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1.
J Biol Chem ; 299(10): 105222, 2023 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-37673337

RESUMO

Many microorganisms use both biological and nonbiological molecules as sources of carbon and energy. This resourcefulness means that some microorganisms have mechanisms to assimilate pollutants found in the environment. One such organism is Comamonas testosteroni, which metabolizes 4-methylbenzenesulfonate and 4-methylbenzoate using the TsaMBCD pathway. TsaM is a Rieske oxygenase, which in concert with the reductase TsaB consumes a molar equivalent of NADH. Following this step, the annotated short-chain dehydrogenase/reductase and aldehyde dehydrogenase enzymes TsaC and TsaD each regenerate a molar equivalent of NADH. This co-occurrence ameliorates the need for stoichiometric addition of reducing equivalents and thus represents an attractive strategy for integration of Rieske oxygenase chemistry into biocatalytic applications. Therefore, in this work, to overcome the lack of information regarding NADH recycling enzymes that function in partnership with Rieske non-heme iron oxygenases (Rieske oxygenases), we solved the X-ray crystal structure of TsaC to a resolution of 2.18 Å. Using this structure, a series of substrate analog and protein variant combination reactions, and differential scanning fluorimetry experiments, we identified active site features involved in binding NAD+ and controlling substrate specificity. Further in vitro enzyme cascade experiments demonstrated the efficient TsaC- and TsaD-mediated regeneration of NADH to support Rieske oxygenase chemistry. Finally, through in-depth bioinformatic analyses, we illustrate the widespread co-occurrence of Rieske oxygenases with TsaC-like enzymes. This work thus demonstrates the utility of these NADH recycling enzymes and identifies a library of short-chain dehydrogenase/reductase enzyme prospects that can be used in Rieske oxygenase pathways for in situ regeneration of NADH.


Assuntos
Proteínas de Bactérias , Comamonas testosteroni , Oxigenases , Aldeído Desidrogenase/metabolismo , NAD/metabolismo , Oxigenases/metabolismo , Especificidade por Substrato , Comamonas testosteroni/enzimologia , Comamonas testosteroni/genética , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Ferroproteínas não Heme/química , Ferroproteínas não Heme/genética , Ferroproteínas não Heme/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Estrutura Terciária de Proteína , Modelos Moleculares , Estabilidade Proteica , Biologia Computacional
2.
J Am Chem Soc ; 143(50): 21425-21432, 2021 12 22.
Artigo em Inglês | MEDLINE | ID: mdl-34881885

RESUMO

Talaromyolides (1-6) are a group of unusual 6/6/6/6/6/6 hexacyclic meroterpenoids with (3R)-6-hydroxymellein and 4,5-seco-drimane substructures, isolated from the marine fungus Talaromyces purpureogenus. We have identified the biosynthetic gene cluster tlxA-J by heterologous expression in Aspergillus, in vitro enzyme assays, and CRISPR-Cas9-based gene inactivation. Remarkably, the heterodimer of non-heme iron (NHI) enzymes, TlxJ-TlxI, catalyzes three steps of oxidation including a key reaction, hydroxylation at C-5 and C-9 of 12, the intermediate with 3-ketohydroxydrimane scaffold, to facilitate a retro-aldol reaction, leading to the construction of the 4,5-secodrimane skeleton and characteristic ketal scaffold of 1-6. The products of TlxJ-TlxI, 1 and 4, were further hydroxylated at C-4'ß by another NHI heterodimer, TlxA-TlxC, and acetylated by TlxB to yield the final products, 3 and 6. The X-ray structural analysis coupled with site-directed mutagenesis provided insights into the heterodimer TlxJ-TlxI formation and its catalysis. This is the first report to show that two NHI proteins form a heterodimer for catalysis and utilizes a novel methodology to create functional oxygenase structures in secondary metabolite biosynthesis.


