The Mechanism-based Inactivation of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase by Catecholic Substrates

Vaillancourt, Frédéric H.; Labbé, Geneviève; Drouin, Nathalie M.; Fortin, Pascal D.; Eltis, Lindsay D.

doi:10.1074/jbc.m106890200

Cited by 112 publications

(117 citation statements)

References 66 publications

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“…The negative charge on HPCA O3 may also be stabilized by hydrogen bonding from Y257 OH (ϳ2.7 Å ). A similar role has been proposed for the analogous tyrosine residues in BPHC_PS102 and BPHC_ LB400 (66,81). The notion of a monoanionic ES complex for extradiol dioxygenases has been suggested previously by X-ray absorption spectroscopy studies of 2,3-CTD (71), UV resonance Raman and crystallographic studies of BPHC_LB400 (79), and studies of 4-nitrocatechol binding to these enzymes (64,78).…”

Section: Discussionmentioning

confidence: 80%

Crystallographic Comparison of Manganese- and Iron-Dependent Homoprotocatechuate 2,3-Dioxygenases

et al. 2004

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The X-ray crystal structures of homoprotocatechuate 2,3-dioxygenases isolated from Arthrobacter globiformis and Brevibacterium fuscum have been determined to high resolution. These enzymes exhibit 83% sequence identity, yet their activities depend on different transition metals, Mn 2؉ and Fe 2؉ , respectively. The structures allow the origins of metal ion selectivity and aspects of the molecular mechanism to be examined in detail. The homotetrameric enzymes belong to the type I family of extradiol dioxygenases (vicinal oxygen chelate superfamily); each monomer has four ␤␣␤␤␤ modules forming two structurally homologous N-terminal and C-terminal barrel-shaped domains. The active-site metal is located in the C-terminal barrel and is ligated by two equatorial ligands, H214 NE1 and E267 OE1 ; one axial ligand, H155 NE1 ; and two to three water molecules. The first and second coordination spheres of these enzymes are virtually identical (root mean square difference over all atoms, 0.19 Å), suggesting that the metal selectivity must be due to changes at a significant distance from the metal and/or changes that occur during folding. The substrate (2,3-dihydroxyphenylacetate [HPCA]) chelates the metal asymmetrically at sites trans to the two imidazole ligands and interacts with a unique, mobile C-terminal loop. The loop closes over the bound substrate, presumably to seal the active site as the oxygen activation process commences. An "open" coordination site trans to E267 is the likely binding site for O 2 . The geometry of the enzyme-substrate complexes suggests that if a transiently formed metal-superoxide complex attacks the substrate without dissociation from the metal, it must do so at the C-3 position. Second-sphere active-site residues that are positioned to interact with the HPCA and/or bound O 2 during catalysis are identified and discussed in the context of current mechanistic hypotheses.Bacterial ring-cleaving dioxygenases are critical enzymes in the catabolism of aromatic compounds that enter the environment from a myriad of sources (9,17,18,44). The substrates for most of these enzymes are ortho-or para-dihydroxylated aromatics and molecular oxygen. Both atoms of oxygen from O 2 are incorporated into the product as the ring is cleaved. The resulting aliphatic products are further metabolized to intermediates of core metabolic cycles through well-established pathways (18,55,74).Dioxygenases that act on ortho-dihydroxylated aromatic compounds are divided into two classes, termed intradiol and extradiol, which differ in their mode of ring cleavage and the oxidation state of the active-site metal (44, 63). Intradiol dioxygenases utilize Fe 3ϩ and cleave the bond between the carbons bearing the two hydroxyls; extradiol dioxygenases utilize Fe 2ϩ or, rarely, Mn 2ϩ and cleave one of the carbon-carbon bonds adjacent to the ortho-hydroxyl substituents. Although intradiol and extradiol dioxygenases oxidize an overlapping set of substrates, they are not structurally related and are proposed to have fundamentally differ...

