scholarly journals Oxidative Inactivation of Ring-Cleavage Extradiol Dioxygenases: Mechanism and Ferredoxin-Mediated Reactivation

2012 ◽  
Keyword(s):  
Ring Cleavage ◽  
Oxidative Inactivation ◽  
Extradiol Dioxygenases

scholarly journals Identification of an Extradiol Dioxygenase Involved in Tetralin Biodegradation: Gene Sequence Analysis and Purification and Characterization of the Gene Product

2000 ◽  
Vol 182 (3) ◽  
pp. 789-795 ◽  
Author(s):  
Eloísa Andújar ◽  
María José Hernáez ◽  
Stefan R. Kaschabek ◽  
Walter Reineke ◽  
Eduardo Santero
Keyword(s):  
Gene Product ◽  
Biochemical Properties ◽  
Genomic Region ◽  
Quinoline Derivative ◽  
Ring Cleavage ◽  
Insertion Mutant ◽  
Significant Activity ◽  
Extradiol Dioxygenase ◽  
Group 2 ◽  
Extradiol Dioxygenases

ABSTRACT A genomic region involved in tetralin biodegradation was recently identified in Sphingomonas strain TFA. We have cloned and sequenced from this region a gene designated thnC, which codes for an extradiol dioxygenase required for tetralin utilization. Comparison to similar sequences allowed us to define a subfamily of 1,2-dihydroxynaphthalene extradiol dioxygenases, which comprises two clearly different groups, and to show that ThnC clusters within group 2 of this subfamily. 1,2-Dihydroxy-5,6,7,8-tetrahydronaphthalene was found to be the metabolite accumulated by a thnC insertion mutant. The ring cleavage product of this metabolite exhibited behavior typical of a hydroxymuconic semialdehyde toward pH-dependent changes and derivatization with ammonium to give a quinoline derivative. The gene product has been purified, and its biochemical properties have been studied. The enzyme is a decamer which requires Fe(II) for activity and shows high activity toward its substrate (V max, 40.5 U mg−1;Km , 18.6 μM). The enzyme shows even higher activity with 1,2-dihydroxynaphthalene and also significant activity toward 1,2-dihydroxybiphenyl or methylated catechols. The broad substrate specificity of ThnC is consistent with that exhibited by other extradiol dioxygenases of the same group within the subfamily of 1,2-dihydroxynaphthalene dioxygenases.

scholarly journals Ring-Cleaving Dioxygenases with a Cupin Fold

2012 ◽  
Vol 78 (8) ◽  
pp. 2505-2514 ◽  
Author(s):  
Susanne Fetzner
Keyword(s):  
Electron Transfer ◽  
Metal Ion ◽  
Direct Electron Transfer ◽  
Heterocyclic Ring ◽  
Divalent Metal ◽  
Ring Cleavage ◽  
Type I ◽  
Divalent Metal Ions ◽  
Canonical Type ◽  
Extradiol Dioxygenases

ABSTRACTRing-cleaving dioxygenases catalyze key reactions in the aerobic microbial degradation of aromatic compounds. Many pathways converge to catecholic intermediates, which are subject toorthoormetacleavage by intradiol or extradiol dioxygenases, respectively. However, a number of degradation pathways proceed via noncatecholic hydroxy-substituted aromatic carboxylic acids like gentisate, salicylate, 1-hydroxy-2-naphthoate, or aminohydroxybenzoates. The ring-cleaving dioxygenases active toward these compounds belong to the cupin superfamily, which is characterized by a six-stranded β-barrel fold and conserved amino acid motifs that provide the 3His or 2- or 3His-1Glu ligand environment of a divalent metal ion. Most cupin-type ring cleavage dioxygenases use an FeIIcenter for catalysis, and the proposed mechanism is very similar to that of the canonical (type I) extradiol dioxygenases. The metal ion is presumed to act as an electron conduit for single electron transfer from the metal-bound substrate anion to O2, resulting in activation of both substrates to radical species. The family of cupin-type dioxygenases also involves quercetinase (flavonol 2,4-dioxygenase), which opens up two C-C bonds of the heterocyclic ring of quercetin, a wide-spread plant flavonol. Remarkably, bacterial quercetinases are capable of using different divalent metal ions for catalysis, suggesting that the redox properties of the metal are relatively unimportant for the catalytic reaction. The major role of the active-site metal ion could be to correctly position the substrate and to stabilize transition states and intermediates rather than to mediate electron transfer. The tentative hypothesis that quercetinase catalysis involves direct electron transfer from metal-bound flavonolate to O2is supported by model chemistry.

