Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 242
Filtrar
Más filtros










Base de datos
Intervalo de año de publicación
1.
Curr Opin Chem Biol ; 80: 102467, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38772214

RESUMEN

Multinuclear non-heme iron dependent oxidative enzymes (MNIOs), formerly known as domain of unknown function 692 (DUF692), are involved in the post-translational modification of peptides during the biosynthesis of peptide-based natural products. These enzymes catalyze highly unusual and diverse chemical modifications. Several class-defining features of this large family (>14 000 members) are beginning to emerge. Structurally, the enzymes are characterized by a TIM-barrel fold and a set of conserved residues for a di- or tri-iron binding site. They use molecular oxygen to modify peptide substrates, often in a four-electron oxidation taking place at a cysteine residue. This review summarizes the current understanding of MNIOs. Four modifications are discussed in detail: oxazolone-thioamide formation, ß-carbon excision, hydantoin-macrocycle formation, and 5-thiooxazole formation. Briefly discussed are two other reactions that do not take place on Cys residues.


Asunto(s)
Oxidación-Reducción , Péptidos , Procesamiento Proteico-Postraduccional , Péptidos/química , Péptidos/metabolismo , Proteínas de Hierro no Heme/metabolismo , Proteínas de Hierro no Heme/química , Hierro/metabolismo , Hierro/química , Tioamidas/química , Tioamidas/metabolismo , Humanos
2.
Methods Enzymol ; 696: 231-247, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38658081

RESUMEN

Nonheme iron enzymes stand out as one of the most versatile biocatalysts for molecular functionalization. They facilitate a wide array of chemical transformations within biological processes, including hydroxylation, chlorination, epimerization, desaturation, cyclization, and more. Beyond their native biological functions, these enzymes possess substantial potential as powerful biocatalytic platforms for achieving abiological metal-catalyzed reactions, owing to their functional and structural diversity and high evolvability. To this end, our group has recently engineered a series of nonheme iron enzymes to employ non-natural radical-relay mechanisms for abiological radical transformations not previously known in biology. Notably, we have demonstrated that a nonheme iron enzyme, (S)-2-hydroxypropylphosphonate epoxidase from Streptomyces viridochromogenes (SvHppE), can be repurposed into an efficient and selective biocatalyst for radical fluorine transfer reactions. This marks the first known instance of a redox enzymatic process for C(sp3)F bond formation. This chapter outlines the detailed experimental protocol for engineering SvHPPE for fluorination reactions. Furthermore, the provided protocol could serve as a general guideline that might facilitate other engineering endeavors targeting nonheme iron enzymes for novel catalytic functions.


Asunto(s)
Biocatálisis , Flúor , Halogenación , Ingeniería de Proteínas , Streptomyces , Flúor/química , Ingeniería de Proteínas/métodos , Streptomyces/enzimología , Streptomyces/genética , Oxidorreductasas/metabolismo , Oxidorreductasas/genética , Oxidorreductasas/química , Oxidación-Reducción , Proteínas de Hierro no Heme/química , Proteínas de Hierro no Heme/metabolismo , Proteínas de Hierro no Heme/genética , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Proteínas Bacterianas/química
3.
J Biol Chem ; 299(10): 105222, 2023 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-37673337

RESUMEN

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.


Asunto(s)
Proteínas Bacterianas , Comamonas testosteroni , Oxigenasas , Aldehído Deshidrogenasa/metabolismo , NAD/metabolismo , Oxigenasas/metabolismo , Especificidad por Sustrato , Comamonas testosteroni/enzimología , Comamonas testosteroni/genética , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Proteínas de Hierro no Heme/química , Proteínas de Hierro no Heme/genética , Proteínas de Hierro no Heme/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Estructura Terciaria de Proteína , Modelos Moleculares , Estabilidad Proteica , Biología Computacional
4.
Science ; 376(6595): 869-874, 2022 05 20.
Artículo en Inglés | MEDLINE | ID: mdl-35587977

RESUMEN

We report the reprogramming of nonheme iron enzymes to catalyze an abiological C(sp3)‒H azidation reaction through iron-catalyzed radical relay. This biocatalytic transformation uses amidyl radicals as hydrogen atom abstractors and Fe(III)‒N3 intermediates as radical trapping agents. We established a high-throughput screening platform based on click chemistry for rapid evolution of the catalytic performance of identified enzymes. The final optimized variants deliver a range of azidation products with up to 10,600 total turnovers and 93% enantiomeric excess. Given the prevalence of radical relay reactions in organic synthesis and the diversity of nonheme iron enzymes, we envision that this discovery will stimulate future development of metalloenzyme catalysts for synthetically useful transformations unexplored by natural evolution.


