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The work presented here investigates whether the TpMesFe+ moiety, which had been previously found to mediate the dioxygenation of cysteine and cysteamine, can do the same with simple thiols, which are not functionalized by an amine group. Accordingly, the complexes TpMesFeSR (R=Ph, iPr) were synthesized and after full characterization exposed to O2. They were found to react unselectively to yield sulfinates, disulfides, and thiosulfones as products. The sulfinate complex TpMesFeO2S‐p‐Tol was prepared independently and found to be air‐stable, suggesting that the additional products are not formed via overoxidation or subsequent reactions of coordinated sulfinate product. To investigate whether the larger reaction space, opened up due to the missing amine donor is responsible, a Tp‐ligand functionalized by a pyridyl donor was employed. A corresponding Tp‐iron(II) chlorido complex was prepared and converted through salt metathesis reactions into the respective thiolate analogues, which were fully characterized and structurally authenticated. However, subsequent O2 reactivity studies did not show an improved selectivity. The reason may lie in a more open reaction pocket in combination with an electronic situation which is less ideal than in case of TpMesFe(cysteamine). [ABSTRACT FROM AUTHOR]

Vanillin is a popular and versatile flavor compound, almost entirely produced from petroleum‐derived phenol by a multi‐step chemical synthesis. The process is hazardous to the environment and unsustainable for its fossil oil usage. Therefore, developing environmentally friendly, efficient, and sustainable routes to biobased vanillin is essential. Here, we report on vanillin production from 4‐n‐propylguaiacol (4PG), one of the main components in lignin oil obtained through reductive catalytic fractionation (RCF) of soft wood, by employing recombinant Escherichia coli cells. Conversion is based on the expression of two engineered oxidative enzymes: a 4‐n‐propylguaiacol oxidase and an isoeugenol dioxygenase. A high yield of vanillin, 66% from 4PG in RCF lignin oil was achieved through rounds of optimisation of the whole‐cell conversion process. This high‐performance strategy was readily scaled up to produce vanillin at an unprecedented 18% and 3% yield based on lignin oil and spruce wood respectively. The whole‐cell bioconversion process shows good tolerance even at high loadings of starting material, showcasing the robustness and applicability of the employed biocatalysts. This work paves the way for further development towards the efficient production of high‐titer biobased vanillin using depolymerised lignin as the feedstock. [ABSTRACT FROM AUTHOR]

The vicinal oxygen chelate (VOC) metalloenzyme superfamily catalyzes a highly diverse set of reactions with the mechanism characterized by the bidentate coordination of vicinal oxygen atoms to metal ion centers, but there remains a lack of a platform to steer the reaction trajectories, especially for o‐quinone metabolizing pathways. Herein, we present the directed‐evolution‐enabled bifunctional turnover of ChaP, which is a homotetramer and represents an unprecedented VOC enzyme class. Unlike the ChaP catalysis of extradiol‐like o‐quinone cleavage and concomitant α‐keto acid decarboxylation, a group of ChaP variants (CVs) catalyze intradiol‐like o‐quinone deconstruction and CO2 liberation from the resulting o‐hydroxybenzoic acid scaffolds with high regioselectivity. Enzyme crystal structures, labeling experiments and computational simulations corroborated that the D49L mutation allows the metal ion to change its coordination with the tyrosine phenoxy atoms in different monomers, thereby altering the reaction trajectory with the regiospecificity further improved by the follow‐up replacement of the Y92 residue with any of alanine, glycine, threonine, and serine. The study highlights the unpredicted catalytic versatility and enzymatic plasticity of VOC enzymes with biotechnological significance. [ABSTRACT FROM AUTHOR]

DNA alkylation damage, emanating from the exposure to environmental alkylating agents or produced by certain endogenous metabolic processes, affects cell viability and genomic stability. Fe(II)/2‐oxoglutarate‐dependent dioxygenase enzymes, such as Escherichia coli AlkB, are involved in protecting DNA from alkylation damage. Inspired by the natural product indenone derivatives reported to inhibit this class of enzymes, and a set of 2‐chloro‐3‐amino indenone derivatives was synthesized and screened for their inhibitory properties against AlkB. The synthesis of 2‐chloro‐3‐amino indenone derivatives was achieved from 2,3‐dichloro indenones through addition–elimination method using alkyl/aryl amines under catalyst‐free conditions. Using an in vitro reconstituted DNA repair assay, we have identified a 2‐chloro‐3‐amino indenone compound 3o to be an inhibitor of AlkB. We have determined the binding affinity, mode of interaction, and kinetic parameters of inhibition of 3o and tested its ability to sensitize cells to methyl methanesulfonate that mainly produce DNA alkylation damage. This study established the potential of indenone‐derived compounds as inhibitors of Fe(II)/2‐oxoglutarate‐dependent dioxygenase AlkB. [ABSTRACT FROM AUTHOR]

