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1.
Nature ; 574(7780): 722-725, 2019 10.
Artículo en Inglés | MEDLINE | ID: mdl-31645759

RESUMEN

The enzyme protochlorophyllide oxidoreductase (POR) catalyses a light-dependent step in chlorophyll biosynthesis that is essential to photosynthesis and, ultimately, all life on Earth1-3. POR, which is one of three known light-dependent enzymes4,5, catalyses reduction of the photosensitizer and substrate protochlorophyllide to form the pigment chlorophyllide. Despite its biological importance, the structural basis for POR photocatalysis has remained unknown. Here we report crystal structures of cyanobacterial PORs from Thermosynechococcus elongatus and Synechocystis sp. in their free forms, and in complex with the nicotinamide coenzyme. Our structural models and simulations of the ternary protochlorophyllide-NADPH-POR complex identify multiple interactions in the POR active site that are important for protochlorophyllide binding, photosensitization and photochemical conversion to chlorophyllide. We demonstrate the importance of active-site architecture and protochlorophyllide structure in driving POR photochemistry in experiments using POR variants and protochlorophyllide analogues. These studies reveal how the POR active site facilitates light-driven reduction of protochlorophyllide by localized hydride transfer from NADPH and long-range proton transfer along structurally defined proton-transfer pathways.


Asunto(s)
Clorofila/biosíntesis , Oxidorreductasas actuantes sobre Donantes de Grupo CH-CH/química , Oxidorreductasas actuantes sobre Donantes de Grupo CH-CH/metabolismo , Synechococcus/enzimología , Synechocystis/enzimología , Catálisis , Clorofila/química , Estructura Molecular , Fotoquímica , Protoclorofilida/metabolismo , Relación Estructura-Actividad , Especificidad por Sustrato
2.
Proc Natl Acad Sci U S A ; 119(30): e2205664119, 2022 07 26.
Artículo en Inglés | MEDLINE | ID: mdl-35862453

RESUMEN

Many enzymes utilize redox-coupled centers for performing catalysis where these centers are used to control and regulate the transfer of electrons required for catalysis, whose untimely delivery can lead to a state incapable of binding the substrate, i.e., a dead-end enzyme. Copper nitrite reductases (CuNiRs), which catalyze the reduction of nitrite to nitric oxide (NO), have proven to be a good model system for studying these complex processes including proton-coupled electron transfer (ET) and their orchestration for substrate binding/utilization. Recently, a two-domain CuNiR from a Rhizobia species (Br2DNiR) has been discovered with a substantially lower enzymatic activity where the catalytic type-2 Cu (T2Cu) site is occupied by two water molecules requiring their displacement for the substrate nitrite to bind. Single crystal spectroscopy combined with MSOX (multiple structures from one crystal) for both the as-isolated and nitrite-soaked crystals clearly demonstrate that inter-Cu ET within the coupled T1Cu-T2Cu redox system is heavily gated. Laser-flash photolysis and optical spectroscopy showed rapid ET from photoexcited NADH to the T1Cu center but little or no inter-Cu ET in the absence of nitrite. Furthermore, incomplete reoxidation of the T1Cu site (∼20% electrons transferred) was observed in the presence of nitrite, consistent with a slow formation of NO species in the serial structures of the MSOX movie obtained from the nitrite-soaked crystal, which is likely to be responsible for the lower activity of this CuNiR. Our approach is of direct relevance for studying redox reactions in a wide range of biological systems including metalloproteins that make up at least 30% of all proteins.


Asunto(s)
Cobre , Nitrito Reductasas , Nitritos , Catálisis , Cobre/química , Nitrito Reductasas/química , Nitritos/química , Oxidación-Reducción , Análisis Espectral
3.
Metab Eng ; 82: 238-249, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38401747

