Structure of the Terminal Oxygenase Component of Angular Dioxygenase, Carbazole 1,9a-Dioxygenase

Nojiri, Hideaki; Ashikawa, Yuji; Noguchi, Hiroshi; Nam, Jeong-Won; Urata, Masaaki; Fujimoto, Zui; Uchimura, Hidemasa; Terada, Tohru; Nakamura, Shugo; Shimizu, Kentaro; Yoshida, Takako; Habe, Hiroshi; Omori, Toshio

doi:10.1016/j.jmb.2005.05.059

Cited by 86 publications

(113 citation statements)

References 37 publications

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“…Sequence identity of structurally analogous residues lining the catalytic pocket for different dioxygenases of known crystallographic structure shows that PhnI presents the highest sequence identity with NDO-O 9816 and the lowest with carbazole-1-9α-dioxygenase from P. resinovorans strain CA10 (CARDO-O CA10 ) [17]. The classification presented in Table 1, based on α-subunit sequence homology and substrate specificity, is consistent with current classifications [18].…”

Section: The Catalytic Pocketsupporting

confidence: 74%

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The catalytic pocket of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1

Jakoncic

Jouanneau

Meyer

et al. 2007

Biochemical and Biophysical Research Communications

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Ring-hydroxylating dioxygenases are multicomponent bacterial enzymes that catalyze the first step in the oxidative degradation of aromatic hydrocarbons. The dioxygenase from Sphingomonas CHY-1 is unique in that it can oxidize a wide range of polycyclic aromatic hydrocarbons (PAHs). With a crystal structure similar to that of the seven other known dioxygenases, its catalytic domain features the largest hydrophobic substrate binding cavity characterized so far. Molecular modeling studies indicated that the catalytic cavity is large enough to accommodate a five-ring benzo [a]pyrene molecule. The predicted positions of this and other PAHs in the substrate binding pocket are consistent with the product regio-and stereo-selectivity of the enzyme. Keywordsdioxygenase; catalytic domain; mononuclear iron; bioremediation; high molecular weight polycyclic aromatic hydrocarbons The first step in the biodegradation of aromatic hydrocarbons by aerobic bacteria often involves a dihydroxylation on two adjacent carbon atoms of the aromatic ring, catalyzed by a ringhydroxylating dioxygenase (RHD). RHDs form a large family of enzymes, very diverse in terms of substrate specificity and protein sequence [1]. Their role is crucial in the degradation of many organic pollutants, including polycyclic aromatic hydrocarbons (PAHs), which are notorious for their resistance to biodegradation. Several bacteria were found to degrade PAHs but only a few have been reported to attack four and five ring PAHs [2,3]. In Sphingomonas strain CHY-1 a single RHD has been shown to be responsible for the oxidation of a wide range of PAHs [4]. This dioxygenase consists of three components, a NADH-dependent reductase (PhnA4), a ferredoxin containing a Rieske type [2Fe-2S] cluster (PhnA3), and a terminal oxygenase, PhnI, containing both a mononuclear iron [Fe 2+ ] and a [2Fe-2S] Rieske cluster [5]. Recent biochemical studies showed that the dioxygenase from strain CHY-1 was able to oxidize at least eight PAHs made of 2 to 5 aromatic rings, in contrast to most other dioxygenases, whose selectivity is limited to 2 and 3 ring PAHs [6,7,8]. A positive electron density observed in the PhnI refined three-dimensional structure served as probe in modeling different substrates in the catalytic pocket. This study presents evidence that the broad substrateCorresponding author: Vivian Stojanoff, Brookhaven National Laboratory, Upton NY 11973 US, Tel.: 1 631 344 8375; Fax: 1 631 344 3238, Email : vivian.stojanoff@gmail.gov. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. NIH Public AccessAuthor Manuscript Biochem Biophy...

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Section: The Catalytic Pocketsupporting

confidence: 74%

“…(--) no structurally equivalent residues were observed. Substrate free structures were used in the comparison [6,16,7,12,15,17,18].…”

Section: Substrate Specificitymentioning

confidence: 99%

The catalytic pocket of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1

Jakoncic

Jouanneau

Meyer

et al. 2007

Biochemical and Biophysical Research Communications

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“…The X-ray structures of naphthalene (NDO) [9], biphenyl (BPDO) [10], nitrobenzene (NBDO) [11], and cumene (CumDO) [12;13] dioxygenases, as well as 2-oxoquinoline-8-monooxygenase (OMO) [14], and the ring-hydroxylating dioxygenase from Sphingomonas CHY-1 (RHD) [15;16] all indicated that these enzymes are α 3 β 3 multimers, with the α subunits containing both the Rieske and the mononuclear centers. An exception is carbazole 1,9-dioxygenase (CarDO) [12], which is an α 3 trimer. In each case, the α subunits of the trimer are arranged with the subunits oriented head-to-tail, with the Rieske center of one subunit being close (∼ 12 Å) to the mononuclear center of the adjacent subunit.…”