SUMMARY: Ectopic expression of the apple 2‐oxoglutarate‐dependent dioxygenase (DOX, 2ODD) gene, designated MdDOX‐Co, is thought to cause the columnar shape of apple trees. However, the mechanism underlying the formation of such a unique tree shape remains unclear. To solve this problem, we demonstrated that Arabidopsis thaliana overexpressing MdDOX‐Co contained reduced levels of biologically active gibberellin (GA) compared with wild type. In summary: (i) with biochemical approaches, the gene product MdDOX‐Co was shown to metabolize active GA A4 (GA4) to GA58 (12‐OH‐GA4) in vitro. MdDOX‐Co also metabolized its precursors GA12 and GA9 to GA111 (12‐OH‐GA12) and GA70 (12‐OH‐GA9), respectively; (ii) Of the three 12‐OH‐GAs, GA58 was still active physiologically, but not GA70 or GA111; (iii) Arabidopsis MdDOX‐Co OE transformants converted exogenously applied deuterium‐labeled (d2)‐GA12 to d2‐GA111 but not to d2‐GA58, whereas transformants converted applied d2‐GA9 to d2‐GA58; (iv) GA111 is converted poorly to GA70 by GA 20‐oxidases in vitro when GA12 is efficiently metabolized to GA9; (v) no GA58 was detected endogenously in MdDOX‐Co OE transformants. Overall, we conclude that 12‐hydroxylation of GA12 by MdDOX‐Co prevents the biosynthesis of biologically active GAs in planta, resulting in columnar phenotypes. [ABSTRACT FROM AUTHOR]

Agricultural straw is abundant worldwide, but efficient production of lactic acid from straw is still challenging. In this paper, Trichoderma viride R16 was cultivated using corncob as the substrate in a fed‐batch process, after which the enzymes from T. viride R16 broth were analyzed through protein mass spectrometry and used for lactic acid production. Dioxygenase activity was found in the T. viride R16 enzymes, and 0.2 g/L phenolics (vanillin, 4‐hydroxybenzaldehyde, syringaldehyde) was degraded during enzyme production. Lactic acid production and yield from NH3‐H2O2 pretreated and washed corncob were increased by more than 24% and total phenolics was significantly lower using T. viride R16 enzymes compared with commercial enzymes in batch and fed‐batch fermentation. These characteristics of T. viride R16 support industrial applications with efficient in situ detoxification of phenolic inhibitors without adding an extra step during lactic acid production from pretreated agricultural straw using simultaneous saccharification and fermentation. © 2020 Society of Chemical Industry and John Wiley & Sons, Ltd [ABSTRACT FROM AUTHOR]

4‐Hydroxyphenylpyruvate dioxygenase (HPPD) catalyzes the second reaction in the tyrosine catabolism and is linked to the production of cofactors plastoquinone and tocopherol in plants. This important biological role has put HPPD in the focus of current herbicide design efforts including the development of herbicide‐tolerant mutants. However, the molecular mechanisms of substrate binding and herbicide tolerance have yet to be elucidated. In this work, we performed molecular dynamics simulations and free energy calculations to characterize active site gating by the C‐terminal helix H11 in HPPD. We compared gating equilibria in Arabidopsis thaliana (At) and Zea mays (Zm) wild‐type proteins retrieving the experimentally observed preferred orientations from the simulations. We investigated the influence of substrate and product binding on the open–closed transition and discovered a ligand‐mediated conformational switch in H11 that mediates rapid substrate access followed by active site closing and efficient product release through H11 opening. We further studied H11 gating in At mutant HPPD, and found large differences with correlation to experimentally measured herbicide tolerance. The computational findings were then used to design a new At mutant HPPD protein that showed increased tolerance to six commercially available HPPD inhibitors in biochemical in vitro experiments. Our results underline the importance of protein flexibility and conformational transitions in substrate recognition and enzyme inhibition by herbicides. [ABSTRACT FROM AUTHOR]

Abstract: A combination of genomic and metabolomic approaches recently resulted in the identification of a nonribosomal tetrapeptide tambromycin, which possesses promising antiproliferative activity and several unusual structural features, including a densely substituted indole, a methyloxazoline ring, and an unusual pyrrolidine‐containing amino acid called tambroline. In this work, we identify a concise synthetic route to access tambromycin, which relies on the strategic use of biocatalytic and chemocatalytic C−H functionalization methods to prepare two key precursors to the natural product in an efficient and scalable manner. The success of our study highlights the benefits of applying the principles of biocatalytic retrosynthesis as well as C−H functionalization logic to the synthesis of complex molecular scaffolds. [ABSTRACT FROM AUTHOR]

Salicylate 1,2-dioxygenase (SDO) was the first enzyme discovered, in the family of iron dioxygenases, to catalyze the ring cleavage of a monohydroxylated aromatic compound, salicylate, without a proton donor. Salicylate is not electron-rich like the familiar dihydroxy or aromatic substrates with an electron-donating group that are utilized in the well-known dioxygenases. SDO carries out the intramolecular C−C bond cleavage in salicylate bearing the OH and COOH groups with high regioselectivity in comparison with the extradiol and intradiol dioxygenases. The catalytic cleavage of a nonactivated substrate like salicylate that lacks an electron-donating group, also in the absence of a proton source, raises many puzzling questions about the oxy intermediates in the reaction pathway of dioxygenase enzymes in general. To answer these fundamental queries, we have investigated the full catalytic mechanism of SDO by a combination of quantum mechanics and molecular mechanics (QM/MM) calculations. Herein, our QM/MM study has several unexpected and interesting implications for the mechanistic pathway of SDO in comparison to the experimental observations. Importantly, it unravels the basis for the unexpected 'intra'-cleavage regioselectivity in SDO. Ostensibly a similar alkylperoxo intermediate is formed in SDO much like in the extradiol and intradiol dioxygenases. In stark contrast to the two diol enzymes, the O−O bond breaking leads to an unprotonated gem-hydroxy carboxylate intermediate, a paradigm analogue of the elusive gem diol intermediate. This unprotonated gem-hydroxy carboxylate intermediate exclusively dictates the C−C cleavage regiospecificity in SDO, which is unprecedented in the family of dioxygenases. It forms a seven-membered lactone species, which eventually forms the ring-cleavage final product by incorporation of two oxygen atoms in the salicylate. Thus, our computational study unravels a detailed reaction pathway of the oxidative cleavage of salicylate without a proton source by identifying the hitherto elusive intermediates in the catalytic cycle of SDO with testable predictions. Moreover, we describe the atomistic origin of the new catalytic role of Arg127 in the catalysis and regioselectivity of SDO. It also rationalizes the formation of a side product without invoking a dioxetane intermediate. This study is important from a fundamental perspective and opens up a new window in the mechanism of the family of dioxygenase enzymes. [ABSTRACT FROM AUTHOR]