Assuntos
Fungos/genética , Ferroproteínas não Heme/metabolismo , Terpenos/metabolismo , Aspergillus/química , Aspergillus/metabolismo , Biocatálise , Dimerização , Fungos/enzimologia , Hidroxilação , Família Multigênica , Mutagênese Sítio-Dirigida , Ferroproteínas não Heme/química , Ferroproteínas não Heme/genética , Oxirredução , Terpenos/química
3.
Inorg Chem ; 60(11): 7719-7731, 2021 Jun 07.
Artigo em Inglês | MEDLINE | ID: mdl-34004115

RESUMO

The non-heme iron-dependent enzyme SznF catalyzes a critical N-nitrosation step during the N-nitrosourea pharmacophore biosynthesis in streptozotocin. The intramolecular oxidative rearrangement process is known to proceed at the FeII-containing active site in the cupin domain of SznF, but its mechanism has not been elucidated to date. In this study, based on the density functional theory calculations, a unique mechanism was proposed for the N-nitrosation reaction catalyzed by SznF in which a four-electron oxidation process is accomplished through a series of complicated electron transferring between the iron center and substrate to bypass the high-valent FeIV═O species. In the catalytic reaction pathway, the O2 binds to the iron center and attacks on the substrate to form the peroxo bridge intermediate by obtaining two electrons from the substrate exclusively. Then, instead of cleaving the peroxo bridge, the Cε-Nω bond of the substrate is homolytically cleaved first to form a carbocation intermediate, which polarizes the peroxo bridge and promotes its heterolysis. After O-O bond cleavage, the following reaction steps proceed effortlessly so that the N-nitrosation is accomplished without NO exchange among reaction species.


Assuntos
Compostos de Nitrosoureia/metabolismo , Ferroproteínas não Heme/metabolismo , Biocatálise , Compostos Ferrosos/química , Compostos Ferrosos/metabolismo , Conformação Molecular , Nitrosação , Compostos de Nitrosoureia/química , Ferroproteínas não Heme/química , Oxirredução , Streptomyces/enzimologia
4.
Biomed Pharmacother ; 139: 111579, 2021 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-33845375

RESUMO

Alzheimer's disease (AD) is the most common type of dementia worldwide, characterized by the deposition of neurofibrillary tangles and amyloid-ß (Aß) peptides in the brain. Additionally, increasing evidence demonstrates that a neuroinflammatory state and oxidative stress, iron-dependent, play a crucial role in the onset and disease progression. Besides conventional therapies, the use of natural-based products represents a future medical option for AD treatment and/or prevention. We, therefore, evaluated the effects of a ribonucleotides-based ingredient (Ribodiet®) in a non-genetic mouse model of AD. To this aim, mice were injected intracerebroventricularly (i.c.v.) with Aß1-42 peptide (3 µg/3 µl) and after with Ribodiet® (0.1-10 mg/mouse) orally (p.o.) 3 times weekly for 21 days following the induction of experimental AD. The mnemonic and cognitive decline was then evaluated, and, successively, we have assessed ex vivo the modulation of different cyto-chemokines on mice brain homogenates. Finally, the level of GFAP, S100ß, and iron-related metabolic proteins were monitored as markers of reactive gliosis, neuro-inflammation, and oxidative stress. Results indicate that Ribodiet® lessens oxidative stress, brain inflammation, and amyloid pathology via modulation of iron-related metabolic proteins paving the way for its rationale use for the treatment of AD and other age-related diseases.


Assuntos
Doença de Alzheimer/prevenção & controle , Angiopatia Amiloide Cerebral/prevenção & controle , Suplementos Nutricionais , Encefalite/prevenção & controle , Estresse Oxidativo/efeitos dos fármacos , Ribonucleotídeos/uso terapêutico , Doença de Alzheimer/psicologia , Peptídeos beta-Amiloides , Animais , Comportamento Animal/efeitos dos fármacos , Biomarcadores , Angiopatia Amiloide Cerebral/psicologia , Dieta , Encefalite/psicologia , Gliose/prevenção & controle , Injeções Intraventriculares , Masculino , Camundongos , Ferroproteínas não Heme/metabolismo , Fragmentos de Peptídeos , Desempenho Psicomotor/efeitos dos fármacos , Ribonucleotídeos/farmacologia
5.
J Nutr ; 151(5): 1073-1083, 2021 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-33693820

