Structure of an aromatic-ring-hydroxylating dioxygenase – naphthalene 1,2-dioxygenase

Kauppi, Björn; Lee, Kyung Ho; Carredano, Enrique; Parales, Rebecca E.; Gibson, David T.; Eklund, Hans; Ramaswamy, S.

doi:10.1016/s0969-2126(98)00059-8

Cited by 518 publications

(577 citation statements)

References 75 publications

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“…1) related to the other by a noncrystallographic three-fold axis [6]. Each α-subunit can be divided into a Rieske-cluster containing domain and a catalytic domain hosting one mononuclear iron.…”

Section: Resultsmentioning

confidence: 99%

“…The 3D structure was determined by molecular replacement, using the α-subunit from naphthalene dioxygenase from Pseudomonas sp. Strain NCIB 9816-4, NDO-O 9816-4 [6] and the β-subunit from cumene dioxygenase from P. fluorescens strain IP01, CDO-O IP01 [11] as templates. The model was refined using REFMAC [12] and COOT [13] to R and R free factors of 19.7 and 23.6 %, respectively (Fig.…”

Section: Methodsmentioning

confidence: 99%

“…The smallest pocket size with an estimated volume of 45 Å 3 was determined for biphenyl dioxygenase from Rhodococcus sp. Strain RHA1, BPDO-O RHA1 (PDB access code 1ULI) [15], while the catalytic pocket volume for naphthalene dioxygenase, NDO-O 9816 (PDB access code 1NDO) [6], found to be 65 Å 3 , is significantly larger. The Phn1 catalytic pocket, with its 91 Å 3 , is the largest reported so far.…”

Section: The Catalytic Pocketmentioning

confidence: 99%

“…(--) 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%

“…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.…”

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confidence: 99%

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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: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: The Catalytic Pocketmentioning

confidence: 99%

“…(--) 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%

mentioning

confidence: 99%

See 3 more Smart Citations

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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High-resolution structures of scytalone dehydratase-inhibitor complexes crystallized at physiological pH

et al. 1999

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Scytalone dehydratase is a molecular target of inhibitor design efforts aimed at preventing the fungal disease caused by Magnaporthe grisea. A method for cocrystallization of enzyme with inhibitors at neutral pH has produced several crystal structures of enzyme-inhibitor complexes at resolutions ranging from 1.5 to 2.2 Å . Four high resolution structures of different enzyme-inhibitor complexes are described. In contrast to the original X-ray structure of the enzyme, the four new structures have well-defined electron density for the loop region comprising residues 115-119 and a different conformation between residues 154 and 160. The structure of the enzyme complex with an aminoquinazoline inhibitor showed that the inhibitor is in a position to form a hydrogen bond with the amide of the Asn131 side chain and with two water molecules in a fashion similar to the salicylamide inhibitor in the original structure, thus confirming design principles. The aminoquinazoline structure also allows for a more confident assignment of donors and acceptors in the hydrogen bonding network.

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High‐resolution structures of scytalone dehydratase‐inhibitor complexes crystallized at physiological pH

Wawrzak¹,

Sandalova²,

Steffens³

et al. 1999

Proteins

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Structure of an aromatic-ring-hydroxylating dioxygenase – naphthalene 1,2-dioxygenase

Cited by 518 publications

References 75 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

High-resolution structures of scytalone dehydratase-inhibitor complexes crystallized at physiological pH

High‐resolution structures of scytalone dehydratase‐inhibitor complexes crystallized at physiological pH

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