The enzyme 2,4′-dihydroxyacetophenone dioxygenase (DAD) catalyses the conversion of 2,4′-dihydroxyacetophenone to 4-hydroxybenzoic acid and formic acid. This enzyme is a very unusual dioxygenase in that it cleaves a C-C bond in a substituent of the aromatic ring rather than within the ring itself. Whilst it has been shown that DAD is a tetramer in solution, the recently solved crystal structure of the Alcaligenes sp. 4HAP enzyme was in fact dimeric rather than tetrameric. Since the use of limited chymotrypsinolysis, which apparently results in removal of the first 20 or so N-terminal residues of DAD, was necessary for crystallization of the protein, it was investigated whether this was responsible for the change in its oligomerization state. Gel-filtration and analytical ultracentrifugation studies were conducted, which confirmed that chymotrypsinolysed DAD has an apparent molecular weight of around 40 kDa, corresponding to a dimer. In contrast, the native enzyme has a molecular weight in the 70-80 kDa region, as expected for the tetramer. The structural basis for tetramerization has been investigated by the use of several docking servers, and the results are remarkably consistent with the tetrameric structure of a homologous cupin protein from Ralstonia eutropha (PDB entry ). [ABSTRACT FROM AUTHOR]

Increased glucose metabolism in cancer cells is a phenomenon that has been known for over 90 years, allowing maximal cell growth through faster ATP production and redistribution of carbons towards nucleotide, protein and fatty acid synthesis. Recently, metabolites that can promote tumorigeneis by altering the epigenome have been identified. These 'oncometabolites' include the tricarboxylic acid cycle metabolites succinate and fumarate, whose levels are elevated in rare tumours with succinate dehydrogenase and fumarate hydratase mutations, respectively. 2-Hydroxyglutarate is another oncometabolite; it is produced de novo as a result of the mutation of isocitrate dehydrogenase, and is commonly found in gliomas and acute myeloid leukaemia. Interestingly, the structural similarity of these oncometabolites to their precursor metabolite, α-ketoglutarate, explains the tumorigenic potential of these metabolites, by competitive inhibition of a superfamily of enzymes called the α-ketoglutarate-dependent dioxygenases. These enzymes utilize α-ketoglutarate as a cosubstrate, and are involved in fatty acid metabolism, oxygen sensing, collagen biosynthesis, and modulation of the epigenome. They include enzymes that are involved in regulating gene expression via DNA and histone tail demethylation. In this review, we will focus on the link between metabolism and epigenetics, and how we may target oncometabolite-induced tumorigenesis in the future. [ABSTRACT FROM AUTHOR]

Although melatonin biosynthetic genes from plants have been cloned, the melatonin catabolism mechanisms remain unclear. To clone the genes responsible for melatonin metabolism, we ectopically expressed 35 full-length cDNAs of rice 2-oxoglutarate-dependent dioxygenase (2- ODD) in Escherichia coli and purified the corresponding recombinant proteins. In vitro 2- ODD assays showed four independent 2- ODD proteins that were able to catalyze melatonin into 2-hydroxymelatonin, exhibiting melatonin 2-hydroxylase (M2H). These M2H proteins had peak activities at pH 8.0 and 30°C. The Km ranged from 121 μ m to 371 μ m with the Vmax ranging from 1.7 to 18.5 pkat/mg protein, respectively. The M2H enzyme activities were dependent on cofactors such as α-ketoglutarate, ascorbate, and Fe2+, similar to the 2- ODD enzymes. M2H activity was inhibited by prohexadione-Ca, an inhibitor of 2- ODD, in a dose-dependent manner. M2H activity was high in the roots of rice seedlings, concurrent with high transcription levels of 2- ODD 21, suggesting that 2- ODD 21 was a major gene for M2H activity. Analogous to the high M2H activity in the roots, 2-hydroxymelatonin was found in large quantities in roots treated with melatonin. These results suggest that melatonin was metabolized into 2-hydroxymelatonin by the M2H genes in plants, but the physiological significance of 2-hydroxymelatonin remains to be examined in the future. [ABSTRACT FROM AUTHOR]

ABSTRACT Tryptophan 2,3-dioxygenase (TDO), one of the two key enzymes in the kynurenine pathway, catalyzes the indole ring cleavage at the C2-C3 bond of l-tryptophan. This is a rate-limiting step in the regulation of tryptophan concentration in vivo, and is thus important in drug discovery for cancer and immune diseases. Here, we report the crystal structure of human TDO (hTDO) without the heme cofactor to 2.90 Å resolution. The overall fold and the tertiary assembly of hTDO into a tetramer, as well as the active site architecture, are well conserved and similar to the structures of known orthologues. Kinetic and mutational studies confirmed that eight residues play critical roles in l-tryptophan oxidation. Proteins 2014; 82:3210-3216. © 2014 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