RESUMEN

Ectoine, a crucial osmoprotectant for salt adaptation in halophiles, has gained growing interest in cosmetics and medical industries. However, its production remains challenged by stringent fermentation process in model microorganisms and low production level in its native producers. Here, we systematically engineered the native ectoine producer Halomonas bluephagenesis for ectoine production by overexpressing ectABC operon, increasing precursors availability, enhancing product transport system and optimizing its growth medium. The final engineered H. bluephagenesis produced 85 g/L ectoine in 52 h under open unsterile incubation in a 7 L bioreactor in the absence of plasmid, antibiotic or inducer. Furthermore, it was successfully demonstrated the feasibility of decoupling salt concentration with ectoine synthesis and co-production with bioplastic P(3HB-co-4HB) by the engineered H. bluephagenesis. The unsterile fermentation process and significantly increased ectoine titer indicate that H. bluephagenesis as the chassis of Next-Generation Industrial Biotechnology (NGIB), is promising for the biomanufacturing of not only intracellular bioplastic PHA but also small molecular compound such as ectoine.


Asunto(s)
Aminoácidos Diaminos , Halomonas , Halomonas/genética , Aminoácidos Diaminos/genética , Antibacterianos , Biopolímeros
4.
Metab Eng ; 84: 95-108, 2024 Jun 18.
Artículo en Inglés | MEDLINE | ID: mdl-38901556

RESUMEN

Microbial instability is a common problem during bio-production based on microbial hosts. Halomonas bluephagenesis has been developed as a chassis for next generation industrial biotechnology (NGIB) under open and unsterile conditions. However, the hidden genomic information and peculiar metabolism have significantly hampered its deep exploitation for cell-factory engineering. Based on the freshly completed genome sequence of H. bluephagenesis TD01, which reveals 1889 biological process-associated genes grouped into 84 GO-slim terms. An enzyme constrained genome-scale metabolic model Halo-ecGEM was constructed, which showed strong ability to simulate fed-batch fermentations. A visible salt-stress responsive landscape was achieved by combining GO-slim term enrichment and CVT-based omics profiling, demonstrating that cells deploy most of the protein resources by force to support the essential activity of translation and protein metabolism when exposed to salt stress. Under the guidance of Halo-ecGEM, eight transposases were deleted, leading to a significantly enhanced stability for its growth and bioproduction of various polyhydroxyalkanoates (PHA) including 3-hydroxybutyrate (3HB) homopolymer PHB, 3HB and 3-hydroxyvalerate (3HV) copolymer PHBV, as well as 3HB and 4-hydroxyvalerate (4HB) copolymer P34HB. This study sheds new light on the metabolic characteristics and stress-response landscape of H. bluephagenesis, achieving for the first time to construct a long-term growth stable chassis for industrial applications. For the first time, it was demonstrated that genome encoded transposons are the reason for microbial instability during growth in flasks and fermentors.

5.
J Am Chem Soc ; 145(37): 20672-20682, 2023 09 20.
Artículo en Inglés | MEDLINE | ID: mdl-37688545

RESUMEN

Oxygenase and peroxygenase enzymes generate intermediates at their active sites which bring about the controlled functionalization of inert C-H bonds in substrates, such as in the enzymatic conversion of methane to methanol. To be viable catalysts, however, these enzymes must also prevent oxidative damage to essential active site residues, which can occur during both coupled and uncoupled turnover. Herein, we use a combination of stopped-flow spectroscopy, targeted mutagenesis, TD-DFT calculations, high-energy resolution fluorescence detection X-ray absorption spectroscopy, and electron paramagnetic resonance spectroscopy to study two transient intermediates that together form a protective pathway built into the active sites of copper-dependent lytic polysaccharide monooxygenases (LPMOs). First, a transient high-valent species is generated at the copper histidine brace active site following treatment of the LPMO with either hydrogen peroxide or peroxyacids in the absence of substrate. This intermediate, which we propose to be a CuII-(histidyl radical), then reacts with a nearby tyrosine residue in an intersystem-crossing reaction to give a ferromagnetically coupled (S = 1) CuII-tyrosyl radical pair, thereby restoring the histidine brace active site to its resting state and allowing it to re-enter the catalytic cycle through reduction. This process gives the enzyme the capacity to minimize damage to the active site histidine residues "on the fly" to increase the total turnover number prior to enzyme deactivation, highlighting how oxidative enzymes are evolved to protect themselves from deleterious side reactions during uncoupled turnover.