Asunto(s)
Evolución Molecular Dirigida , Enzimas , Proteínas de Hierro no Heme , Biocatálisis , Carbono/química , Enzimas/química , Hidrógeno/química , Proteínas de Hierro no Heme/química
5.
J Am Chem Soc ; 143(50): 21425-21432, 2021 12 22.
Artículo en Inglés | MEDLINE | ID: mdl-34881885

RESUMEN

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.


Asunto(s)
Hongos/genética , Proteínas de Hierro no Heme/metabolismo , Terpenos/metabolismo , Aspergillus/química , Aspergillus/metabolismo , Biocatálisis , Dimerización , Hongos/enzimología , Hidroxilación , Familia de Multigenes , Mutagénesis Sitio-Dirigida , Proteínas de Hierro no Heme/química , Proteínas de Hierro no Heme/genética , Oxidación-Reducción , Terpenos/química
6.
Inorg Chem ; 60(11): 7719-7731, 2021 Jun 07.
Artículo en Inglés | MEDLINE | ID: mdl-34004115

RESUMEN

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.


Asunto(s)
Compuestos de Nitrosourea/metabolismo , Proteínas de Hierro no Heme/metabolismo , Biocatálisis , Compuestos Ferrosos/química , Compuestos Ferrosos/metabolismo , Conformación Molecular , Nitrosación , Compuestos de Nitrosourea/química , Proteínas de Hierro no Heme/química , Oxidación-Reducción , Streptomyces/enzimología
7.
J Phys Chem A ; 125(8): 1720-1737, 2021 Mar 04.
Artículo en Inglés | MEDLINE | ID: mdl-33620220

RESUMEN

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.


Asunto(s)
Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Hierro/metabolismo , Proteínas de Hierro no Heme/química , Proteínas de Hierro no Heme/metabolismo , Oxigenasas/química , Oxigenasas/metabolismo , Electricidad Estática , Viomicina/biosíntesis , Dominio Catalítico , Hidroxilación , Modelos Moleculares
8.
Proc Natl Acad Sci U S A ; 118(4)2021 01 26.
Artículo en Inglés | MEDLINE | ID: mdl-33468680

RESUMEN

In biosynthesis of the pancreatic cancer drug streptozotocin, the tridomain nonheme-iron oxygenase SznF hydroxylates Nδ and Nω' of Nω-methyl-l-arginine before oxidatively rearranging the triply modified guanidine to the N-methyl-N-nitrosourea pharmacophore. A previously published structure visualized the monoiron cofactor in the enzyme's C-terminal cupin domain, which promotes the final rearrangement, but exhibited disorder and minimal metal occupancy in the site of the proposed diiron cofactor in the N-hydroxylating heme-oxygenase-like (HO-like) central domain. We leveraged our recent observation that the N-oxygenating µ-peroxodiiron(III/III) intermediate can form in the HO-like domain after the apo protein self-assembles its diiron(II/II) cofactor to solve structures of SznF with both of its iron cofactors bound. These structures of a biochemically validated member of the emerging heme-oxygenase-like diiron oxidase and oxygenase (HDO) superfamily with intact diiron cofactor reveal both the large-scale conformational change required to assemble the O2-reactive Fe2(II/II) complex and the structural basis for cofactor instability-a trait shared by the other validated HDOs. During cofactor (dis)assembly, a ligand-harboring core helix dynamically (un)folds. The diiron cofactor also coordinates an unanticipated Glu ligand contributed by an auxiliary helix implicated in substrate binding by docking and molecular dynamics simulations. The additional carboxylate ligand is conserved in another N-oxygenating HDO but not in two HDOs that cleave carbon-hydrogen and carbon-carbon bonds to install olefins. Among ∼9,600 sequences identified bioinformatically as members of the emerging HDO superfamily, ∼25% conserve this additional carboxylate residue and are thus tentatively assigned as N-oxygenases.


Asunto(s)
Hemo Oxigenasa (Desciclizante)/ultraestructura , Proteínas de Hierro no Heme/ultraestructura , Oxigenasas/ultraestructura , Estreptozocina/química , Catálisis/efectos de los fármacos , Cristalografía por Rayos X , Hemo Oxigenasa (Desciclizante)/química , Humanos , Ligandos , Compuestos de Nitrosourea/toxicidad , Proteínas de Hierro no Heme/química , Oxidación-Reducción , Oxígeno/química , Oxigenasas/química , Neoplasias Pancreáticas/inducido químicamente , Neoplasias Pancreáticas/enzimología , Neoplasias Pancreáticas/patología , Conformación Proteica/efectos de los fármacos , Dominios Proteicos/genética , Estreptozocina/toxicidad
9.
Inorg Chem ; 59(9): 6000-6009, 2020 May 04.
Artículo en Inglés | MEDLINE | ID: mdl-32309932

RESUMEN

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.


