Crystal Structure of Naphthalene Dioxygenase: Side-on Binding of Dioxygen to Iron

Karlsson, Andreas; Parales, Juanito V.; Parales, Rebecca E.; Gibson, David T.; Eklund, Hans; Ramaswamy, S.

doi:10.1126/science.1078020

Cited by 517 publications

(522 citation statements)

References 25 publications

(16 reference statements)

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“…The observation of dioxygen molecules near enzyme active sites is precedented in other structures (10,11). Dioxygen is associated with metal atoms in naphthalene dioxygenase and cytochromes P450 (10,12). The proposed dioxygen in this FMO structure is bound to Asn-91.…”

Section: Discussionmentioning

confidence: 99%

Mechanism of action of a flavin-containing monooxygenase

Eswaramoorthy

Bonanno

Burley³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

172

170

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Elimination of nonnutritional and insoluble compounds is a critical task for any living organism. Flavin-containing monooxygenases (FMOs) attach an oxygen atom to the insoluble nucleophilic compounds to increase solubility and thereby increase excretion. Here we analyze the functional mechanism of FMO from Schizosaccharomyces pombe using the crystal structures of the wild type and protein–cofactor and protein–substrate complexes. The structure of the wild-type FMO revealed that the prosthetic group FAD is an integral part of the protein. FMO needs NADPH as a cofactor in addition to the prosthetic group for its catalytic activity. Structures of the protein–cofactor and protein–substrate complexes provide insights into mechanism of action. We propose that FMOs exist in the cell as a complex with a reduced form of the prosthetic group and NADPH cofactor, readying them to act on substrates. The 4α-hydroperoxyflavin form of the prosthetic group represents a transient intermediate of the monooxygenation process. The oxygenated and reduced forms of the prosthetic group help stabilize interactions with cofactor and substrate alternately to permit continuous enzyme turnover.

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Section: Discussionmentioning

confidence: 99%

Mechanism of action of a flavin-containing monooxygenase

Eswaramoorthy

Bonanno

Burley³

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

172

170

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“…[19] This implies that the BDEOH of the [Fe IV (O)(Por +• )] + system will be considerably smaller than that of P450 CpdI and unable to react via hydrogen atom abstraction. Indeed, we calculate a BDEOH for the reaction of 3 [Fe III (OH)(Por +• )] + into CpdI and a hydrogen atom of DE+ZPE = 66.3 kcal mol -1 , whereas for a P450 CpdI model a value of 88.9 kcal mol -1 was obtained. [20] In aliphatic hydroxylation the energy of the hydrogen atom abstraction step is equal to the difference in BDECH of the substrate and the BDEOH of the oxidant.…”

Section: Theorymentioning

confidence: 99%

“…[2] Highly relevant for environmental purposes are, for instance, the naphthalene dioxygenases that have functions in biotechnology that include the cleaning up of oil-spills and removal of aromatic compounds from soil. [3] Also, in the human body applications of heme and nonheme iron dioxygenases are found, for instance, for the biodegradation of aromatic amino acids starting with a mono-or dihydroxylation reaction. [4] Further arene activating enzymes in the body include the thiolate-ligated heme mono-oxygenases called cytochromes P450 (P450) that have been shown to hydroxylate arenes to phenols as a means to metabolize drugs as well as xenobiotic molecules in the liver.…”

Section: Introductionmentioning

confidence: 99%

A Systematic Account on Aromatic Hydroxylation by a Cytochrome P450 Model Compound I: A Low‐Pressure Mass Spectrometry and Computational Study

Reinhard

Sainna

Upadhyay

et al. 2016

Chemistry A European J

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Cytochrome P450 enzymes are heme containing monooxygenases that mainly react through oxygen atom transfer. Specific features of substrate and oxidant that determine the reaction rate constant for oxygen atom transfer are still poorly understood and, therefore, we did a systematic gas-phase study on reactions by iron(IV)-oxo porphyrin cation radical structures with arenes. We present here the first results obtained by using Fourier transform-ion cyclotron resonance mass spectrometry and provide rate constants and product distributions for the assayed reactions. Product distributions and kinetic isotope effect studies implicate a rate determining aromatic hydroxylation reaction that correlates with the ionization energy of the substrate and no evidence of aliphatic hydroxylation products is observed. To further understand the details of the reaction mechanism, a computational study on a model complex was performed. These studies confirm the experimental hypothesis of dominant aromatic over aliphatic hydroxylation and show that the lack of an axial ligand affects the aliphatic pathways. Moreover, a two parabola valence bond model is used to rationalize the rate constant and identify key properties of the oxidant and substrate that drive the reaction. In particular, the work shows that aromatic hydroxylation rates correlate with the ionization energy of the substrate as well as with the electron affinity of the oxidant.