RESUMO

BACKGROUND: Maternal iron deficiency (ID) is associated with poor pregnancy and fetal outcomes. The effect is thought to be mediated by the placenta but there is no comprehensive assessment of placental responses to maternal ID. Additionally, whether the influence of maternal ID on the placenta differs by fetal sex is unknown. OBJECTIVES: To identify gene and protein signatures of ID mouse placentas at mid-gestation. A secondary objective was to profile the expression of iron genes in mouse placentas across gestation. METHODS: We used a real-time PCR-based array to determine the mRNA expression of all known iron genes in mouse placentas at embryonic day (E) 12.5, E14.5, E16.5, and E19.5 (n = 3 placentas/time point). To determine the effect of maternal ID, we performed RNA sequencing and proteomics in male and female placentas from ID and iron-adequate mice at E12.5 (n = 8 dams/diet). RESULTS: In female placentas, 6 genes, including transferrin receptor (Tfrc) and solute carrier family 11 member 2, were significantly changed by maternal ID. An additional 154 genes were altered in male ID placentas. A proteomic analysis quantified 7662 proteins in the placenta. Proteins translated from iron-responsive element (IRE)-containing mRNA were altered in abundance; ferritin and ferroportin 1 decreased, while TFRC increased in ID placentas. Less than 4% of the significantly altered genes in ID placentas occurred both at the transcriptional and translational levels. CONCLUSIONS: Our data demonstrate that the impact of maternal ID on placental gene expression in mice is limited in scope and magnitude at mid-gestation. We provide strong evidence for IRE-based transcriptional and translational coordination of iron gene expression in the mouse placenta. Finally, we discover sexually dimorphic effects of maternal ID on placental gene expression, with more genes and pathways altered in male compared with female mouse placentas.


Assuntos
Anemia Ferropriva/metabolismo , Placenta/metabolismo , Complicações na Gravidez/metabolismo , Proteoma/metabolismo , Transcriptoma/fisiologia , Animais , Feminino , Regulação da Expressão Gênica , Ferro/metabolismo , Ferro/farmacologia , Camundongos , Ferroproteínas não Heme/genética , Ferroproteínas não Heme/metabolismo , Gravidez , RNA Mensageiro/genética , RNA Mensageiro/metabolismo
6.
J Phys Chem A ; 125(8): 1720-1737, 2021 Mar 04.
Artigo em Inglês | MEDLINE | ID: mdl-33620220

RESUMO

The viomycin biosynthesis enzyme VioC is a nonheme iron and α-ketoglutarate-dependent dioxygenase involved in the selective hydroxylation of l-arginine at the C3-position for antibiotics biosynthesis. Interestingly, experimental studies showed that using the substrate analogue, namely, l-homo-arginine, a mixture of products was obtained originating from C3-hydroxylation, C4-hydroxylation, and C3-C4-desaturation. To understand how the addition of one CH2 group to a substrate can lead to such a dramatic change in selectivity and activity, we decided to perform a computational study using quantum mechanical (QM) cluster models. We set up a large active-site cluster model of 245 atoms that includes the oxidant with its first- and second-coordination sphere influences as well as the substrate binding pocket. The model was validated against experimental work from the literature on related enzymes and previous computational studies. Thereafter, possible pathways leading to products and byproducts were investigated for a model containing l-Arg and one for l-homo-Arg as substrate. The calculated free energies of activation predict product distributions that match the experimental observation and give a low-energy C3-hydroxylation pathway for l-Arg, while for l-homo-Arg, several barriers are found to be close in energy leading to a mixture of products. We then analyzed the origins of the differences in product distributions using thermochemical, valence bond, and electrostatic models. Our studies show that the C3-H and C4-H bond strengths of l-Arg and l-homo-Arg are similar; however, external perturbations from an induced electric field of the protein affect the relative C-H bond strengths of l-Arg dramatically and make the C3-H bond the weakest and guide the reaction to a selective C3-hydroxylation channel. Therefore, the charge distribution in the protein and the induced electric dipole field of the active site of VioC guides the l-Arg substrate activation to C3-hydroxylation and disfavors the C4-hydroxylation pathway, while this does not occur for l-homo-Arg. Tight substrate positioning and electrostatic perturbations from the second-coordination sphere residues in VioC also result in a slower overall reaction for l-Arg; however, they enable a high substrate selectivity. Our studies highlight the importance of the second-coordination sphere in proteins that position the substrate and oxidant, perturb charge distributions, and enable substrate selectivity.