Section: Nih Public Accessmentioning

confidence: 99%

Similar enzymes, different structures: Phthalate dioxygenase is an α3α3 stacked hexamer, not an α3β3 trimer like “normal” Rieske oxygenases

Tarasev

Kaddis

Yin

et al. 2007

Archives of Biochemistry and Biophysics

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Phthalate dioxygenase is an α 3 α 3 stacked hexamer, not an α 3 β 3 trimer like "normal" Rieske oxygenases.Michael Tarasev AbstractPhthalate dioxygenase (PDO) is a member of a class of bacterial oxygenases that contain both Rieske [2Fe-2S] and Fe(II) mononuclear centers. Recent crystal structures of several Rieske dioxygenases showed that they exist as α 3 β 3 multimers with subunits arranged head-to-tail in α and β stacked planar consists of only α-subunits, remains to be solved. Although similar to other Rieske dioxygenases in many aspects, PDO was shown to differ in the mechanism of catalysis. Gel filtration and analytical centrifugation experiments, supplemented with mass spectrometric analysis (both ESI-MS and ESI-GEMMA), in this work showed a hexameric arrangement of subunits in the PDO multimer. Our proposed model for the subunit arrangement in PDO postulates two α 3 planar rings one on top the other, similar to the α 3 β 3 arrangement in other Rieske dioxygenases. Unlike other Rieske dioxygenases, this arrangement brings two Rieske and two mononuclear centers, all on separate subunits, into proximity, allowing their cooperation for catalysis. Potential reasons necessitating this unusual structural arrangement are discussed. KeywordsPhthalate Dioxygenase; Rieske center; Rieske dioxygenase; structure; subunit arrangement Rieske aromatic ring-hydroxylating dioxygenase systems facilitate the degradation of various aromatic hydrocarbons. These enzymes contain Rieske-type redox-active iron-sulfur clusters ) and mononuclear ferrous centers, and catalyze the formation of cis-dihydrodiols by enantiospecific addition of two hydroxyl groups onto aromatic substrates. This is a first step in many aerobic biodegradation pathways that typically lead to breaching of aromatic rings of otherwise recalcitrant substrates.Phthalate dioxygenase (PDO), an oxygenase from Burkholderia cepacia (DB01), catalyzes the first step in the breakdown of the aromatic compound phthalate to form the dihydrodiol of * To whom correspondence should be addressed. Email: dballou@umich.edu Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. . It is a member of the Although similar to other Rieske dioxygenases in many aspects, PDO was shown to differ somewhat in its mechanism of catalysis. For example, after reduced NDO is exposed to oxygen in the presence of the substrate, the mononuclear iron was found to be in the ferric state [6]. One cis-dihydrodiol product was found per Rieske and mononuclear center that was oxidized. NIH Public AccessIn contrast, upon completion of the reaction in PDO, phthe mononucle...

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“…J3 has been determined, and several hydrophobic residues, such as Ile184, Ile186, Leu270, Val272, Phe275, Phe329, and Ile334, were found to constitute substrate-binding pockets. 23) In the case of strain IC177, the residues corresponding to Ile186 and Ile334 of J3 were replaced by Met192 and Val338, respectively. 24) In the case of strain OC11, Ile186 and Ile334 of J3 were replaced by Leu194 and Val340, respectively (Fig.…”

Section: )mentioning

confidence: 99%

Characterization and genetic analyses of a carbazole-degrading gram-positive marine isolate, Janibacter sp. strain OC11

Oba

Suzuki

Maeda

et al. 2014

Bioscience, Biotechnology, and Biochemistry

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Strain OC11 was isolated from seawater sampled at the coast of Chiba, Japan, in artificial seawater medium with carbazole (CAR) as the sole carbon source. Its 16S ribosomal RNA gene sequence suggested that strain OC11 belongs to the genus Janibacter. The CAR-degradation genes (car genes) of strain OC11 were PCR amplified, using degenerate primers designed based on the car gene sequences of other CAR-degrading bacteria. Complete nucleotide sequences encoding six complete open reading frames were determined, and the first known ferredoxin reductase gene (carAd) was found from a CAR-degrading bacterium isolated from the marine environment. An experiment using a mutant strain suggested that the car genes of strain OC11 are functional in CAR degradation. Southern hybridization indicated that strain OC11 had one car gene cluster in vivo. RT-PCR revealed that transcription of carOC11 constitutes an operon.

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Structure of the Terminal Oxygenase Component of Angular Dioxygenase, Carbazole 1,9a-Dioxygenase

Cited by 86 publications

References 37 publications

The catalytic pocket of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1

The catalytic pocket of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1

Similar enzymes, different structures: Phthalate dioxygenase is an α3α3 stacked hexamer, not an α3β3 trimer like “normal” Rieske oxygenases

Characterization and genetic analyses of a carbazole-degrading gram-positive marine isolate, Janibacter sp. strain OC11

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