Iron(II)/α-ketoacid-dependent oxygenases (αKAOs) are enzymes that mainly catalyse hydroxylation reaction. By using a genomic approach combining sequence comparison and protein-domain sharing, a set of 131 αKAO enzymes was prepared. The screening of various substrates revealed five new αKAOs. Four αKAOs were found to be active towards L-lysine, L-ornithine and L-arginine with total regio- and stereoselectivities and yielding the corresponding 3- or 4-hydroxyamino acids. The enzymatic cascade reaction with two stereoselective regiodivergent αKAOs enabled the synthesis of 3,4-dihydroxy- L-lysine. [ABSTRACT FROM AUTHOR]

The enzyme 2,4′-dihydroxyacetophenone dioxygenase (DAD) catalyses the conversion of 2,4′-dihydroxyacetophenone to 4-hydroxybenzoic acid and formic acid with the incorporation of molecular oxygen. Whilst the vast majority of dioxygenases cleave within the aromatic ring of the substrate, DAD is very unusual in that it is involved in C-C bond cleavage in a substituent of the aromatic ring. There is evidence that the enzyme is a homotetramer of 20.3 kDa subunits, each containing nonhaem iron, and its sequence suggests that it belongs to the cupin family of dioxygenases. In this paper, the first X-ray structure of a DAD enzyme from the Gram-negative bacterium Alcaligenes sp. 4HAP is reported, at a resolution of 2.2 Å. The structure establishes that the enzyme adopts a cupin fold, forming dimers with a pronounced hydrophobic interface between the monomers. The catalytic iron is coordinated by three histidine residues (76, 78 and 114) within a buried active-site cavity. The iron also appears to be tightly coordinated by an additional ligand which was putatively assigned as a carbonate dianion since this fits the electron density optimally, although it might also be the product formate. The modelled carbonate is located in a position which is highly likely to be occupied by the α-hydroxyketone group of the bound substrate during catalysis. Modelling of a substrate molecule in this position indicates that it will interact with many conserved amino acids in the predominantly hydrophobic active-site pocket where it undergoes peroxide radical-mediated heterolysis. [ABSTRACT FROM AUTHOR]

The 2-oxoglutarate-dependent dioxygenase (2 OGD) superfamily is the second largest enzyme family in the plant genome, and its members are involved in various oxygenation/hydroxylation reactions. Despite their biochemical significance in metabolism, a systematic analysis of plant 2 OGDs remains to be accomplished. We present a phylogenetic classification of 479 2 OGDs in six plant models, ranging from green algae to angiosperms. These were classified into three classes - DOXA, DOXB and DOXC - based on amino acid sequence similarity. The DOXA class includes plant homologs of Escherichia coli Alk B, which is a prototype of 2 OGD involved in the oxidative demethylation of alkylated nucleic acids and histones. The DOXB class is conserved across all plant taxa and is involved in proline 4-hydroxylation in cell wall protein synthesis. The DOXC class is involved in specialized metabolism of various phytochemicals, including phytohormones and flavonoids. The vast majority of 2 OGDs from land plants were classified into the DOXC class, but only seven from Chlamydomonas, suggesting that this class has diversified during land plant evolution. Phylogenetic analysis assigned DOXC-class 2 OGDs to 57 phylogenetic clades. 2 OGD genes involved in gibberellin biosynthesis were conserved among vascular plants, and those involved in flavonoid and ethylene biosynthesis were shared among seed plants. Several angiosperm-specific clades were found to be involved in various lineage-specific specialized metabolisms, but 31 of the 57 DOXC-class clades were only found in a single species. Therefore, the evolution and diversification of DOXC-class 2 OGDs is partly responsible for the diversity and complexity of specialized metabolites in land plants. [ABSTRACT FROM AUTHOR]

The salicylate 1,2-dioxygenase ( SDO) from the bacterium Pseudaminobacter salicylatoxidans BN12 is a versatile gentisate 1,2-dioxygenase ( GDO) that converts both gentisate (2,5-dihydroxybenzoate) and various monohydroxylated substrates. Several variants of this enzyme were rationally designed based on the previously determined enzyme structure and sequence differences between the SDO and the 'conventional' GDO from Corynebacterium glutamicum. This was undertaken in order to define the structural elements that give the SDO its unique ability to dioxygenolytically cleave (substituted) salicylates. SDO variants M103 L, G106 A, G111 A, R113 G, S147 R and F159 Y were constructed and it was found that G106 A oxidized only gentisate; 1-hydroxy-2-naphthoate and salicylate were not converted. This indicated that this enzyme variant behaves like previously known 'conventional' GDOs. Crystals of the G106 A SDO variant and its complexes with salicylate and gentisate were obtained under anaerobic conditions, and the structures were solved and analyzed. The amino acid residue Gly106 is located inside the SDO active site cavity but does not directly interact with the substrates. Crystal structures of G106 A SDO complexes with gentisate and salicylate showed a different binding mode for salicylate when compared with the wild-type enzyme. Thus, salicylate coordinated in the G106 A variant with the catalytically active Fe(II) ion in an unusual and unproductive manner because of the inability of salicylate to displace a hydrogen bond that was formed between Trp104 and Asp174 in the G106 A variant. It is proposed that this type of unproductive substrate binding might generally limit the substrate spectrum of 'conventional' GDOs. Database Structural data are available in the Protein Data Bank databases under the accession numbers 3NST, 3NWA, 3NVC [ABSTRACT FROM AUTHOR]

Vitamin C is an antioxidant that maintains the activity of iron and α-ketoglutarate-dependent dioxygenases. Despite these enzymes being implicated in a wide range of biological pathways, vitamin C is rarely included in common cell culture media. Recent studies show that reprogramming of pluripotent stem cells is enhanced when vitamin C is present, thereby illustrating previous limitations in reprogramming cultures. Here, we summarize understanding of dioxygenase function in reprogramming and epigenetic regulation. The available data suggest a link between dioxygenase function and stem cell differentiation, which is exposed to environmental influence and is relevant for human disease. [ABSTRACT FROM AUTHOR]

Indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenase catalyze the O2-dependent oxidation of l-tryptophan to N-formylkynurenine. Both are heme-containing enzymes, with a proximal histidine ligand, as found in the globins and peroxidases. From the structural information available so far, the distal heme pockets of these enzymes can contain a histidine residue (in tryptophan 2,3-dioxygenases), an arginine residue and numerous hydrophobic residues that line the pocket. We have examined the functional role of each of these residues in both human indoleamine 2,3-dioxygenase and human tryptophan 2,3-dioxygenase. We found that the distal histidine does not play an essential catalytic role, although substrate binding can be affected by removing the distal arginine and reducing the hydrophobic nature of the binding pocket. We collate the information obtained in the present study with that reported in the available literature to draw comparisons across the family and to provide a more coherent picture of how the heme pocket is optimized for tryptophan binding. [ABSTRACT FROM AUTHOR]

A white-rot fungus of Polyporus sp. S133 was isolated from an oil-polluted soil. The metabolism of pyrene by this fungus was investigated in liquid medium with 5 mg of the compound. Depletion of pyrene was evident during the 30-day growth period and was 21% and 90%, respectively, in cometabolism and metabolism of pyrene alone. Pyrene was absorbed to fungal cells or biodegraded to form simpler structural compounds. Seventy-one percent of eliminated pyrene was transformed by Polyporus sp. S133 into other compounds, whereas only 18% was absorbed in the fungal cell. The effects of pH and temperature on biomass production of Polyporus sp. S133 for pyrene were examined; the properties of laccase and 1,2-dioxygenase produced by Polyporus sp. S133 during pyrene degradation were investigated. The optimal values of pH were 3, 5, and 4 for laccase, 1,2-dioxygenase, and biomass production, respectively, whereas the optimal values of temperature were 25 °C for laccase and 50 °C for 1,2-dioxygenase and biomass production. Under optimal conditions, pyrene was mainly metabolized to 1-hydroxypyrene and gentisic acid. The structure of 1-hydroxypyrene and gentisic acid was determined by gas chromatography-mass spectrometry after identification using thin-layer chromatography. [ABSTRACT FROM AUTHOR]

Background: Although adolescent major depressive disorder (MDD) is acknowledged to be a heterogeneous disorder, no studies have reported on biological correlates of its clinical subgroups. This study addresses this issue by examining whether adolescent MDD with and without melancholic features (M-MDD and NonM-MDD) have distinct biological features in the kynurenine pathway (KP). The KP is initiated by pro-inflammatory cytokines via induction of the enzyme indoleamine 2,3-dioxygenase (IDO), which degrades tryptophan (TRP) into kynurenine (KYN). KYN is further metabolized into neurotoxins linked to neuronal dysfunction in MDD. Hypotheses were that, compared to healthy controls and to NonM-MDD adolescents, adolescents with M-MDD would exhibit: (i) increased activation of the KP [i.e., increased KYN and KYN/TRP (reflecting IDO activity)]; (ii) greater neurotoxic loads [i.e., increased 3-hydroxyanthranilic acid (3-HAA, neurotoxin) and 3-HAA/KYN (reflecting production of neurotoxins)]; and (iii) decreased TRP. We also examined relationships between severity of MDD and KP metabolites. Methods: Subjects were 20 adolescents with M-MDD, 30 adolescents with NonM-MDD, and 22 healthy adolescents. MDD episode duration had to be ≥ 6 weeks and Children’s Depression Rating Scale-Revised (CDRS-R) scores were ≥ 36. Blood samples were collected at AM after an overnight fast and analyzed using high-performance liquid chromatography. Group contrasts relied on analysis of covariance based on ranks, adjusted for age, gender, and CDRS-R scores. Analyses were repeated excluding medicated patients. Fisher’s protected least significant difference was used for multiple comparisons. Results: As hypothesized, KYN/TRP ratios were elevated and TRP concentrations were reduced in adolescents with M-MDD compared to NonM-MDD adolescents ( p = .001 and .006, respectively) and to healthy controls ( p = .008 and .022, respectively). These findings remained significant when medicated patients were excluded from the analyses. Significant correlations were obtained exclusively in the M-MDD group between KYN and 3-HAA/KYN and CDRS-R. Conclusions: Findings support the notion that adolescent M-MDD may represent a biologically distinct clinical syndrome. [ABSTRACT FROM AUTHOR]

Citation Nishizawa H, Kato T, Ota S, Nishiyama S, Pryor-Koishi K, Suzuki M, Tsutsumi M, Inagaki H, Kurahashi H, Udagawa Y. Genetic variation in the indoleamine 2,3-Dioxygenase gene in pre-eclampsia. Am J Reprod Immunol 2010; 64: 68–76 Problem To investigate the contribution of genomic variations in the indoleamine 2,3-dioxygenase (IDO) gene to the onset of pre-eclampsia. Method of study We examined sequence variations in the IDO1 gene using placental genomic DNA from 35 pre-eclamptic patients and 32 normotensive pregnant women. Results A case–control study revealed that none of the common variants influences the risk of disease. Sequencing of each IDO1 exon in diseased subjects revealed rare variants. This variation, c.-147_150delGAAA, was located within the 5′-untranslated region of the IDO1 gene, and its homozygote was identified only in pre-eclamptic subjects. However, despite the low levels of IDO expression and enzyme activity in the c.-147_150delGAAA homozygote, reporter assays indicated that this variation does not affect gene expression. Conclusion Our findings indicate that genetic alteration of fetal IDO gene does not appear to be a primary cause of pre-eclampsia. [ABSTRACT FROM AUTHOR]

The article presents research on the determination of naphthalene dioxygenase activity (NDO) with the use of indole biotransformation and indigo production by Pseudomonas species J26 strain. It says that J26 strain was chosen as a dark blue colony by indole test and indigo concentration extracted from J26 whole cells was calculated. The results suggest that indigo production was achieved at 25 °C using mM indole while indole concentrations higher than four mM were proved toxic for cells.