Asunto(s)
Dioxigenasas/química , Proteínas de Hierro no Heme/química , Sitios de Unión , Dioxigenasas/metabolismo , Compuestos Férricos/química , Compuestos Férricos/metabolismo , Ligandos , Conformación Molecular , Proteínas de Hierro no Heme/metabolismo
10.
Phys Chem Chem Phys ; 22(16): 8699-8712, 2020 Apr 29.
Artículo en Inglés | MEDLINE | ID: mdl-32270839

RESUMEN

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.


Asunto(s)
Enzimas/metabolismo , Proteínas de Hierro no Heme/metabolismo , Halogenación , Hidroxilación , Proteínas de Hierro no Heme/química , Especificidad por Sustrato
11.
Dalton Trans ; 49(14): 4266-4276, 2020 Apr 07.
Artículo en Inglés | MEDLINE | ID: mdl-32141456

RESUMEN

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.


Asunto(s)
ADN/química , Dioxigenasas/química , Proteínas de Hierro no Heme/química , Teoría Cuántica , Sitios de Unión , ADN/metabolismo , Reparación del ADN , Dioxigenasas/metabolismo , Hidroxilación , Modelos Moleculares , Estructura Molecular , Proteínas de Hierro no Heme/metabolismo , Oxígeno/química , Oxígeno/metabolismo
12.
Proc Natl Acad Sci U S A ; 117(10): 5152-5159, 2020 03 10.
Artículo en Inglés | MEDLINE | ID: mdl-32094179

RESUMEN

Determining the requirements for efficient oxygen (O2) activation is key to understanding how enzymes maintain efficacy and mitigate unproductive, often detrimental reactivity. For the α-ketoglutarate (αKG)-dependent nonheme iron enzymes, both a concerted mechanism (both cofactor and substrate binding prior to reaction with O2) and a sequential mechanism (cofactor binding and reaction with O2 precede substrate binding) have been proposed. Deacetoxycephalosporin C synthase (DAOCS) is an αKG-dependent nonheme iron enzyme for which both of these mechanisms have been invoked to generate an intermediate that catalyzes oxidative ring expansion of penicillin substrates in cephalosporin biosynthesis. Spectroscopy shows that, in contrast to other αKG-dependent enzymes (which are six coordinate when only αKG is bound to the FeII), αKG binding to FeII-DAOCS results in ∼45% five-coordinate sites that selectively react with O2 relative to the remaining six-coordinate sites. However, this reaction produces an FeIII species that does not catalyze productive ring expansion. Alternatively, simultaneous αKG and substrate binding to FeII-DAOCS produces five-coordinate sites that rapidly react with O2 to form an FeIV=O intermediate that then reacts with substrate to produce cephalosporin product. These results demonstrate that the concerted mechanism is operative in DAOCS and by extension, other nonheme iron enzymes.


Asunto(s)
Transferasas Intramoleculares/química , Hierro/química , Ácidos Cetoglutáricos/química , Proteínas de Hierro no Heme/química , Proteínas de Unión a las Penicilinas/química , Especies Reactivas de Oxígeno/química , Activación Enzimática , Oxidación-Reducción , Penicilina G/química , Especificidad por Sustrato
13.
Chemphyschem ; 21(5): 385-396, 2020 03 04.
Artículo en Inglés | MEDLINE | ID: mdl-31926045

RESUMEN

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.


Asunto(s)
Metano/biosíntesis , Proteínas de Hierro no Heme/metabolismo , Compuestos Organofosforados/metabolismo , Oxigenasas/metabolismo , Metano/química , Proteínas de Hierro no Heme/química , Compuestos Organofosforados/química , Oxigenasas/química
14.
Biochim Biophys Acta Mol Cell Biol Lipids ; 1865(11): 158590, 2020 11.
Artículo en Inglés | MEDLINE | ID: mdl-31874225

RESUMEN

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.


Asunto(s)
Carotenoides/química , Dioxigenasas/genética , Proteínas de Hierro no Heme/genética , Oxígeno/metabolismo , Carbono/metabolismo , Carotenoides/metabolismo , Dioxigenasas/química , Dioxigenasas/metabolismo , Humanos , Luz , Proteínas de Hierro no Heme/química , Proteínas de Hierro no Heme/metabolismo , Resveratrol/farmacología , Especificidad por Sustrato
15.
FEBS J ; 287(14): 2998-3011, 2020 07.
Artículo en Inglés | MEDLINE | ID: mdl-31876382

RESUMEN

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.