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Section: Discussionmentioning

confidence: 80%

Crystallographic Comparison of Manganese- and Iron-Dependent Homoprotocatechuate 2,3-Dioxygenases

et al. 2004

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“…For example, catechol-type metabolites have an inhibitory effect against PAH dioxygenase, which is a first enzyme in PAH metabolism (Vaillancourt et al 2002). In most of metabolisms of PAHs and heteroaromatic compounds (e.g., polychlorinated dibenzo-p-dioxins, dibenzofurans, carbazoles), catecholic metabolites are produced both in initial reaction and intermediary metabolisms by different type of dioxygenase.…”

Section: Discussionmentioning

confidence: 99%

Comparative metabolomic analysis of Sinorhizobium sp. C4 during the degradation of phenanthrene

Keum

Seo

et al. 2008

Appl Microbiol Biotechnol

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Comparative metabolic responses of Sinorhizobium sp. C4 were investigated. Comprehensive metabolites profiles, including polar metabolites, fatty acids, and polyhydroxyalkanoates were evaluated through untargeted metabolome analyses. Intracellular metabolomes during the degradation of phenanthrene were compared with those from natural carbon sources. Principal component analysis showed a clear separation of metabolomes of phenanthrene degradation from other carbon sources. Shift to more hydrophobic fatty acid was observed from the analysis of fatty acid methyl ester. Polyhydroxyalkanoate from strain C4 was composed mainly with 3-hydroxybutyric acid and small amount of 3-hydroxypentanoic acid, while the monomeric composition was independent on carbon sources. However, the amount of polyhydroxyalkanoates during degradation of phenanthrene was 50-210% less than those from other carbon sources. Among 207 gas chromatography-mass spectrometry peaks from the polar metabolite fraction, 60% of the peaks were identified and compared. Several intermediates in tricarboxylic acid cycles and glycolysis were increased during phenanthrene degradation. Accumulation of trehalose was also evident in the phenanthrene-treated bacterium. Some amino acid, including branched amino acids, glycine, homoserine, and valine, were also increased, while more than 70% of identified metabolites were decreased during the phenanthrene metabolism. Accumulation of sulfur amino acids and nicotinic acid suggested the possible oxidative stress conditions during phenanthrene metabolism.

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“…The stability of the enzymes in the presence of oxygen was calculated by incubation of enzyme solutions corresponding to 5 mU/ml under standard assay conditions and monitoring the remaining activity after different intervals as previously described (43). Partition ratios were determined spectrophotometrically under standard conditions using 0.5 to 10 mU/ml of enzyme and substrate concentrations of 100 to 200 M and calculated by dividing the amount of product formed by the amount of enzyme added to the assay.…”

Section: Methodsmentioning

confidence: 99%

Substrate Specificity and Expression of Three 2,3-Dihydroxybiphenyl 1,2-Dioxygenases from Rhodococcus globerulus Strain P6

et al. 2003

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Rhodococcus globerulus strain P6 contains at least three genes, bphC1, bphC2, and bphC3, coding for 2,3-dihydroxybiphenyl 1,2-dioxygenases; the latter two specify enzymes of the family of one-domain extradiol dioxygenases. In order to assess the importance of these different isoenzymes for the broad catabolic activity of this organism towards the degradation of polychlorinated biphenyls (PCBs), the capacities of recombinant enzymes expressed in Escherichia coli to transform different chlorosubstituted dihydroxybiphenyls formed by the action of R. globerulus P6 biphenyl dioxygenase and biphenyl 2,3-dihydrodiol dehydrogenase were determined. Whereas both BphC2 and BphC3 showed similar activities for 2,3-dihydroxybiphenyl and all monochlorinated 2,3-dihydroxybiphenyls, BphC1 exhibited only weak activity for 2-chloro-2,3-dihydroxybiphenyl. More highly chlorinated 2-chlorosubstituted 2,3-dihydroxybiphenyls were also transformed at high rates by BphC2 and BphC3 but not BphC1. In R. globerulus P6, BphC2 was constitutively expressed, BphC1 expression was induced during growth on biphenyl, and BphC3 was not expressed at significant levels under the experimental conditions. Although we cannot rule out the expression of BphC3 under certain environmental conditions, it seems that the contrasting substrate specificities of BphC1 and BphC2 contribute significantly to the versatile PCB-degrading phenotype of R. globerulus P6.

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The Mechanism-based Inactivation of 2,3-Dihydroxybiphenyl 1,2-Dioxygenase by Catecholic Substrates

Cited by 112 publications

References 66 publications

Crystallographic Comparison of Manganese- and Iron-Dependent Homoprotocatechuate 2,3-Dioxygenases

Crystallographic Comparison of Manganese- and Iron-Dependent Homoprotocatechuate 2,3-Dioxygenases

Comparative metabolomic analysis of Sinorhizobium sp. C4 during the degradation of phenanthrene

Substrate Specificity and Expression of Three 2,3-Dihydroxybiphenyl 1,2-Dioxygenases from Rhodococcus globerulus Strain P6

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