Renilla luciferase (RLUC) is a versatile tool for gene expression assays and in vivo biosensor applications, but its catalytic mechanism remains to be elucidated. RLUC is evolutionarily related to the α/β hydrolase family. Its closest known homologs are bacterial dehalogenases, raising the question of how a protein with a hydrolase fold can function as a decarboxylating oxygenase. Molecular docking simulations with the coelenterazine substrate against an RLUC homology model as well as a recently determined RLUC crystal structure were used to build hypotheses to identify functionally important residues, which were subsequently tested by site-directed mutagenesis, heterologous expression, and bioluminescence emission spectroscopy. The data highlighted two triads of residues that are critical for catalysis. The putative catalytic triad residues D120, E144, and H285 bear only limited resemblance to those found in the active site of aequorin, a coelenterazine-utilizing photoprotein, suggesting that the reaction scheme employed by RLUC differs substantially from the one established for aequorin. The role of H285 in catalysis was further supported by inhibition using diethylpyrocarbonate. Multiple substitutions of N53, W121, and P220-three other residues implicated in product binding in the homologous dehalogenase Sphingomonas LinB-also supported their involvement in catalysis. Together with luminescence spectra, our data lead us to propose that the conserved catalytic triad of RLUC is directly involved in the decarboxylation reaction of coelenterazine to produce bioluminescence, while the other active-site residues are used for binding of the substrate. [ABSTRACT FROM AUTHOR]

Bioremediation strategies use microorganisms to remove hazardous substances, such as aromatic molecules, from polluted sites. The applicability of these techniques would greatly benefit from the expansion of the catabolic ability of these bacteria in transforming a variety of aromatic compounds. Catechol-2,3-dioxygenase (C2,3O) from Pseudomonas stutzeri OX1 is a key enzyme in the catabolic pathway for aromatic molecules. Its specificity and regioselectivity control the range of molecules degraded through the catabolic pathway of the microorganism that is able to use aromatic hydrocarbons as growth substrates. We have used in silico substrate docking procedures to investigate the molecular determinants that direct the enzyme substrate specificity. In particular, we looked for a possible molecular explanation of the inability of catechol-2,3-dioxygenase to cleave 3,5-dimethylcatechol and 3,6-dimethylcatechol and of the efficient cleavage of 3,4-dimethylcatechol. The docking study suggested that reduction in the volume of the side chain of residue 249 could allow the binding of 3,5-dimethylcatechol and 3,6-dimethylcatechol. This information was used to prepare and characterize mutants at position 249. The kinetic and regiospecificity parameters of the mutants confirm the docking predictions, and indicate that this position controls the substrate specificity of catechol-2,3-dioxygenase. Moreover, our results suggest that Thr249 also plays a previously unsuspected role in the catalytic mechanism of substrate cleavage. The hypothesis is advanced that a water molecule bound between one of the hydroxyl groups of the substrate and the side chain of Thr249 favors the deprotonation/protonation of this hydroxyl group, thus assisting the final steps of the cleavage reaction. [ABSTRACT FROM AUTHOR]

Abstract: Hydroxymandelate synthase (HmaS) and hydroxyphenylpyruvate dioxygenase (HppD) are non-heme iron-dependent dioxygenases, which share a common substrate and first catalytic step. The catalytic pathways then diverge to yield hydroxymandelate for secondary metabolism, or homogentisate in tyrosine catabolism. To probe the differences between these related active sites that channel a common intermediate down alternative pathways, we attempted to interconvert their activities by directed evolution. HmaS activity was readily introduced to HppD by just two amino acid changes. A parallel attempt to engineer HppD activity in HmaS was unsuccessful, suggesting that homogentisate synthesis places greater chemical and steric demands on the active site. [Copyright &y& Elsevier]

( R)- and ( S)-dichlorprop/α-ketoglutarate dioxygenases (RdpA and SdpA) catalyze the oxidative cleavage of 2-(2,4-dichlorophenoxy)propanoic acid (dichlorprop) and 2-(4-chloro-2-methyl-phenoxy)propanoic acid (mecoprop) to form pyruvate plus the corresponding phenol concurrent with the conversion of α-ketoglutarate (αKG) to succinate plus CO2. RdpA and SdpA are strictly enantiospecific, converting only the ( R) or the ( S) enantiomer, respectively. Homology models were generated for both enzymes on the basis of the structure of the related enzyme TauD (PDB code 1OS7). Docking was used to predict the orientation of the appropriate mecoprop enantiomer in each protein, and the predictions were tested by characterizing the activities of site-directed variants of the enzymes. Mutant proteins that changed at residues predicted to interact with (R)- or (S)-mecoprop exhibited significantly reduced activity, often accompanied by increased Km values, consistent with roles for these residues in substrate binding. Four of the designed SdpA variants were (slightly) active with ( R)-mecoprop. The results of the kinetic investigations are consistent with the identification of key interactions in the structural models and demonstrate that enantiospecificity is coordinated by the interactions of a number of residues in RdpA and SdpA. Most significantly, residues Phe171 in RdpA and Glu69 in SdpA apparently act by hindering the binding of the wrong enantiomer more than the correct one, as judged by the observed decreases in Km when these side chains are replaced by Ala. [ABSTRACT FROM AUTHOR]