Asunto(s)
Cobre , Histidina , Oxigenasas de Función Mixta , Estrés Oxidativo , Catálisis
6.
Crit Rev Biotechnol ; : 1-18, 2023 Nov 06.
Artículo en Inglés | MEDLINE | ID: mdl-37932016

RESUMEN

The circular economy is anticipated to bring a disruptive transformation in manufacturing technologies. Robust and industrial scalable microbial strains that can simultaneously assimilate and valorize multiple carbon substrates are highly desirable, as waste bioresources contain substantial amounts of renewable and fermentable carbon, which is diverse. Lignocellulosic biomass (LCB) is identified as an inexhaustible and alternative resource to reduce global dependence on oil. Glucose, xylose, and arabinose are the major monomeric sugars in LCB. However, primary research has focused on the use of glucose. On the other hand, the valorization of pentose sugars, xylose, and arabinose, has been mainly overlooked, despite possible assimilation by vast microbial communities. The present review highlights the research efforts that have explicitly proven the suitability of arabinose as the starting feedstock for producing various chemical building blocks via biological routes. It begins by analyzing the availability of various arabinose-rich biorenewable sources that can serve as potential feedstocks for biorefineries. The subsequent section outlines the current understanding of arabinose metabolism, biochemical routes prevalent in prokaryotic and eukaryotic systems, and possible products that can be derived from this sugar. Further, currently, exemplar products from arabinose, including arabitol, 2,3-butanediol, 1,2,3-butanetriol, ethanol, lactic acid, and xylitol are discussed, which have been produced by native and non-native microbial strains using metabolic engineering and genome editing tools. The final section deals with the challenges and obstacles associated with arabinose-based production, followed by concluding remarks and prospects.

7.
Biochemistry ; 61(17): 1735-1742, 2022 09 06.
Artículo en Inglés | MEDLINE | ID: mdl-35979922

RESUMEN

Calmodulin (CaM) is a highly dynamic Ca2+-binding protein that exhibits large conformational changes upon binding Ca2+ and target proteins. Although it is accepted that CaM exists in an equilibrium of conformational states in the absence of target protein, the physiological relevance of an elongated helical linker region in the Ca2+-replete form has been highly debated. In this study, we use PELDOR (pulsed electron-electron double resonance) EPR measurements of a doubly spin-labeled CaM variant to assess the conformational states of CaM in the apo-, Ca2+-bound, and Ca2+ plus target peptide-bound states. Our findings are consistent with a three-state conformational model of CaM, showing a semi-open apo-state, a highly extended Ca2+-replete state, and a compact target protein-bound state. Molecular dynamics simulations suggest that the presence of glycerol, and potentially other molecular crowding agents, has a profound effect on the relative stability of the different conformational states. Differing experimental conditions may explain the discrepancies in the literature regarding the observed conformational state(s) of CaM, and our PELDOR measurements show good evidence for an extended conformation of Ca2+-replete CaM similar to the one observed in early X-ray crystal structures.


Asunto(s)
Calmodulina , Simulación de Dinámica Molecular , Calcio/metabolismo , Calmodulina/química , Electrones , Unión Proteica , Conformación Proteica , Marcadores de Spin
8.
Nat Prod Rep ; 39(1): 90-118, 2022 01 26.
Artículo en Inglés | MEDLINE | ID: mdl-34231643

RESUMEN

Covering: up to 2021Terpenoids are a diverse group of chemicals used in a wide range of industries. Microbial terpenoid production has the potential to displace traditional manufacturing of these compounds with renewable processes, but further titre improvements are needed to reach cost competitiveness. This review discusses strategies to increase terpenoid titres in Escherichia coli with a focus on alternative metabolic pathways. Alternative pathways can lead to improved titres by providing higher orthogonality to native metabolism that redirects carbon flux, by avoiding toxic intermediates, by bypassing highly-regulated or bottleneck steps, or by being shorter and thus more efficient and easier to manipulate. The canonical 2-C-methyl-D-erythritol 4-phosphate (MEP) and mevalonate (MVA) pathways are engineered to increase titres, sometimes using homologs from different species to address bottlenecks. Further, alternative terpenoid pathways, including additional entry points into the MEP and MVA pathways, archaeal MVA pathways, and new artificial pathways provide new tools to increase titres. Prenyl diphosphate synthases elongate terpenoid chains, and alternative homologs create orthogonal pathways and increase product diversity. Alternative sources of terpenoid synthases and modifying enzymes can also be better suited for E. coli expression. Mining the growing number of bacterial genomes for new bacterial terpenoid synthases and modifying enzymes identifies enzymes that outperform eukaryotic ones and expand microbial terpenoid production diversity. Terpenoid removal from cells is also crucial in production, and so terpenoid recovery and approaches to handle end-product toxicity increase titres. Combined, these strategies are contributing to current efforts to increase microbial terpenoid production towards commercial feasibility.