Assuntos
Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Ferro/metabolismo , Ferroproteínas não Heme/química , Ferroproteínas não Heme/metabolismo , Oxigenases/química , Oxigenases/metabolismo , Eletricidade Estática , Viomicina/biossíntese , Domínio Catalítico , Hidroxilação , Modelos Moleculares
7.
Chemistry ; 27(5): 1795-1809, 2021 Jan 21.
Artigo em Inglês | MEDLINE | ID: mdl-32965733

RESUMO

The nonheme iron enzyme OrfP reacts with l-Arg selectively to form the 3R,4R-dihydroxyarginine product, which in mammals can inhibit the nitric oxide synthase enzymes involved in blood pressure control. To understand the mechanisms of dioxygen activation of l-Arg by OrfP and how it enables two sequential oxidation cycles on the same substrate, we performed a density functional theory study on a large active site cluster model. We show that substrate binding and positioning in the active site guides a highly selective reaction through C3 -H hydrogen atom abstraction. This happens despite the fact that the C3 -H and C4 -H bond strengths of l-Arg are very similar. Electronic differences in the two hydrogen atom abstraction pathways drive the reaction with an initial C3 -H activation to a low-energy 5 σ-pathway, while substrate positioning destabilizes the C4 -H abstraction and sends it over the higher-lying 5 π-pathway. We show that substrate and monohydroxylated products are strongly bound in the substrate binding pocket and hence product release is difficult and consequently its lifetime will be long enough to trigger a second oxygenation cycle.


Assuntos
Arginina/química , Arginina/metabolismo , Ferroproteínas não Heme/metabolismo , Domínio Catalítico , Hidrogênio/química , Hidrogênio/metabolismo , Hidroxilação , Oxirredução
8.
Dalton Trans ; 49(48): 17745-17757, 2020 Dec 22.
Artigo em Inglês | MEDLINE | ID: mdl-33241840

RESUMO

Two mononuclear iron(ii)-thiolate complexes have been prepared that represent structural models of the nonheme iron enzymes EgtB and OvoA, which catalyze the O2-dependent formation of carbon-sulfur bonds in the biosynthesis of thiohistidine compounds. The series of Fe(ii) complexes reported here feature tripodal N4 chelates (LA and LB) that contain both pyridyl and imidazolyl donors (LA = (1H-imidazol-4-yl)-N,N-bis((pyridin-2-yl)methyl)methanamine; LB = N,N-bis((1-methylimidazol-2-yl)methyl)-2-pyridylmethylamine). Further coordination with monodentate aromatic or aliphatic thiolate ligands yielded the five-coordinate, high-spin Fe(ii) complexes [FeII(LA)(SMes)]BPh4 (1) and [FeII(LB)(SCy)]BPh4 (2), where SMes = 2,4,6-trimethylthiophenolate and SCy = cyclohexanethiolate. X-ray crystal structures revealed that 1 and 2 possess trigonal bipyramidal geometries formed by the N4S ligand set. In each case, the thiolate ligand is positioned cis to an imidazole donor, replicating the arrangement of Cys- and His-based substrates in the active site of EgtB. The geometric and electronic structures of 1 and 2 were analyzed with UV-vis absorption and Mössbauer spectroscopies in tandem with density functional theory (DFT) calculations. Exposure of 1 and 2 to nitric oxide (NO) yielded six-coordinate FeNO adducts that were characterized with infrared and electron paramagnetic resonance (EPR) spectroscopies, confirming that these complexes are capable of binding diatomic molecules. Reaction of 1 and 2 with O2 causes oxidation of the thiolate ligands to disulfide products. The implications of these results for the development of functional models of EgtB and OvoA are discussed.


Assuntos
Compostos Ferrosos/farmacologia , Ferroproteínas não Heme/metabolismo , Oxirredutases/metabolismo , Compostos de Sulfidrila/farmacologia , Domínio Catalítico/efeitos dos fármacos , Cristalografia por Raios X , Teoria da Densidade Funcional , Compostos Ferrosos/síntese química , Compostos Ferrosos/química , Modelos Moleculares , Estrutura Molecular , Mycobacteriaceae/enzimologia , Compostos de Sulfidrila/química
9.
Chem Pharm Bull (Tokyo) ; 68(9): 823-831, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32879222

RESUMO

This review summarizes the recent progress in research on the non-heme Fe(II)- and 2-oxoglutarate-dependent dioxygenases, which are involved in the biosynthesis of pharmaceutically important fungal meroterpenoids. This enzyme class activates a selective C-H bond of the substrate and catalyzes a wide range of chemical reactions, from simple hydroxylation to dynamic carbon skeletal rearrangements, thereby significantly contributing to the structural diversification and complexification of the molecules. Structure-function studies of these enzymes provide an excellent platform for the development of useful biocatalysts for synthetic biology to create novel molecules for future drug discovery.