scholarly journals Crystal structures of alkylperoxo and anhydride intermediates in an intradiol ring-cleaving dioxygenase

2014 ◽  
Vol 112 (2) ◽  
pp. 388-393 ◽  
Author(s):  
Cory J. Knoot ◽  
Vincent M. Purpero ◽  
John D. Lipscomb
Keyword(s):  
Ring Cleavage ◽  
Site Specificity ◽  
Computational Studies ◽  
Structural Comparison ◽  
Alternative Substrate ◽  
Extradiol Dioxygenase ◽  
X Ray ◽  
Solution Studies ◽  
Extradiol Dioxygenases ◽  
Peroxo Intermediate

Intradiol aromatic ring-cleaving dioxygenases use an active site, nonheme Fe3+ to activate O2 and catecholic substrates for reaction. The inability of Fe3+ to directly bind O2 presents a mechanistic conundrum. The reaction mechanism of protocatechuate 3,4-dioxygenase is investigated here using the alternative substrate 4-fluorocatechol. This substrate is found to slow the reaction at several steps throughout the mechanistic cycle, allowing the intermediates to be detected in solution studies. When the reaction was initiated in an enzyme crystal, it was found to halt at one of two intermediates depending on the pH of the surrounding solution. The X-ray crystal structure of the intermediate at pH 6.5 revealed the key alkylperoxo-Fe3+ species, and the anhydride-Fe3+ intermediate was found for a crystal reacted at pH 8.5. Intermediates of these types have not been structurally characterized for intradiol dioxygenases, and they validate four decades of spectroscopic, kinetic, and computational studies. In contrast to our similar in crystallo crystallographic studies of an Fe2+-containing extradiol dioxygenase, no evidence for a superoxo or peroxo intermediate preceding the alkylperoxo was found. This observation and the lack of spectroscopic evidence for an Fe2+ intermediate that could bind O2 are consistent with concerted formation of the alkylperoxo followed by Criegee rearrangement to yield the anhydride and ultimately ring-opened product. Structural comparison of the alkylperoxo intermediates from the intra- and extradiol dioxygenases provides a rationale for site specificity of ring cleavage.

scholarly journals High aromatic ring-cleavage diversity in birch rhizosphere: PAH treatment-specific changes of I.E.3 group extradiol dioxygenases and 16S rRNA bacterial communities in soil

2008 ◽  
Vol 2 (9) ◽  
pp. 968-981 ◽  
Author(s):  
Timo P Sipilä ◽  
Anna-Kaisa Keskinen ◽  
Marja-Leena Åkerman ◽  
Carola Fortelius ◽  
Kielo Haahtela ◽  
...  
Keyword(s):  
16S Rrna ◽  
Aromatic Ring ◽  
Bacterial Communities ◽  
Ring Cleavage ◽  
Aromatic Ring Cleavage ◽  
Extradiol Dioxygenases

scholarly journals Elucidation of the 4-Hydroxyacetophenone Catabolic Pathway in Pseudomonas fluorescens ACB

2008 ◽  
Vol 190 (15) ◽  
pp. 5190-5198 ◽  
Author(s):  
Mariëlle J. H. Moonen ◽  
Nanne M. Kamerbeek ◽  
Adrie H. Westphal ◽  
Sjef A. Boeren ◽  
Dick B. Janssen ◽  
...  
Keyword(s):  
Pseudomonas Fluorescens ◽  
Efflux Pump ◽  
Intermediate Formation ◽  
Open Reading Frames ◽  
Ring Cleavage ◽  
Semialdehyde Dehydrogenase ◽  
Genes Encoding ◽  
Intradiol Dioxygenase ◽  
Extradiol Dioxygenases ◽  
Reading Frames

