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EC Number
Crystallization
Reference
CARDO of Novosphingobium sp. KA1 consists of a terminal oxygenase, a putidaredoxin-type ferredoxin and a ferredoxin-NADH oxidoreductase. Crystallization of the ferredoxin reductase component to 1.58 A resolution, space group P32, with unit-cell parameters a = b = 92.2, c = 78.6 A
CARDO of Novosphingobium sp. KA1 consists of a terminal oxygenase, Oxy, a putidaredoxin-type ferredoxin and a ferredoxin-NADH oxidoreductase. Crystallization of the oxygenase component to 2.1 A resolution, space group P21
comparison of crystal structures of the oxygenase and ferredoxin components to the CARDOs from Pseudomonas resinovorans CA10, Janthinobacterium sp. J3, Novosphingobium sp. KA1, and Nocardioides aromaticivorans IC177 which are grouped into classes III, III, IIA, and IIB, respectively. The comparison suggests residues in common between class IIB and class III CARDOs that are important for interactions between ferredoxin and oxygenase. In the class IIB CARDOs, these include His75 and Glu71 in ferredoxin and Lys20 and Glu357 in the oxygenase for electrostatic interactions, and Phe74 and Pro90 in ferredoxin and Trp21, Leu359, and Val367 in the oxygenase for hydrophobic interactions
crystal structure of ferredoxin component CarAc at 1.9 A resolution by molecular replacement using the structure of BphF, the biphenyl 2,3-dioxygenase ferredoxin from Burkholderia cepacia strain LB400 as a search model. CarAc is composed of three beta-sheets, and the structure can be divided into a cluster-binding domain and a basal domain. The Rieske [2Fe-2S] cluster is located at the tip of the cluster-binding domain, where it is exposed to solvent. While the overall folding of CarAc and BphF is strongly conserved, the properties of their surfaces are very different from each other. The structure of the cluster-binding domain of CarAc is more compact and protruding than that of BphF
crystal structure of oxygenase component CARDO-O at a resolution of 1.95 A, and of selenomethione derivative to 2.3 A resolution. The alpha3 trimeric overall structure of the CARDO-O molecule roughly corresponds to the alpha3 partial structures of other terminal oxygenase components of Rieske non-heme iron oxygenase systems that have the alpha3beta3 configuration and reveals the presence of the specific loops that interact with a neighboring subunit. The shape of the substrate-binding pocket of CARDO-O is markedly different from those of other oxygenase components involved in naphthalene and biphenyl degradation pathways. Docking simulations suggest that carbazole binds to the substrate-binding pocket in a manner suitable for catalysis of angular dioxygenation
crystal structures of the nonreduced, reduced, and substrate-bound binary complexes of terminal oxygenase CARDO-O from Janthinobacterium sp. J3 with its electron donor, ferredoxin CARDO-F from Pseudomonas resinovorans CA10 at 1.9, 1.8, and 2.0 A resolutions, respectively. The structures provide a structure-based interpretation of intercomponent electron transfer between two Rieske [2Fe-2S] clusters of ferredoxin and oxygenase in a Rieske nonheme iron oxygenase system. Three molecules of CARDO-F bind to the subunit boundary of one CARDO-O trimeric molecule, and specific binding created by electrostatic and hydrophobic interactions with conformational changes suitably aligns the two Rieske clusters for electron transfer. Additionally, conformational changes upon binding carbazole results in the closure of a lid over the substrate-binding pocket, thereby seemingly trapping carbazole at the substrate-binding site
crystal structures of the reduced carbazole-bound, dioxygen-bound, and both carbazole- and dioxygen-bound subunits CARDO-O:CARDO-F binary complex structures at 1.95, 1.85, and 2.00 A resolution, using the catalytic terminal oxygenase subunit from Janthinobacterium sp. J3 and ferredoxin from Pseudomonas resinovorans CA10. Catalytic mechanism is as follows: When the Rieske cluster is reduced, substrate binding induces several conformational changes that create room for oxygen binding. Dioxygen bound in a side-on fashion onto nonheme iron is activated by reduction to the peroxo state [Fe(III)-(hydro)peroxo]. This state may react directly with the bound substrate, or OÂľO bond cleavage may occur to generate Fe(V)-oxo-hydroxo species prior to the reaction. After producing a cis-dihydrodiol, the product is released by reducing the nonheme iron
crystallization of ferredoxin component, to 2.0 A resolution, space group P41212; terminal oxygenase component, to 2.3 A resolution, space group C2
crystallization of ferredoxin reductase subunit CARDO-R using the hanging-drop vapour-diffusion method with the precipitant PEG 8000 results in two crystal types. The type I crystal diffract to a maximum resolution of 2.80 A and belong to space group P42212, with unit cell parameters a, b of 158.7, c of 81.4 A. The type II crystal diffracts to 2.60 A resolution and belongs to the same space group, with unit-cell parameters a, b of 161.8, c of 79.5 A
docking simulation of dibenzo-p-dioxin to wild-type CARDO oxygenase
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