Asunto(s)
Escherichia coli/metabolismo , Ingeniería Metabólica , Redes y Vías Metabólicas , Terpenos/metabolismo , Ingeniería Metabólica/métodos
9.
Chembiochem ; 23(5): e202100484, 2022 03 04.
Artículo en Inglés | MEDLINE | ID: mdl-34669250

RESUMEN

Terpenoids are a highly diverse group of natural products with considerable industrial interest. Increasingly, engineered microbes are used for the production of terpenoids to replace natural extracts and chemical synthesis. Terpene synthases (TSs) show a high level of functional plasticity and are responsible for the vast structural diversity observed in natural terpenoids. Their relatively inert active sites guide intrinsically reactive linear carbocation intermediates along one of many cyclisation paths via exertion of subtle steric and electrostatic control. Due to the absence of a strong protein interaction with these intermediates, there is a remarkable lack of sequence-function relationship within the TS family, making product-outcome predictions from sequences alone challenging. This, in combination with the fact that many TSs produce multiple products from a single substrate hampers the design and use of TSs in the biomanufacturing of terpenoids. This review highlights recent advances in genome mining, computational modelling, high-throughput screening, and machine-learning that will allow more predictive engineering of these fascinating enzymes in the near future.


Asunto(s)
Transferasas Alquil y Aril , Transferasas Alquil y Aril/genética , Transferasas Alquil y Aril/metabolismo , Dominio Catalítico , Ciclización , Terpenos/metabolismo
10.
Chembiochem ; 23(5): e202100688, 2022 03 04.
Artículo en Inglés | MEDLINE | ID: mdl-35005823

RESUMEN

Monoterpene synthases are often promiscuous enzymes, yielding product mixtures rather than pure compounds due to the nature of the branched reaction mechanism involving reactive carbocations. Two previously identified bacterial monoterpene synthases, a linalool synthase (bLinS) and a cineole synthase (bCinS), produce nearly pure linalool and cineole from geranyl diphosphate, respectively. We used a combined experimental and computational approach to identify critical residues involved in bacterial monoterpenoid synthesis. Phe77 is essential for bCinS activity, guiding the linear carbocation intermediate towards the formation of the cyclic α-terpinyl intermediate; removal of the aromatic ring results in variants that produce acyclic products only. Computational chemistry confirmed the importance of Phe77 in carbocation stabilisation. Phe74, Phe78 and Phe179 are involved in maintaining the active site shape in bCinS without a specific role for the aromatic ring. Phe295 in bLinS, and the equivalent Ala301 in bCinS, are essential for linalool and cineole formation, respectively. Where Phe295 places steric constraints on the carbocation intermediates, Ala301 is essential for bCinS initial cyclisation and activity. Our multidisciplinary approach gives unique insights into how carefully placed amino acid residues in the active site can direct carbocations down specific paths, by placing steric constraints or offering stabilisation via cation-π interactions.


Asunto(s)
Eucaliptol , Dominio Catalítico , Ciclización
11.
Nature ; 539(7630): 593-597, 2016 11 24.
Artículo en Inglés | MEDLINE | ID: mdl-27851736

RESUMEN

The universal Per-ARNT-Sim (PAS) domain functions as a signal transduction module involved in sensing diverse stimuli such as small molecules, light, redox state and gases. The highly evolvable PAS scaffold can bind a broad range of ligands, including haem, flavins and metal ions. However, although these ligands can support catalytic activity, to our knowledge no enzymatic PAS domain has been found. Here we report characterization of the first PAS enzyme: a haem-dependent oxidative N-demethylase. Unrelated to other amine oxidases, this enzyme contains haem, flavin mononucleotide, 2Fe-2S and tetrahydrofolic acid cofactors, and specifically catalyses the NADPH-dependent oxidation of dimethylamine. The structure of the α subunit reveals that it is a haem-binding PAS domain, similar in structure to PAS gas sensors. The dimethylamine substrate forms part of a highly polarized oxygen-binding site, and directly assists oxygen activation by acting as both an electron and proton donor. Our data reveal that the ubiquitous PAS domain can make the transition from sensor to enzyme, suggesting that the PAS scaffold can support the development of artificial enzymes.


