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Fig. 39 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 39. Reaction catalyzed by indole cyanohydrin oxidase (AtBBE3/ FOX1). The product of the reaction is further hydroxylated to 4-hydroxyindole- 3-carbonyl nitrile, a cyanogenic metabolite involved in pathogen defense. According to the analysis by (Zafred et al., 2015), the enzyme should be able to react with dioxygen directly and thus the reoxidation of the reduced FAD would produce hydrogen peroxide (see also discussion below).
Fig. 30 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 30. Reaction of lycopene cyclases in A. thaliana. Lycopene ε-cyclase generates a single ε-ring, whereas the β-cyclase introduces two β-rings at both ends of the all-trans lycopene. The β-cyclase may also add a β-ring at the 1′-end of δ-carotene (not shown). All of these reactions employ reduced FAD as the catalytically active cofactor, which is probably generated at the expense of NAD (P)H, similar to carotene cis-trans isomerase (see Fig. 29).
Fig. 17 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 17. Reduction of 5,10-methylene tetrahydrofolate to 5-methyl-tetrahydrofolate by methylenetetrahydrofolate reductase. In the plant enzyme, NADH is used to reduce the FAD cofactor. The reaction proceeds via hydride transfer, probably to the carbon (highlighted in red) and subsequent protonation of the nitrogen (reductive cleavage). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 34 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 34. Postulated reaction catalyzed by indole-3-butyryl-CoA dehydrogenase. This conversion of indole-3-butyryl-CoA to indole-3-butenoyl-CoA constitutes the first step toward the release of indole-3-acetic acid from indole butyric acid through side chain shortening. Due to its peroxisomal localization, it is likely that reoxidation of the reduced FAD is achieved by direct reaction with dioxygen to yield hydrogen peroxide (Zolman et al, 2007, 2008).
Fig. 16 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 16. Reaction catalyzed by chorismate synthase. The 1,4-anti-elimination of the 6(proR)-hydrogen and phosphate converts 5-enolpyruvylshikimate 3-phosphate to chorismate, the final metabolite of the common shikimate pathway. In the case of bacteria and plants, the required reduced FMN is probably produced by unidentified NAD(P)-dependent FMN reductases and then taken up by chorismate synthase.
Fig. 15 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 15. Reactions catalyzed by glutamate synthase. In the first reaction step, catalyzed by the glutaminase, ammonia is released from the amide group of L-glutamine yielding L-glutamate (top reaction). The ammonia (shown in red) then attacks the keto group of α-ketoglutarate to form an imine intermediate (bottom reaction), which is then reduced by FMN, as shown on the right side. Note that two molecules of L-glutamate are generated, one as a result of the glutaminase reaction and another one as a result of the glutamate synthase reaction. In plants, the FMN cofactor is either reduced by NADH or reduced ferredoxin (see also text for references). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 13 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 13. Reaction of farnesylcysteine lyase. In the first step the proS- hydrogen (shown in red) is transferred as a hydride to the FAD cofactor, which is reoxidized by dioxygen to yield hydrogen peroxide as a by-product. The thiocarbenium is nucleophilically attacked by water generating a hemithioacetal intermediate, which subsequently decomposes to the products farnesal and L-cysteine. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 12 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 12. Back-conversion reactions catalyzed by FAD-dependent polyamine oxidases. The oxidative cleavage of spermine to putrescine occurs in two consecutive steps via spermidine. In the initial oxidation of the -N-C-bond to the imine, the FAD cofactor is reduced and reoxidation occurs by direct reaction with dioxygen producing hydrogen peroxide. The imine is subsequently hydrolyzed to the amine and the aldehyde products.
Fig. 10 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 10. α,β-dehydrogenation of acyl-CoA derivatives as the first step of fatty acid degradation (β-oxidation). Note that the reduced FAD is directly reoxidized by dioxygen to yield hydrogen peroxide. The peroxisomal acyl-CoA oxidases catalyze the first step in β-oxidation by mediating the dehydrogenation of acyl-CoAs of different chain lengths to the corresponding enoyl-CoAs.
Fig. 8 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 8. Reaction catalyzed by D-2-hydroxyglutarate dehydrogenase. The oxidation of D-2-hydroxyglutarate yields α-ketoglutarate and reduced FAD. As a client of ETF, the electrons of the reduced FAD are eventually transferred to the mitochondrial mETC via ETF-QO.
Fig. 14 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 14. Reduction of nitrate to nitrite at the expense of NAD(P)H. After reduction of the Moco, nitrate displaces the hydroxyl group bound to the molybdenum atom and is directly reduced to nitrite (for mechanistic details see Hille, 2013). Nitrite can also be reduced to nitric oxide involving a one-electron reduction. However, the mechanism of this reaction is currently unknown.