Assuntos
Fungos/enzimologia , Oxigenases de Função Mista/metabolismo , Ferroproteínas não Heme/metabolismo , Terpenos/metabolismo , Fungos/metabolismo , Terpenos/química
10.
Biochim Biophys Acta Bioenerg ; 1861(10): 148256, 2020 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-32622739

RESUMO

Flavodiiron proteins (FDPs) of photosynthetic organisms play a photoprotective role by reducing oxygen to water and thus avoiding the accumulation of excess electrons on the photosystem I (PSI) acceptor side under stress conditions. In Synechocystis sp. PCC 6803 grown under high CO2, both FDPs Flv1 and Flv3 are indispensable for oxygen reduction. We performed a detailed in vivo kinetic study of wild-type (WT) and Δflv1/3 strains of Synechocystis using light-induced NADPH fluorescence and near-infrared absorption of iron-sulfur clusters from ferredoxin and the PSI acceptors (FAFB), collectively named FeS. These measurements were performed under conditions where the Calvin-Benson cycle is inactive or poorly activated. Under such conditions, the NADPH decay following a short illumination decays in parallel in both strains and exhibits a time lag which is correlated to the presence of reduced FeS. On the contrary, reduced FeS decays much faster in WT than in Δflv1/3 (13 vs 2 s-1). These data unambiguously show that reduced ferredoxin, or possibly reduced FAFB, is the direct electron donor to the Flv1/Flv3 heterodimer. Evidences for large reduction of (FAFB) and recombination reactions within PSI were also provided by near-infrared absorption. Mutants lacking either the NDH1-L complex, the homolog of complex I of respiration, or the Pgr5 protein show no difference with WT in the oxidation of reduced FeS following a short illumination. These observations question the participation of a significant cyclic electron flow in cyanobacteria during the first seconds of the induction phase of photosynthesis.


Assuntos
Proteínas de Bactérias/metabolismo , Ferroproteínas não Heme/metabolismo , Synechocystis/metabolismo , Proteínas de Bactérias/genética , Transporte de Elétrons , Cinética , Mutação , NADP/metabolismo , Ferroproteínas não Heme/genética , Espectrometria de Fluorescência
11.
Phys Chem Chem Phys ; 22(16): 8699-8712, 2020 Apr 29.
Artigo em Inglês | MEDLINE | ID: mdl-32270839

RESUMO

The selectivity of halogenation versus hydroxylation in α-KG de-pendent halogenases is vital to their function and has been widely studied, particularly using the halogenase SyrB2 as a model. WelO5, a new member of α-KG dependent halogenases, catalyzes the chlorination of 12-epi-fischerindole U in the welwitindolinone biosynthetic pathway. Herein, we give a detailed insight into the selectivity of WelO5 through combined quantum mechanical/molecular mechanical (QM/MM) calculations for the whole catalytic cycle. O2 activation leads to a Fe(iv)[double bond, length as m-dash]O moiety which adopts an equatorial conformation (in the plane consisting of His164, chloride and Fe atom), in contrast to axial conformation (perpendicular to the plane). Key to the conformational selectivity is a serine residue (Ser189) in the equatorial plane, that brings the precursor of the Fe(iv)[double bond, length as m-dash]O intermediate (a Fe(ii)-peracid complex) to the equatorial conformation through hydrogen bonding. Hydrogen abstraction of the substrate by the equatorial Fe(iv)[double bond, length as m-dash]O leads to a five-coordinated HO-Fe(iii)-Cl complex, where the hydroxyl ligand is still equatorial and thus relatively far from the substrate radical in the axial direction compared to the chloride ligand. This smoothly explains the extremely high selectivity of chlorination in WelO5 and provides a microscopic explanation for the experimental finding that S189A WelO5 ceases to display any chlorination selectivity versus hydroxylation. Notably, although Ser189 is vital for the selectivity of the enzyme, it is not part of the substrate binding pocket. Therefore, WelO5 serves as an excellent example how chemoselectivity can be achieved in directed evolution without the tedious redesign of the substrate binding pocket.