Asunto(s)
Oxidorreductasas N-Desmetilantes/química , Oxidorreductasas N-Desmetilantes/metabolismo , Pseudomonas mendocina/enzimología , Sitios de Unión , Coenzimas/metabolismo , Cristalografía por Rayos X , Dimetilaminas/metabolismo , Mononucleótido de Flavina/metabolismo , Hemo/metabolismo , Proteínas Hierro-Azufre/química , Proteínas Hierro-Azufre/metabolismo , Modelos Moleculares , NADP/metabolismo , Oxidación-Reducción , Oxígeno/metabolismo , Dominios Proteicos , Subunidades de Proteína/química , Subunidades de Proteína/metabolismo , Tetrahidrofolatos/metabolismo
12.
Biochem J ; 478(18): 3423-3428, 2021 09 30.
Artículo en Inglés | MEDLINE | ID: mdl-34554213

RESUMEN

Nitroreductases catalyse the NAD(P)H-dependent nitro reduction in nitrofuran antibiotics, which activates them into cytotoxic molecules leading to cell death. The design of new effective nitrofuran antibiotics relies on knowledge of the kinetic mechanism and nitrofuran binding mode of microbial nitroreductases NfsA and NfsB. This has been hampered by multiple co-crystallisation studies revealing ligand binding in non-electron transfer competent states. In a recent study by Day et al. (2021) the authors investigated the likely reaction mechanism and mode of nitrofurantoin binding to NfsA using potentiometry, global kinetics analysis, crystallography and molecular dynamics simulations. Their findings suggest nitrofurantoin reduction proceeds via a direct hydride transfer from reduced FMN, while the crystallographic binding orientation is an inhibitory complex. Molecular dynamics simulations suggest ligand binding orientations is dependent on the oxidation state of the FMN. This study highlights the importance of utilising computational studies alongside traditional crystallographic approaches, when multiple stable ligand binding orientations can occur.


Asunto(s)
Antibacterianos , Nitrofuranos , Escherichia coli/metabolismo , Flavinas , Cinética , Nitrorreductasas/metabolismo , Oxidación-Reducción
13.
Chembiochem ; 22(13): 2325-2334, 2021 07 01.
Artículo en Inglés | MEDLINE | ID: mdl-33938632

RESUMEN

Linalool is a monoterpenoid used as a fragrance ingredient, and is a promising source for alternative fuels. Synthetic biology offers attractive alternative production methods compared to extraction from natural sources and chemical synthesis. Linalool/nerolidol synthase (bLinS) from Streptomyces clavuligerus is a bifunctional enzyme, producing linalool as well as the sesquiterpenoid nerolidol when expressed in engineered Escherichia coli harbouring a precursor terpenoid pathway such as the mevalonate (MVA) pathway. Here we identified two residues important for substrate selection by bLinS, L72 and V214, where the introduction of bulkier residues results in variants with reduced nerolidol formation. Terpenoid production using canonical precursor pathways is usually limited by numerous and highly regulated enzymatic steps. Here we compared the canonical MVA pathway to the non-canonical isopentenol utilization (IU) pathway to produce linalool using the optimised bLinS variant. The IU pathway uses isoprenol and prenol to produce linalool in only five steps. Adjusting substrate, plasmid system, inducer concentration, and cell strain directs the flux towards monoterpenoids. Our integrated approach, combining enzyme engineering with flux control using the artificial IU pathway, resulted in high purity production of the commercially attractive monoterpenoid linalool, and will guide future efforts towards efficient optimisation of terpenoid production in engineered microbes.