Fig. 25 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 25. Reaction catalyzed by 4′-phosphopantothenoylcysteine decarboxylase. The enzyme uses non-covalently bound FMN, which is transiently reduced in the first half-reaction (substrate oxidation) yielding a thioaldehyde intermediate (top). At this stage, decarboxylation occurs (right) and the generated enethiolate is then subject to reduction to the final product 4′-phosphopantetheine (bottom). Thus the flavin serves as a transient electron sink during the decarboxylation reaction.
Fig. 9 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 9. The first step of proline degradation. Proline dehydrogenase 1 and 2 catalyze the two-electron oxidation of the C–N bond in the pyrollidine-ring as shown. The enzymes are peripherally associated with the inner mitochondrial membrane enabling direct transfer of the electrons to CoQ.
Fig. 11 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 11. Reactions catalyzed by xanthine dehydrogenase. The enzyme oxidizes hypoxanthine to xanthine and further to uric acid. The initial oxidation occurs at the Moco and electrons are transferred to two iron-sulfur-complexes operating in-line to reduce the FAD cofactor, which in turn reduces NAD+ to NADH. Alternatively, the enzyme may reduce dioxygen either to hydrogen peroxide or superoxide when present in its oxidase conformation. The oxygen atom incorporated in the products is derived from water (shown in red, for details of the reaction mechanism, see Nishino et al., 2013). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 4 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 4. Reaction catalyzed by the lipoamide dehydrogenase subunit (E3). This subunit is present in the pyruvate, α-ketoglutarate and branched-chain α-keto acid dehydrogenase complex where the dithiol of the lipoamide moiety first reduces the internal disulfide bridge (top) and subsequently the reduced internal dithiol reduces the FAD (right), which in turn reduces NAD+ (left) leading to the resting state of the enzyme.
Fig. 22 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 22. Reactions catalyzed by pyridoxamine/pyridine 5′-phosphate oxidase. The enzyme accepts pyridoxamine and pyridoxine 5′-phosphate as substrate. The oxidation of pyridoxamine 5-phosphate leads to the imine, which is hydrolyzed to the aldehyde and ammonia (upper curved arrow). In both reactions the reduced cofactor FMN is re-oxidized by dioxygen resulting in the generation of hydrogen peroxide (upper and lower curved arrow).
Fig. 3 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 3. Oxidation of succinate to fumarate catalyzed by succinate dehydrogenase (complex II). The reduced FAD donates the electrons to a pair of iron-sulfur clusters from where they are finally delivered to a cytochrome leading to the reduction of ubiquinone (CoQ) in the inner mitochondrial membrane.
Fig. 6 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 6. Reaction catalyzed by D-lactate dehydrogenase. The reduced FAD cofactor is reoxidized by cytochrome c in the intermembrane space of mitochondria and the electrons are transferred to cytochrome c oxidase (complex IV) of the mETC.
Fig. 2 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 2. Biosynthesis of riboflavin in A. thaliana. The biosynthesis of riboflavin starts with GTP (top left), which is converted in four enzymatic steps to 5-amino-6- ribityl-aminouracil (center). The second component needed is D-ribulose-5-phosphate (center, left), which is converted to 3,4-dihydroxy-2-butanone-4-phosphate (shown in blue). The second ring is generated by condensation of the two intermediates, a reaction catalyzed by lumazine synthase (RibE) yielding 6,7-dimethyl- 8-ribityl lumazine. The last step of the biosynthesis is a dismutation reaction involving two lumazine molecules resulting in the generation of riboflavin and 5- amino-6-ribityl-aminouracil, which reenters riboflavin biosynthesis. For clarity, the two lumazine molecules are highlighted in red/blue and red/green, respectively. The double headed green arrow (top, right) indicates the swap of reactions compared to riboflavin biosynthesis in E. coli and S. cerevisiae. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)
Fig. 42 in The scope of flavin-dependent reactions and processes in the model plant Arabidopsis thaliana
Fig. 42. Reaction catalyzed by monolignol oxidoreductases. The enzymes were shown to accept monolignols with different substitution patterns in the aromatic ring (R1 and R2 = H, p-coumaryl alcohol; R1 = H and R2 = methoxy, coniferyl alcohol; R1 and R2 = methoxy, sinapyl alcohol) (Daniel et al., 2015). In contrast to the other members of the BBE-like enzyme family, most of the enzymes catalyzing this reaction are dehydrogenases, with the exception of AtBBE24 (Zafred et al., 2015). The electron acceptor for the dehydogenases is yet unknown.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.