Quercetin 2,3-dioxygenase (2,3QD) is a copper-containing dioxygenase that catalyses the oxidation of the flavonol quercetin to 2-protocatechuoylphloroglucinol carboxylic acid with concomitant production of carbon monoxide. In contrast to iron dioxygenases, very little is known about copper dioxygenases. We have characterized 2,3QD from the fungus Aspergillus japonicus by electron paramagnetic resonance spectroscopy (EPR). At pH 6.0, 2,3QD shows a mixture of two EPR species. The major form has parameters typical of type 2 Cu sites (g // = 2.330, A // = 13.7 mT), the minor one has a more distorted geometry (g // = 2.290, A // = 12.5 mT). Anaerobic addition of the substrate quercetin results in a different, single species EPR spectrum with g // = 2.336, A // = 11.4 mT, parameters, which are in-between those of the type 2 and type 1 Cu sites in the Peisach–Blumberg (g // vs. A // ) plot. After turnover, a new EPR signal is observed, which is ascribed to the carboxylic acid ester product complex. This spectrum is similar to that of the native enzyme at pH 10.0 and has g -tensor parameters suggesting a trigonal bipyramidal site. Of a variety of flavonoids studied, only flavonols are able to bind to the copper centre of 2,3QD. Nine flavonols with different hydroxylation patterns at the A- and B-ring have been analysed. They cluster in two different regions of the Peisach–Blumberg plot and show that the presence of a 5-OH group has a large effect on the A // parameter. Several differences are noted between A. japonicus 2,3QD and the enzyme from A. niger German Collection of Microorganisms 821. [ABSTRACT FROM AUTHOR]

Manganese lipoxygenase was isolated to homogeneity from the take-all fungus, Gaeumannomyces graminis . The C-terminal amino acids and several internal peptides were sequenced, and the information was used to obtain a cDNA probe by RT/PCR. Screening of a genomic library of G. graminis yielded a full-length clone of the Mn-Lipoxygenase gene. cDNA analysis showed that the gene spanned 2.6 kb and contained one intron (133 bp). Northern blot analyses indicated two transcripts (2.7 and 3.1 kb). The deduced amino-acid sequence of the Mn-Lipoxygenase precursor (618 amino acids, 67.7 kDa) could be aligned with mammalian and plant lipoxygenases with 23–28% identity over 350–400 amino-acid residues of the catalytic domains. Lipoxygenases have one water molecule and five amino acids as Fe ligands. These are two histidine residues in the highly conserved 30 amino-acid sequence WLLAK-X15 -H-X4 -H-X3 -E of α helix 9, one histidine and usually an asparaine residue in the sequence H-X3 -N-X-G of α helix 18, and the carboxyl oxygen of the C-terminal isoleucine (or valine) residue. The homologous sequence of α helix 9 of Mn-Lipoxygenase [WLLAK-X14 -H(294)-X3 -H(297)-X3 -E] contained two single-amino-acid gaps, but otherwise His294 and His297 aligned with the two His residues, which coordinate iron. Mn-Lipoxygenase [H(478)-X3 -N(482)-X-G] could be aligned with the two metal ligands of α helix 18, and the C-terminal residue was Val618. We conclude that Mn-Lipoxygenase belongs to the lipoxygenase gene family and that its unique biochemical properties might be related to structural differences in the metal centre and α helix 9 of lipoxygenases rather than to the metal ligands. [ABSTRACT FROM AUTHOR]

Clavaminate synthase (CAS), a 2-oxoglutarate (2OG) dependent dioxygenase, catalyses three steps in the biosynthesis of clavulanic acid. Crystals of CAS complexed with Fe(II), 2OG and deoxyguanidinoproclavaminate were exposed to nitric oxide (NO) acting as a dioxygen analogue. Prior to exposure with NO, the active site Fe(II) is octahedrally coordinated by a water molecule, the 2-oxo and 1-carboxylate groups of 2OG, and the side-chains of an aspartyl and two histidinyl residues. NO binds to the position previously occupied by the 2OG 1-carboxylate concomitant with rearrangement of the latter to the position previously occupied by the displaced water. [Copyright &y& Elsevier]

Patients with generalized peroxisomal disorders, rhizomelic chondrodysplasia punctata, and Refsum disease are all unable to α-oxidize 3,7,11,15-tetramethylhexadecanoic (phytanic) acid. The exact cause of the oxidation defect in these patients is not well characterized, in part because there is only limited knowledge of the biochemical pathway. In 1969, the α-oxidation of phytanic acid was reported [Tsai, S.-C., Avigan, J. & Steinberg, D. (1969) Studies on the α-oxidation of phytanic acid by rat liver mitochondria, J. Biol. Chem. 244, 2682-2692] to involve the formation of an α-hydroxyphytanic acid intermediate prior to removal of the alpha carbon. Subsequently, most researchers have had difficulty detecting this intermediate. In the present study, cofactors known to form hydroxy intermediates by both monooxygenase and dioxygenase reaction mechanisms were incubated with purified rat liver peroxisomes and either [2,3-3H]phytanic acid or [1-14C]phytanic acid. Reaction products were separated by reverse-phase HPLC. A single reaction product, identified as α-hydroxyphytanoyl-CoA rather than the free fatty acid, was detected when 2-oxoglutarate/Fe+2/ascorbate, cofactors associated with a dioxygenase reaction mechanism, were present. Concomitant with α-hydroxyphytanoyl-CoA production, there was an increased accumulation of formate and CO2. This increase in α-oxidation products is evidence that α-hydroxyphytanoyl-CoA is a true pathway intermediate and that the entire pathway functions in peroxisomes. In contrast, α-hydroxyphytanoyl-CoA was not formed in any quantity in mitochondria. These studies suggest that the α-hydroxylation step of phytanic acid oxidation, which has been shown to be defective in Refsum disease, is located in peroxisomes. [ABSTRACT FROM AUTHOR]