Asunto(s)
Monoterpenos Acíclicos/química , Pentanoles/química , Sesquiterpenos/metabolismo , Transferasas/metabolismo , Monoterpenos Acíclicos/metabolismo , Secuencia de Aminoácidos , Escherichia coli/genética , Hemiterpenos/metabolismo , Ácido Mevalónico/metabolismo , Pentanoles/metabolismo , Conformación Proteica , Ingeniería de Proteínas , Transducción de Señal , Streptomyces/enzimología , Terpenos/metabolismo , Transferasas/genética
14.
Biochem Soc Trans ; 49(3): 1055-1063, 2021 06 30.
Artículo en Inglés | MEDLINE | ID: mdl-34100907

RESUMEN

Metabolic engineering technologies have been employed with increasing success over the last three decades for the engineering and optimization of industrial host strains to competitively produce high-value chemical targets. To this end, continued reductions in the time taken from concept, to development, to scale-up are essential. Design-Build-Test-Learn pipelines that are able to rapidly deliver diverse chemical targets through iterative optimization of microbial production strains have been established. Biofoundries are employing in silico tools for the design of genetic parts, alongside combinatorial design of experiments approaches to optimize selection from within the potential design space of biological circuits based on multi-criteria objectives. These genetic constructs can then be built and tested through automated laboratory workflows, with performance data analysed in the learn phase to inform further design. Successful examples of rapid prototyping processes for microbially produced compounds reveal the potential role of biofoundries in leading the sustainable production of next-generation bio-based chemicals.


Asunto(s)
Bacterias/genética , Productos Biológicos/metabolismo , Microbiología Industrial/métodos , Ingeniería Metabólica/métodos , Redes y Vías Metabólicas/genética , Biología Sintética/métodos , Bacterias/metabolismo , Biotecnología/métodos , Escherichia coli/genética , Escherichia coli/metabolismo , Regulación de la Expresión Génica , Plásmidos/genética , Plásmidos/metabolismo
15.
Arch Biochem Biophys ; 697: 108702, 2021 01 15.
Artículo en Inglés | MEDLINE | ID: mdl-33275878

RESUMEN

Kynurenine-3-monooxygenase (KMO) is an important therapeutic target for several brain disorders that has been extensively studied in recent years. Potent inhibitors towards KMO have been developed and tested within different disease models, showing great therapeutic potential, especially in models of neurodegenerative disease. The inhibition of KMO reduces the production of downstream toxic kynurenine pathway metabolites and shifts the flux to the formation of the neuroprotectant kynurenic acid. However, the efficacy of KMO inhibitors in neurodegenerative disease has been limited by their poor brain permeability. Combined with virtual screening and prodrug strategies, a novel brain penetrating KMO inhibitor has been developed which dramatically decreases neurotoxic metabolites. This review highlights the importance of KMO as a drug target in neurological disease and the benefits of brain permeable inhibitors in modulating kynurenine pathway metabolites in the central nervous system.


Asunto(s)
Encéfalo/metabolismo , Inhibidores Enzimáticos/metabolismo , Inhibidores Enzimáticos/farmacología , Quinurenina 3-Monooxigenasa/antagonistas & inhibidores , Enfermedades Neurodegenerativas/tratamiento farmacológico , Animales , Encéfalo/efectos de los fármacos , Descubrimiento de Drogas , Inhibidores Enzimáticos/uso terapéutico , Humanos , Enfermedades Neurodegenerativas/enzimología , Enfermedades Neurodegenerativas/metabolismo
16.
Nature ; 522(7557): 502-6, 2015 Jun 25.
Artículo en Inglés | MEDLINE | ID: mdl-26083743