Asunto(s)
Proteínas Bacterianas/metabolismo , Vías Biosintéticas , Evolución Molecular , Ingeniería Genética/métodos , Nogalamicina/biosíntesis , Proteínas de Hierro no Heme/metabolismo , Streptomyces/enzimología , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Proteínas de Hierro no Heme/química , Proteínas de Hierro no Heme/genética , Conformación Proteica
16.
Angew Chem Int Ed Engl ; 59(19): 7332-7349, 2020 05 04.
Artículo en Inglés | MEDLINE | ID: mdl-31373120

RESUMEN

Nonheme iron enzymes generate powerful and versatile oxidants that perform a wide range of oxidation reactions, including the functionalization of inert C-H bonds, which is a major challenge for chemists. The oxidative abilities of these enzymes have inspired bioinorganic chemists to design synthetic models to mimic their ability to perform some of the most difficult oxidation reactions and study the mechanisms of such transformations. Iron-oxygen intermediates like iron(III)-hydroperoxo and high-valent iron-oxo species have been trapped and identified in investigations of these bio-inspired catalytic systems, with the latter proposed to be the active oxidant for most of these systems. In this Review, we highlight the recent spectroscopic and mechanistic advances that have shed light on the various pathways that can be accessed by bio-inspired nonheme iron systems to form the high-valent iron-oxo intermediates.


Asunto(s)
Proteínas de Hierro no Heme/química , Oxidantes/química , Carbono/química , Catálisis , Compuestos Férricos/química , Hidrógeno/química , Oxidación-Reducción
17.
J Am Chem Soc ; 141(51): 20269-20277, 2019 12 26.
Artículo en Inglés | MEDLINE | ID: mdl-31840992

RESUMEN

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.


Asunto(s)
Indolquinonas/biosíntesis , Proteínas de Hierro no Heme/metabolismo , Indolquinonas/química , Estructura Molecular , Monascus/enzimología , Proteínas de Hierro no Heme/química , Penicillium/enzimología , Estereoisomerismo
18.
J Am Chem Soc ; 141(50): 19585-19588, 2019 12 18.
Artículo en Inglés | MEDLINE | ID: mdl-31790588

RESUMEN

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.


Asunto(s)
Alquenos/química , Biocatálisis , Proteínas de Hierro no Heme/metabolismo , Pseudomonas/enzimología , Aziridinas/química , Evolución Molecular Dirigida , Ligandos , Modelos Moleculares , Proteínas de Hierro no Heme/química , Proteínas de Hierro no Heme/genética , Conformación Proteica
19.
Artículo en Inglés | MEDLINE | ID: mdl-31564305

RESUMEN

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.


Asunto(s)
Productos Biológicos/metabolismo , Hongos/enzimología , Proteínas de Hierro no Heme/metabolismo , Productos Biológicos/química , Proteínas Fúngicas , Modelos Moleculares , Proteínas de Hierro no Heme/química , Conformación Proteica
20.
J Phys Chem B ; 123(10): 2244-2253, 2019 03 14.
Artículo en Inglés | MEDLINE | ID: mdl-30776233

RESUMEN

An extradiol-cleaving catecholic dioxygenase, 2,3-dihydroxybiphenyl dioxygenase, plays important roles in the catabolism of biphenyl/polychlorinated biphenyl aromatic contaminants in the environment. To better elucidate the biodegradable pathway, a theoretical investigation of the ring-opening degradation of 2,3-dihydroxybiphenyl (DHBP) was performed with the aid of quantum mechanical/molecular mechanical calculations. A quintet state of the DHBP-iron-dioxygen group adducts was found to be the reactive state with a substrate radical-FeII-superoxo (DHBP•↑-FeII-O2•-↓) character. The HOO• species was the reactive oxygen species responsible for the subsequent attack of DHBP. Among the whole reaction energy profile, the first step in proton-coupled electron transfer was determined to be the rate-determining step with a potential energy barrier of 17.2 kcal/mol, which is close to the experimental value (14.7 kcal/mol). Importantly, the residue His194 shows distinct roles in the catalytic cycle, where it acts as an acid-base catalyst to deprotonate the hydroxyl group of DHBP at an early stage, then stabilizes the negative charge on the dioxygen group, and, at the final stage, promotes the semialdehyde product formation as a proton donor.


Asunto(s)
Compuestos de Bifenilo/química , Catecoles/química , Dioxigenasas/química , Contaminantes Ambientales/química , Proteínas de Hierro no Heme/química , Oxigenasas/química , Sitios de Unión , Catálisis , Dioxigenasas/metabolismo , Transporte de Electrón , Modelos Químicos , Simulación de Dinámica Molecular , Proteínas de Hierro no Heme/metabolismo , Oxigenasas/metabolismo , Pseudomonas/enzimología
SELECCIÓN DE REFERENCIAS
DETALLE DE LA BÚSQUEDA
...