The first step in the oxidation of the diaryl ethers dibenzo-p-dioxin and dibenzofuran by the bacterium Sphingomonas sp. RW1 is carried out by an atypical multi-component ring hydroxylating dioxygenase. This heteromeric enzyme requires the participation of a flavoprotein, reductase A2, and an iron-sulfur protein, Fdx1, to mediate the transfer of electrons from NADH to the dioxygenase for oxygen activation [Bünz, P. V. & Cook, A. M. (1993) J. Bacteriol. 175, 6467-6475]. From the type of ferredoxin (Fd) and flavoprotein, this complex is presumed to belong to the class-IIA dioxygenase system which has not been genetically analysed so far. The gene encoding the flavoprotein was identified by screening a genomic library constructed in pLAFR3 with a probe generated by PCR amplification. The nucleotide sequence of a 2.0-kb DNA fragment encompassing the reductase gene, redA2, was determined. The specified protein shares 37-40 % identity with class-I cytochrome P450 reductases and 27-35 % identity with reductases acting with class-IIB dioxygenases. An FAD-binding amino acid consensus sequence, as well as an NADH-binding site were detected by analogy beginning at residues 10 and 153, respectively. The redA2 gene is not linked to the dioxin dioxygenase cistrons. The rare start codon, GTG, of the reductase was changed to ATG and the modified gene hyperexpressed in Escherichia coli using the strong T7 polymerase promoter. The recombinant reductase was purified to homogeneity with an approximate yield of 3.3 mg/g wet mass cells. Flavin analysis confirmed the presence of 1 FAD/mol protein. The Km values for NADH and Fdx1 are 22 ( ± 3) μM and 3.7 ( ± 0.4) μM, respectively. [ABSTRACT FROM AUTHOR]

Recent developments in our knowledge of the biochemistry of 1-aminocyclopropane-1-carboxylate (ACC) oxidase, the enzyme responsible for the final stage in the biosynthesis of ethylene, are reviewed. Particular reference is made to the role of carbon dioxide as an essential cofactor, the activity of ACC oxidase in the plant cell, the enzyme catalytic centre, and the role of ACC oxidase in the evolutionary development of ethylene biosynthesis in plants. Evidence is marshalled to support a proposal that the membrane requirement for ACC oxidase that is observed in vivo is attributable to a need for a charged plasma membrane to maintain ascorbate in the reduced state for an ACC oxidase located in the apoplast. It is argued on biochemical grounds that the acquisition of the ACC oxidase was the crucial evolutionary step in the development by seed plants of an ethylene biosynthesis pathway that could easily be regulated, and that signalled the plant's response to stress and pathogen attack. [ABSTRACT FROM AUTHOR]

Indoleamine 2,3-dioxygenase (IDO) is a haem-containing dioxygenase that catalyzes the oxidative cleavage of the pyrrole ring of indoleamines by the insertion of molecular oxygen. This reaction is the first and the rate-limiting step in the kynurenine pathway, the major Trp catabolic pathway in mammals. Recombinant human IDO was crystallized by the vapour-diffusion technique. The addition of 4-phenylimidazole as a haem ligand was essential for crystallization. The crystals belong to space group P212121, with unit-cell parameters a = 86.1, b = 98.0, c = 131.0 Å. Diffraction data were collected to 2.3 Å resolution. [ABSTRACT FROM AUTHOR]

Summary The anthocyanin and proanthocyanidin (PA) biosynthetic pathways share common intermediates until leucocyanidin, which may be used by leucoanthocyanidin dioxygenase (LDOX) to produce anthocyanin, or the enzyme leucoanthocyanidin reductase (LAR) to produce catechin, a precursor of PA. The Arabidopsis mutant tannin deficient seed 4 (tds4-1 ) has a reduced PA level and altered pattern PA accumulation. We identified the TDS4 gene as LDOX by complementation of the tds4-1 mutation either with a cosmid encoding LDOX or a 35S:LDOX construct. Independent Arabidopsis lines with a T-DNA insertion in the LDOX gene had a similar phenotype, and one was allelic to tds4-1. The seed phenotype of ban tds4 double mutants showed that LDOX precedes BANYULS (BAN) in the PA pathway, confirming recent biochemical characterisation of BAN as an anthocyanidin reductase. Double mutant analysis was also used to order the other TDS genes. Analysis of the PA intermediates in tds4-1 revealed three dimethylaminocinnamaldehyde (DMACA) reacting compounds that accumulated in extracts from developing seeds. Analysis of Arabidopsis PA and its precursors indicates that Arabidopsis , unlike many other plants, exclusively uses the epicatechin and not the catechin pathway to PA. Transmission electron microscopy (TEM) showed that the pattern observed when seeds of tds4 were stained with DMACA was a result of the accumulation of PA intermediates in the cytoplasm of endothelial cells. Fluorescent marker dyes were used to show that tds4 endothelial cells had multiple small vacuoles, instead of a large central vacuole as observed in the wild types (WT). These results show that in addition to its established role in the formation of anthocyanin, LDOX is also part of the PA biosynthesis pathway. [ABSTRACT FROM AUTHOR]