RESUMEN

Ubiquinone (also known as coenzyme Q) is a ubiquitous lipid-soluble redox cofactor that is an essential component of electron transfer chains. Eleven genes have been implicated in bacterial ubiquinone biosynthesis, including ubiX and ubiD, which are responsible for decarboxylation of the 3-octaprenyl-4-hydroxybenzoate precursor. Despite structural and biochemical characterization of UbiX as a flavin mononucleotide (FMN)-binding protein, no decarboxylase activity has been detected. Here we report that UbiX produces a novel flavin-derived cofactor required for the decarboxylase activity of UbiD. UbiX acts as a flavin prenyltransferase, linking a dimethylallyl moiety to the flavin N5 and C6 atoms. This adds a fourth non-aromatic ring to the flavin isoalloxazine group. In contrast to other prenyltransferases, UbiX is metal-independent and requires dimethylallyl-monophosphate as substrate. Kinetic crystallography reveals that the prenyltransferase mechanism of UbiX resembles that of the terpene synthases. The active site environment is dominated by π systems, which assist phosphate-C1' bond breakage following FMN reduction, leading to formation of the N5-C1' bond. UbiX then acts as a chaperone for adduct reorientation, via transient carbocation species, leading ultimately to formation of the dimethylallyl C3'-C6 bond. Our findings establish the mechanism for formation of a new flavin-derived cofactor, extending both flavin and terpenoid biochemical repertoires.


Asunto(s)
Biocatálisis , Carboxiliasas/metabolismo , Dimetilaliltranstransferasa/metabolismo , Flavinas/metabolismo , Pseudomonas aeruginosa/enzimología , Pseudomonas aeruginosa/metabolismo , Ubiquinona/biosíntesis , Transferasas Alquil y Aril/química , Transferasas Alquil y Aril/metabolismo , Aspergillus niger/enzimología , Aspergillus niger/genética , Carboxiliasas/química , Carboxiliasas/genética , Dominio Catalítico , Cristalografía por Rayos X , Reacción de Cicloadición , Descarboxilación , Dimetilaliltranstransferasa/química , Dimetilaliltranstransferasa/genética , Transporte de Electrón , Mononucleótido de Flavina/metabolismo , Flavinas/biosíntesis , Flavinas/química , Modelos Moleculares , Pseudomonas aeruginosa/genética
17.
Nature ; 522(7557): 497-501, 2015 Jun 25.
Artículo en Inglés | MEDLINE | ID: mdl-26083754

RESUMEN

The bacterial ubiD and ubiX or the homologous fungal fdc1 and pad1 genes have been implicated in the non-oxidative reversible decarboxylation of aromatic substrates, and play a pivotal role in bacterial ubiquinone (also known as coenzyme Q) biosynthesis or microbial biodegradation of aromatic compounds, respectively. Despite biochemical studies on individual gene products, the composition and cofactor requirement of the enzyme responsible for in vivo decarboxylase activity remained unclear. Here we show that Fdc1 is solely responsible for the reversible decarboxylase activity, and that it requires a new type of cofactor: a prenylated flavin synthesized by the associated UbiX/Pad1. Atomic resolution crystal structures reveal that two distinct isomers of the oxidized cofactor can be observed, an isoalloxazine N5-iminium adduct and a N5 secondary ketimine species with markedly altered ring structure, both having azomethine ylide character. Substrate binding positions the dipolarophile enoic acid group directly above the azomethine ylide group. The structure of a covalent inhibitor-cofactor adduct suggests that 1,3-dipolar cycloaddition chemistry supports reversible decarboxylation in these enzymes. Although 1,3-dipolar cycloaddition is commonly used in organic chemistry, we propose that this presents the first example, to our knowledge, of an enzymatic 1,3-dipolar cycloaddition reaction. Our model for Fdc1/UbiD catalysis offers new routes in alkene hydrocarbon production or aryl (de)carboxylation.


Asunto(s)
Biocatálisis , Carboxiliasas/metabolismo , Reacción de Cicloadición , Alquenos/química , Alquenos/metabolismo , Aspergillus niger/enzimología , Aspergillus niger/genética , Carboxiliasas/química , Carboxiliasas/genética , Cristalografía por Rayos X , Descarboxilación , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Flavinas/biosíntesis , Flavinas/química , Flavinas/metabolismo , Isomerismo , Ligandos , Modelos Moleculares , Ubiquinona/biosíntesis
18.
Biochemistry ; 59(32): 2909-2915, 2020 08 18.
Artículo en Inglés | MEDLINE | ID: mdl-32786403

