Structural Insight into the Dioxygenation of Nitroarene Compounds: the Crystal Structure of Nitrobenzene Dioxygenase

Friemann, Rosmarie; Ivkovic-Jensen, Maja M.; Lessner, Daniel J.; Yu, Chung Huang; Gibson, David T.; Parales, Rebecca E.; Eklund, Hans; Ramaswamy, S.

doi:10.1016/j.jmb.2005.03.052

Cited by 113 publications

(179 citation statements)

References 57 publications

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“…This conformational shift increases the accessible surface at the metal site and opens a pathway for oxygen to diffuse to the mononuclear center. It should be noted that these results correlate with the observed structures for other Rieske dioxygenases (2,4,5), in which the Rieske centers are likely to have been in the reduced state due to reduction that occurred in the electron beam, similar to that shown for NDO (18).…”

supporting

confidence: 77%

The “Bridging” Aspartate 178 in Phthalate Dioxygenase Facilitates Interactions between the Rieske Center and the Iron(II)−Mononuclear Center

et al. 2006

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Phthalate dioxygenase (PDO) and its reductase are parts of a two-component Rieske dioxygenase system that initiates the aerobic breakdown of phthalate by forming cis-4,5-dihydro-4,5-dihydroxyphthalate (DHD). Aspartate D178 in PDO, located near its ferrous mononuclear center, is highly conserved among Rieske dioxygenases. The analogous aspartate has been implicated in electron transfer between the mononuclear iron and Rieske center in naphthalene dioxygenase (Parales, R.E. et. al. (1999) J Bacteriol 181, 1831-1837 and in substrate binding and oxygen reactivity in anthranilate dioxygenase (Beharry, Z.M. et. al (2003), Biochemistry 42, 13625-13636). The effects of substituting D178 in PDO with alanine or asparagine on the reactivity of the Rieske centers, phthalate hydroxylation, and coupling of Rieske center oxidation to DHD formation were studied previously (Pinto, A., Tarasev, M., and Ballou, D. P. (2006) Biochemistry in press). This work describes effects that D178N and D178A substitutions have on the interactions between the Rieske and mononuclear centers in PDO. The mutations affected protonation of the Rieske center histidine and conformation of subunits within the PDO multimer to create a more open structure with more solvent-accessible Rieske centers. When the Rieske centers in PDO were oxidized, D178N and D178A substitutions disrupted communication between the Rieske and Fe-mononuclear centers. This was shown by the lack of perturbations of the UV-vis spectra on phthalate binding to the D178N and D178A variants, as opposed to that observed in WT PDO. However, when the Rieske center was in the reduced state, communication between the centers was not disrupted. Phthalate binding similarly affected the rates of oxidation of the reduced Rieske center in both WT and mutant PDO. Nitric Oxide binding at the Fe(II) mononuclear center, as detected by EPR spectrometry of the Fe(II) nitrosyl complex, was regulated by the redox state of the Rieske center. When the Rieske center was oxidized in either WT or D178N PDO, NO bound to the mononuclear iron in the presence or absence of phthalate. However, when the Rieske center was reduced, NO bound only when phthalate was present. These findings are discussed in terms of the "communication functions" performed by the bridging Asp-178.Phthalate dioxygenase (PDO) and its reductase are parts of a two-component enzyme system (PDS) in Burkholderia cepacia DB01 that initiates the aerobic breakdown of phthalate by forming cis-4,5-dihydro-4,5-dihydroxyphthalate (DHD). PDS comprises the monomeric phthalate dioxygenase reductase (PDR), an enzyme that contains both FMN and a plant-type [2Fe-2S] ferredoxin, and a Rieske dioxygenase (PDO), an α 6 multimer that contains Rieske and ferrous mononuclear centers. Mononuclear iron and Rieske centers on each subunit in Rieske oxygenases are shown to be separated by more than 40 Å (2), making direct electron *To whom correspondence should be addressed. Email: dballou@umich.edu NIH Public Access transfer unfavorable (3). However, as s...

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confidence: 77%

The “Bridging” Aspartate 178 in Phthalate Dioxygenase Facilitates Interactions between the Rieske Center and the Iron(II)−Mononuclear Center

et al. 2006

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“…However, this remains to be substantiated via cloning of NdmA and NdmB individually. Some Rieske oxygenases are known to be in hexameric a 3 b 3 configuration (Dong et al, 2005;Friemann et al, 2005;Kauppi et al, 1998;Yu et al, 2007) but only the a subunits contain the [2Fe-2S] cluster and the mononuclear ferrous iron, while the b subunits are mainly for structural purposes (Ferraro et al, 2005). The 2-oxo-1,2-dihydroquinoline 8-monooxygenase of P. putida 86 was reported to be in an a 6 configuration, determined by gel filtration chromatography (Rosche et al, 1995), but the crystal structure showed that it is actually a homotrimer (Martins et al, 2005).…”