Assuntos
Enzimas/metabolismo , Ferroproteínas não Heme/metabolismo , Halogenação , Hidroxilação , Ferroproteínas não Heme/química , Especificidade por Substrato
12.
Inorg Chem ; 59(9): 6000-6009, 2020 May 04.
Artigo em Inglês | MEDLINE | ID: mdl-32309932

RESUMO

An important class of non-heme dioxygenases contains a conserved Fe binding site that consists of a 2-His-1-carboxylate facial triad. Results from structural biology show that, in the resting state, these proteins are six-coordinate with aqua ligands occupying the remaining three coordination sites. We have utilized biotin-streptavidin (Sav) technology to design new artificial Fe proteins (ArMs) that have many of the same structural features found within active sites of these non-heme dioxygenases. An Sav variant was isolated that contains the S112E mutation, which installed a carboxylate side chain in the appropriate position to bind to a synthetic FeII complex confined within Sav. Structural studies using X-ray diffraction (XRD) methods revealed a facial triad binding site that is composed of two N donors from the biotinylated ligand and the monodentate coordination of the carboxylate from S112E. Two aqua ligands complete the primary coordination sphere of the FeII center with both involved in hydrogen bond networks within Sav. The corresponding FeIII protein was also prepared and structurally characterized to show a six-coordinate complex with two exogenous acetato ligands. The FeIII protein was further shown to bind an exogenous azido ligand through replacement of one acetato ligand. Spectroscopic studies of the ArMs in solution support the results found by XRD.


Assuntos
Dioxigenases/química , Ferroproteínas não Heme/química , Sítios de Ligação , Dioxigenases/metabolismo , Compostos Férricos/química , Compostos Férricos/metabolismo , Ligantes , Conformação Molecular , Ferroproteínas não Heme/metabolismo
13.
Dalton Trans ; 49(14): 4266-4276, 2020 Apr 07.
Artigo em Inglês | MEDLINE | ID: mdl-32141456

RESUMO

DNA base repair mechanisms of alkylated DNA bases is an important reaction in chemical biology and particularly in the human body. It is typically catalyzed by an α-ketoglutarate-dependent nonheme iron dioxygenase named the AlkB repair enzyme. In this work we report a detailed computational study into the structure and reactivity of AlkB repair enzymes with alkylated DNA bases. In particular, we investigate the aliphatic hydroxylation and C[double bond, length as m-dash]C epoxidation mechanisms of alkylated DNA bases by a high-valent iron(iv)-oxo intermediate. Our computational studies use quantum mechanics/molecular mechanics methods on full enzymatic structures as well as cluster models on active site systems. The work shows that the iron(iv)-oxo species is rapidly formed after dioxygen binding to an iron(ii) center and passes a bicyclic ring structure as intermediate. Subsequent cluster models explore the mechanism of substrate hydroxylation and epoxidation of alkylated DNA bases. The work shows low energy barriers for substrate activation and consequently energetically feasible pathways are predicted. Overall, the work shows that a high-valent iron(iv)-oxo species can efficiently dealkylate alkylated DNA bases and return them into their original form.


Assuntos
DNA/química , Dioxigenases/química , Ferroproteínas não Heme/química , Teoria Quântica , Sítios de Ligação , DNA/metabolismo , Reparo do DNA , Dioxigenases/metabolismo , Hidroxilação , Modelos Moleculares , Estrutura Molecular , Ferroproteínas não Heme/metabolismo , Oxigênio/química , Oxigênio/metabolismo
14.
Chemphyschem ; 21(5): 385-396, 2020 03 04.
Artigo em Inglês | MEDLINE | ID: mdl-31926045

RESUMO

A new methane formation pathway, which uses methylphosphonate (MPn) as the methane precursor, has been discovered in the upper ocean. Methylphosphonate synthase (MPnS) is a key piece in this pathway to produce MPn from 2-hydroxyethylphosphonate (2-HEP), using an untypical 2-His-1-Gln non-heme iron architecture. Herein, the MPnS reaction mechanism was demonstrated by the density functional calculations to mainly include the substrate hydroxyl deprotonation, the formation of a MPn radical and a formate, and the hydrogen abstraction of formate by MPn radical. The second-shell Lys28' may serve as a proton reservoir activating 2-HEP and regenerating the Fe site. The Fe-bound superoxide radical is a bifunctional species to deprotonate the substrate hydroxyl and abstract the substrate methylene hydrogen. Several alternative mechanisms have been ruled out. Furthermore, the catalytic activity of MPnS was found to be inactivated/reduced by the mutation of Gln152E/Gln152H/Gln152D, rendering a significant evolutionary advantage with an uncommon 2-His-1-Gln triad introduced to the ferrous coordination sphere.