ABSTRACT The catabolism of 4-hydroxyacetophenone in Pseudomonas fluorescens ACB is known to proceed through the intermediate formation of hydroquinone. Here, we provide evidence that hydroquinone is further degraded through 4-hydroxymuconic semialdehyde and maleylacetate to β-ketoadipate. The P. fluorescens ACB genes involved in 4-hydroxyacetophenone utilization were cloned and characterized. Sequence analysis of a 15-kb DNA fragment showed the presence of 14 open reading frames containing a gene cluster (hapCDEFGHIBA) of which at least four encoded enzymes are involved in 4-hydroxyacetophenone degradation: 4-hydroxyacetophenone monooxygenase (hapA), 4-hydroxyphenyl acetate hydrolase (hapB), 4-hydroxymuconic semialdehyde dehydrogenase (hapE), and maleylacetate reductase (hapF). In between hapF and hapB, three genes encoding a putative intradiol dioxygenase (hapG), a protein of the Yci1 family (hapH), and a [2Fe-2S] ferredoxin (hapI) were found. Downstream of the hap genes, five open reading frames are situated encoding three putative regulatory proteins (orf10, orf12, and orf13) and two proteins possibly involved in a membrane efflux pump (orf11 and orf14). Upstream of hapE, two genes (hapC and hapD) were present that showed weak similarity with several iron(II)-dependent extradiol dioxygenases. Based on these findings and additional biochemical evidence, it is proposed that the hapC and hapD gene products are involved in the ring cleavage of hydroquinone.

Catalytic Mechanism for 2,3-Dihydroxybiphenyl Ring Cleavage by Nonheme Extradiol Dioxygenases BphC: Insights from QM/MM Analysis

2019 ◽  
Vol 123 (10) ◽  
pp. 2244-2253 ◽  
Author(s):  
Junjie Wang ◽  
Jinfeng Chen ◽  
Xiaowen Tang ◽  
Yanwei Li ◽  
Ruiming Zhang ◽  
...  
Keyword(s):  
Catalytic Mechanism ◽  
Ring Cleavage ◽  
Extradiol Dioxygenases

scholarly journals Structures of an extradiol catechol dioxygenase – C23O64, from 3-nitrotoluene degrading Diaphorobacter sp. strain DS2 in substrate-free, substrate-bound and substrate analog-bound states

2020 ◽  
Vol 1 ◽  
Author(s):  
Keerti Mishra ◽  
Chetan Kumar Arya ◽  
Ramaswamy Subramanian ◽  
Gurunath Ramanathan
Keyword(s):  
Bound States ◽  
Degradation Pathway ◽  
Ring Cleavage ◽  
Molecular Replacement ◽  
Catechol Dioxygenase ◽  
Conserved Residues ◽  
Substrate Analog ◽  
Cleavage Enzyme ◽  
Metabolic Degradation ◽  
Extradiol Dioxygenases

AbstractThis manuscript reports structure–function studies of Catechol 2,3-dioxygenase (C23O64), which is the second enzyme in the metabolic degradation pathway of 3-nitrotoluene by Diaphorobacter sp. strain DS2. The recombinant protein is a ring cleavage enzyme for 3-methylcatechol and 4-methylcatechol products formed after dioxygenation of the aromatic ring. Here we report the substrate-free, substrate-bound, and substrate-analog bound crystal structures of C23O64. The protein crystallizes in the P6(2)22 space-group. The structures were determined by molecular replacement and refined to resolutions of 2.4, 2.4, 2.2 Å, respectively. A comparison of the structures with related extradiol dioxygenases showed 22 conserved residues. A comparison of the active site pocket with catechol 2,3-dioxygenase (LapB) from Pseudomonas sp KL28 and homoprotocatechuate 2,3-dioxygenase (HPCD) from Brevibacterium fuscum shows significant similarities to suggest that the mechanism of enzyme action is similar to HPCD.

Cleavage of the Epimines of 1,6-Anhydrohexoses with Fluoride Anion

2005 ◽  
Vol 70 (12) ◽  
pp. 2075-2085 ◽  
Author(s):  
Jiří Kroutil ◽  
Klára Jeništová
Keyword(s):  
Fluoride Anion ◽  
Ring Cleavage ◽  
Protecting Group ◽  
Reaction Conditions ◽  
Aziridine Ring ◽  
Cleavage Reactions ◽  
Derivatives Of ◽  
Fluoro Derivatives

Aziridine ring cleavage reactions of five N-nosylepimines (2-6) having D-talo, D-galacto, D-manno, and D-allo configurations with potassium hydrogendifluoride under various reaction conditions have been performed. The cleavage regioselectively afforded diaxial isomers of vicinal amino-fluoro derivatives of 1,6-anhydro-β-D-gluco- and mannopyranose 7-11 in 51-94% yields. Removal of 2-nitrobenzenesulfonyl protecting group with benzenethiol has been attempted in the case of compound 10.

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