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“…First, X-ray crystallography has revealed that NDO forms a side-on bound Fe (III)-hydroperoxy substrate intermediate at the mononuclear iron site. 6 Second, the STO experiments have shown that the chemical reaction can be carried out without NDR and NDF. Both metal centers of NDO are oxidized during the STO revealing the sources of the two reducing equivalents required by the stoichiometry of the reaction.…”

mentioning

confidence: 99%

Radical Intermediates in Monooxygenase Reactions of Rieske Dioxygenases

et al. 2007

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Rieske dioxygenases catalyze the cis-dihydroxylation of a wide range of aromatic compounds to initiate their biodegradation. The archetypal Rieske dioxygenase naphthalene 1,2-dioxygenase (NDOS) catalyzes dioxygenation of naphthalene to form (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene. NDOS is composed of three proteins: a reductase, a ferredoxin, and an α 3 β 3 oxygenase (NDO). In each α subunit, NDO contains a Rieske Fe 2 S 2 cluster and a mononuclear iron site where substrate dihydroxylation occurs. NDOS also catalyzes monooxygenase reactions for many substrates. The mechanism of the reaction is unknown for either the mono-or di-oxygenase reactions, but has been postulated to involve either direct reaction of a structurally characterized Fe (III)-hydroperoxy intermediate or the electronically equivalent Fe(V)-oxo-hydroxo intermediate formed by O-O bond cleavage before reaction with substrate. The reaction for the former intermediate is expected to proceed through cationic intermediates while the latter is anticipated to initially form a radical intermediate. Here the monooxygenation reactions of the diagnostic probe molecules norcarane and bicyclohexane are investigated. In each case, a significant amount of the rearrangement product derived from a radical intermediate (lifetime of 11-18 ns) is observed while little or no ring expansion product from a cationic intermediate is formed. Thus, monooxygenation of these molecules appears to proceed via the Fe(V)-oxo-hydroxo intermediate. The formation of this highvalent intermediate shows that it must also be considered as a possible participant in the dioxygenation reaction, in contrast to computational studies but in accord with previous biomimetic studies.Rieske cis-diol forming dioxygenases are among the most versatile of nature's oxidizing catalysts and are often employed to initiate the biodegradation of recalcitrant environmental E-mail: E-mail: lipsc001@umn.edu. Supporting Information Available: Additional methods and characterization of products (PDF). This material is available free of charge via the Internet at http://pubs.acs.org. The natural substrates for these enzymes are unactivated aromatic compounds. These are converted to nonaromatic cis-dihydrodiols with the incorporation of both oxygen atoms from O 2 in a reaction coupled to the oxidation of NADH. NIH Public AccessNaphthalene 1,2-dioxygenase is a Rieske dioxygenase that catalyzes the oxidation of its name substrate to form (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene. 1b The enzyme system (NDOS) consists of an FAD and Fe 2 S 2 cluster-containing reductase (NDR), a ferredoxin (NDF), and an α 3 β 3 oxygenase (NDO) containing a Fe 2 S 2 Rieske cluster and a mononuclear iron center in each α subunit. NDOS exhibits a broad substrate range for aromatic cisdihydroxylation. 1c Moreover, it catalyzes monooxygenase reactions with a diversity rivaling cytochrome P450 (P450) and methane monooxygenase (MMO). 1b-c,2The mechanism for oxygen insertion by Rieske dioxygenases is unknown for both ...

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Crystal Structure of Naphthalene Dioxygenase: Side-on Binding of Dioxygen to Iron

Cited by 517 publications

References 25 publications

Mechanism of action of a flavin-containing monooxygenase

Mechanism of action of a flavin-containing monooxygenase

A Systematic Account on Aromatic Hydroxylation by a Cytochrome P450 Model Compound I: A Low‐Pressure Mass Spectrometry and Computational Study

Radical Intermediates in Monooxygenase Reactions of Rieske Dioxygenases

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