Assuntos
Metano/biossíntese , Ferroproteínas não Heme/metabolismo , Compostos Organofosforados/metabolismo , Oxigenases/metabolismo , Metano/química , Ferroproteínas não Heme/química , Compostos Organofosforados/química , Oxigenases/química
15.
FEBS J ; 287(14): 2998-3011, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-31876382

RESUMO

Microbes are competent chemists that are able to generate thousands of chemically complex natural products with potent biological activities. The key to the formation of this chemical diversity has been the rapid evolution of secondary metabolism. Many enzymes residing on these metabolic pathways have acquired atypical catalytic properties in comparison with their counterparts found in primary metabolism. The biosynthetic pathway of the anthracycline nogalamycin contains two such proteins, SnoK and SnoN, belonging to nonheme iron and 2-oxoglutarate-dependent mono-oxygenases. In spite of structural similarity, the two proteins catalyze distinct chemical reactions; SnoK is a C2-C5″ carbocyclase, whereas SnoN catalyzes stereoinversion at the adjacent C4″ position. Here, we have identified four structural regions involved in the functional differentiation and generated 30 chimeric enzymes to probe catalysis. Our analyses indicate that the carbocyclase SnoK is the ancestral form of the enzyme from which SnoN has evolved to catalyze stereoinversion at the neighboring carbon. The critical step in the appearance of epimerization activity has likely been the insertion of three residues near the C-terminus, which allow repositioning of the substrate in front of the iron center. The loss of the original carbocyclization activity has then occurred with changes in four amino acids near the iron center that prohibit alignment of the substrate for the formation of the C2-C5″ bond. Our study provides detailed insights into the evolutionary processes that have enabled Streptomyces soil bacteria to become the major source of antibiotics and antiproliferative agents. ENZYMES: EC number 1.14.11.


Assuntos
Proteínas de Bactérias/metabolismo , Vias Biossintéticas , Evolução Molecular , Engenharia Genética/métodos , Nogalamicina/biossíntese , Ferroproteínas não Heme/metabolismo , Streptomyces/enzimologia , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Ferroproteínas não Heme/química , Ferroproteínas não Heme/genética , Conformação Proteica
16.
Biochim Biophys Acta Mol Cell Biol Lipids ; 1865(11): 158590, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-31874225

RESUMO

Carotenoid cleavage dioxygenases (CCDs) comprise a superfamily of mononuclear non-heme iron proteins that catalyze the oxygenolytic fission of alkene bonds in carotenoids to generate apocarotenoid products. Some of these enzymes exhibit additional activities such as carbon skeleton rearrangement and trans-cis isomerization. The group also includes a subfamily of enzymes that split the interphenyl alkene bond in molecules such as resveratrol and lignostilbene. CCDs are involved in numerous biological processes ranging from production of light-sensing chromophores to degradation of lignin derivatives in pulping waste sludge. These enzymes exhibit unique features that distinguish them from other families of non-heme iron enzymes. The distinctive properties and biological importance of CCDs have stimulated interest in their modes of catalysis. Recent structural, spectroscopic, and computational studies have helped clarify mechanistic aspects of CCD catalysis. Here, we review these findings emphasizing common and unique properties of CCDs that enable their variable substrate specificity and regioselectivity. This article is part of a Special Issue entitled Carotenoids recent advances in cell and molecular biology edited by Johannes von Lintig and Loredana Quadro.


Assuntos
Carotenoides/química , Dioxigenases/genética , Ferroproteínas não Heme/genética , Oxigênio/metabolismo , Carbono/metabolismo , Carotenoides/metabolismo , Dioxigenases/química , Dioxigenases/metabolismo , Humanos , Luz , Ferroproteínas não Heme/química , Ferroproteínas não Heme/metabolismo , Resveratrol/farmacologia , Especificidade por Substrato
17.
J Am Chem Soc ; 141(51): 20269-20277, 2019 12 26.
Artigo em Inglês | MEDLINE | ID: mdl-31840992

RESUMO

Generation of reactive intermediates and interception of these fleeting species under physiological conditions is a common strategy employed by Nature to build molecular complexity. However, selective formation of these species under mild conditions using classical synthetic techniques is an outstanding challenge. Here, we demonstrate the utility of biocatalysis in generating o-quinone methide intermediates with precise chemoselectivity under mild, aqueous conditions. Specifically, α-ketoglutarate-dependent non-heme iron enzymes, CitB and ClaD, are employed to selectively modify benzylic C-H bonds of o-cresol substrates. In this transformation, biocatalytic hydroxylation of a benzylic C-H bond affords a benzylic alcohol product which, under the aqueous reaction conditions, is in equilibrium with the corresponding o-quinone methide. o-Quinone methide interception by a nucleophile or a dienophile allows for one-pot conversion of benzylic C-H bonds into C-C, C-N, C-O, and C-S bonds in chemoenzymatic cascades on preparative scale. The chemoselectivity and mild nature of this platform is showcased here by the selective modification of peptides and chemoenzymatic synthesis of the chroman natural product (-)-xyloketal D.