Section: Discussionmentioning

confidence: 99%

Characterization of a broad-specificity non-haem iron N-demethylase from Pseudomonas putida CBB5 capable of utilizing several purine alkaloids as sole carbon and nitrogen source

Summers

Louie

et al. 2011

Microbiology

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N-Demethylation of many xenobiotics and naturally occurring purine alkaloids such as caffeine and theobromine is primarily catalysed in higher organisms, ranging from fungi to mammals, by the well-studied membrane-associated cytochrome P450s. In contrast, there is no well-characterized enzyme for N-demethylation of purine alkaloids from bacteria, despite several reports on their utilization as sole source of carbon and nitrogen. Here, we provide what we believe to be the first detailed characterization of a purified N-demethylase from Pseudomonas putida CBB5. The soluble N-demethylase holoenzyme is composed of two components, a reductase component with cytochrome c reductase activity (Ccr) and a two-subunit N-demethylase component (Ndm). Ndm, with a native molecular mass of 240 kDa, is composed of NdmA (40 kDa) and NdmB (35 kDa). Ccr transfers reducing equivalents from NAD(P)H to Ndm, which catalyses an oxygen-dependent N-demethylation of methylxanthines to xanthine, formaldehyde and water. Paraxanthine and 7-methylxanthine were determined to be the best substrates, with apparent K m and kcat values of 50.4±6.8 μM and 16.2±0.6 min−1, and 63.8±7.5 μM and 94.8±3.0 min−1, respectively. Ndm also displayed activity towards caffeine, theobromine, theophylline and 3-methylxanthine, all of which are growth substrates for this organism. Ndm was deduced to be a Rieske [2Fe–2S]-domain-containing non-haem iron oxygenase based on (i) its distinct absorption spectrum and (ii) significant identity of the N-terminal sequences of NdmA and NdmB with the gene product of an uncharacterized caffeine demethylase in P. putida IF-3 and a hypothetical protein in Janthinobacterium sp. Marseille, both predicted to be Rieske non-haem iron oxygenases.

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“…Biochemical and genetic analyses of nitrobenzene dioxygenase (NBDO) showed that it belongs to the naphthalene family of multicomponent Rieske-type dioxygenases (111). Crystal structures and site-directed mutagenesis studies of NBDO identified the active site of the enzyme, as well as key amino acids that bind and direct oxidation specifically to the nitrosubstituted carbon (48,91). JS765 uses a standard meta-cleavage pathway (70,134), like that in P. putida mt-2 (124) and other Pseudomonas strains (32), to metabolize catechol to acetaldehyde and pyruvate (Fig.…”

Section: Pathways For Nitrobenzene Catabolismmentioning

confidence: 99%

Nitroaromatic Compounds, from Synthesis to Biodegradation

Parales

2010

Microbiol Mol Biol Rev

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SUMMARY Nitroaromatic compounds are relatively rare in nature and have been introduced into the environment mainly by human activities. This important class of industrial chemicals is widely used in the synthesis of many diverse products, including dyes, polymers, pesticides, and explosives. Unfortunately, their extensive use has led to environmental contamination of soil and groundwater. The nitro group, which provides chemical and functional diversity in these molecules, also contributes to the recalcitrance of these compounds to biodegradation. The electron-withdrawing nature of the nitro group, in concert with the stability of the benzene ring, makes nitroaromatic compounds resistant to oxidative degradation. Recalcitrance is further compounded by their acute toxicity, mutagenicity, and easy reduction into carcinogenic aromatic amines. Nitroaromatic compounds are hazardous to human health and are registered on the U.S. Environmental Protection Agency's list of priority pollutants for environmental remediation. Although the majority of these compounds are synthetic in nature, microorganisms in contaminated environments have rapidly adapted to their presence by evolving new biodegradation pathways that take advantage of them as sources of carbon, nitrogen, and energy. This review provides an overview of the synthesis of both man-made and biogenic nitroaromatic compounds, the bacteria that have been identified to grow on and completely mineralize nitroaromatic compounds, and the pathways that are present in these strains. The possible evolutionary origins of the newly evolved pathways are also discussed.

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Structural Insight into the Dioxygenation of Nitroarene Compounds: the Crystal Structure of Nitrobenzene Dioxygenase

Cited by 113 publications

References 57 publications

The “Bridging” Aspartate 178 in Phthalate Dioxygenase Facilitates Interactions between the Rieske Center and the Iron(II)−Mononuclear Center

The “Bridging” Aspartate 178 in Phthalate Dioxygenase Facilitates Interactions between the Rieske Center and the Iron(II)−Mononuclear Center

Characterization of a broad-specificity non-haem iron N-demethylase from Pseudomonas putida CBB5 capable of utilizing several purine alkaloids as sole carbon and nitrogen source

Nitroaromatic Compounds, from Synthesis to Biodegradation

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