S] cluster. Both class II and class III ROs contain a ferredoxin component in addition to reductase and oxygenase components. There is variation in the redox-transfer machineries of both the reductase and the ferredoxin, these components transfer electrons from NAD(P)H to oxygenase for dioxygen activation
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