Assuntos
Indolquinonas/biossíntese , Ferroproteínas não Heme/metabolismo , Indolquinonas/química , Estrutura Molecular , Monascus/enzimologia , Ferroproteínas não Heme/química , Penicillium/enzimologia , Estereoisomerismo
18.
J Am Chem Soc ; 141(50): 19585-19588, 2019 12 18.
Artigo em Inglês | MEDLINE | ID: mdl-31790588

RESUMO

Transition-metal catalysis is a powerful tool for the construction of chemical bonds. Here we show that Pseudomonas savastanoi ethylene-forming enzyme, a non-heme iron enzyme, can catalyze olefin aziridination and nitrene C-H insertion, and that these activities can be improved by directed evolution. The non-heme iron center allows for facile modification of the primary coordination sphere by addition of metal-coordinating molecules, enabling control over enzyme activity and selectivity using small molecules.


Assuntos
Alcenos/química , Biocatálise , Ferroproteínas não Heme/metabolismo , Pseudomonas/enzimologia , Aziridinas/química , Evolução Molecular Direcionada , Ligantes , Modelos Moleculares , Ferroproteínas não Heme/química , Ferroproteínas não Heme/genética , Conformação Proteica
19.
Artigo em Inglês | MEDLINE | ID: mdl-31564305

RESUMO

Non-heme iron enzymes catalyze a wide range of chemical transformations, serving as one of the key types of tailoring enzymes in the biosynthesis of natural products. Hydroxylation reaction is the most common type of reactions catalyzed by these enzymes and hydroxylation reactions have been extensively investigated mechanistically. However, the mechanistic details for other types of transformations remain largely unknown or unexplored. In this paper, we present some of the most recently discovered transformations, including endoperoxidation, orthoester formation, cyclopropanation, oxidative C-C and C-S bond formation reactions. In addition, many of them are multi-functional enzymes, which further complicate their mechanistic investigations. In this work, we summarize their biosynthetic pathways, with special emphasis on the mechanistic details available for these newly discovered enzymes.


Assuntos
Produtos Biológicos/metabolismo , Fungos/enzimologia , Ferroproteínas não Heme/metabolismo , Produtos Biológicos/química , Proteínas Fúngicas , Modelos Moleculares , Ferroproteínas não Heme/química , Conformação Proteica
20.
Asia Pac J Clin Nutr ; 28(2): 214-222, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31192549

RESUMO

BACKGROUND AND OBJECTIVES: This study assessed the bioavailability and biological incorporation of nonheme iron from staple food diets in healthy young urban Chinese women and determined the relevant effects of typical regional patterns of staple foods in South and North China. METHODS AND STUDY DESIGN: Twenty-two young urban Chinese women aged 20-23 years were enrolled and randomly allocated to two groups, with rice (rice group) and steamed buns (steamed buns group) as the staple food, respectively. Each participant received three meals daily containing approximately 3.25 mg of stable 57FeSO4 for 2 consecutive days, along with daily intravenous injection of approximately 2.0 mg of 58FeSO4. Nonheme iron absorption and infused iron incorporation rates were assayed. RESULTS: In all participants, the rice group, and the buns group, nonheme iron intake was 7.2±1.6, 5.9±0.6, and 8.4±1.2 mg, respectively; mean 57FeSO4 absorption rate was 22.2%±9.6%, 22.2%±10.6%, and 22.2%±8.9%, respectively; and the mean infused 58FeSO4 incorporation rate was 91.6%±8.2%, 93%±7.3%, and 90%±9.1%, respectively. No substantial differences existed in the nonheme iron intakes and the 57FeSO4 absorption and 58FeSO4 incorporation rates between the rice and buns groups (all p>0.05). CONCLUSIONS: The bioavailability and incorporation rates of nonheme iron from representative comprehensive Chinese diets in healthy young urban Chinese women were evaluated. Our results can facilitate the establishment of dietary reference intake for iron in Chinese women.


Assuntos
Dieta/métodos , Ferro da Dieta/metabolismo , Adulto , Disponibilidade Biológica , China , Feminino , Humanos , Ferroproteínas não Heme/metabolismo , População Urbana/estatística & dados numéricos , Adulto Jovem
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