RESUMEN

Due to the recent advances in X-ray free electron laser techniques, bilin-containing cyanobacteriochrome photoreceptors have become prime targets for the ever-expanding field of time-resolved structural biology. However, to facilitate these challenging studies, it is essential that the time scales of any structural changes during the photocycles of cyanobacteriochromes be established. Here, we have used visible and infrared transient absorption spectroscopy to probe the photocycle of a model cyanobacteriochrome system, TePixJ. The kinetics span multiple orders of magnitude from picoseconds to seconds. Localized changes in the bilin binding pocket occur in picoseconds to nanoseconds, followed by more large-scale changes in protein structure, including formation and breakage of a second thioether linkage, in microseconds to milliseconds. The characterization of the entire photocycle will provide a vital frame of reference for future time-resolved structural studies of this model photoreceptor.


Asunto(s)
Proteínas Bacterianas/metabolismo , Cianobacterias/metabolismo , Cianobacterias/efectos de la radiación , Luz , Proteínas Bacterianas/química , Cinética , Modelos Moleculares , Conformación Proteica
19.
J Am Chem Soc ; 142(37): 15764-15779, 2020 09 16.
Artículo en Inglés | MEDLINE | ID: mdl-32811149

RESUMEN

The cytochromes P450 are heme-dependent enzymes that catalyze many vital reaction processes in the human body related to biodegradation and biosynthesis. They typically act as mono-oxygenases; however, the recently discovered P450 subfamily TxtE utilizes O2 and NO to nitrate aromatic substrates such as L-tryptophan. A direct and selective aromatic nitration reaction may be useful in biotechnology for the synthesis of drugs or small molecules. Details of the catalytic mechanism are unknown, and it has been suggested that the reaction should proceed through either an iron(III)-superoxo or an iron(II)-nitrosyl intermediate. To resolve this controversy, we used stopped-flow kinetics to provide evidence for a catalytic cycle where dioxygen binds prior to NO to generate an active iron(III)-peroxynitrite species that is able to nitrate l-Trp efficiently. We show that the rate of binding of O2 is faster than that of NO and also leads to l-Trp nitration, while little evidence of product formation is observed from the iron(II)-nitrosyl complex. To support the experimental studies, we performed density functional theory studies on large active site cluster models. The studies suggest a mechanism involving an iron(III)-peroxynitrite that splits homolytically to form an iron(IV)-oxo heme (Compound II) and a free NO2 radical via a small free energy of activation. The latter activates the substrate on the aromatic ring, while compound II picks up the ipso-hydrogen to form the product. The calculations give small reaction barriers for most steps in the catalytic cycle and, therefore, predict fast product formation from the iron(III)-peroxynitrite complex. These findings provide the first detailed insight into the mechanism of nitration by a member of the TxtE subfamily and highlight how the enzyme facilitates this novel reaction chemistry.


Asunto(s)
Sistema Enzimático del Citocromo P-450/metabolismo , Compuestos Férricos/metabolismo , Nitrocompuestos/metabolismo , Ácido Peroxinitroso/metabolismo , Biocatálisis , Teoría Funcional de la Densidad , Compuestos Férricos/química , Modelos Moleculares , Conformación Molecular , Nitrocompuestos/química , Ácido Peroxinitroso/química
20.
Chembiochem ; 21(7): 985-990, 2020 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-31682055

RESUMEN

Monoterpenoids are industrially important natural products with applications in the flavours, fragrances, fuels and pharmaceutical industries. Most monoterpenoids are produced by plants, but recently two bacterial monoterpene synthases have been identified, including a cineole synthase (bCinS). Unlike plant cineole synthases, bCinS is capable of producing nearly pure cineole from geranyl diphosphate in a complex cyclisation cascade that is tightly controlled. Here we have used a multidisciplinary approach to show that Asn305 controls water attack on the α-terpinyl cation and subsequent cyclisation and deprotonation of the α-terpineol intermediate, key steps in the cyclisation cascade which direct product formation towards cineole. Mutation of Asn305 results in variants that no longer produce α-terpineol or cineole. Molecular dynamics simulations revealed that water coordination is disrupted in all variants tested. Quantum mechanics calculations indicate that Asn305 is most likely a (transient) proton acceptor for the final deprotonation step. Our synergistic approach gives unique insight into how a single residue, Asn305, tames the promiscuous chemistry of monoterpene synthase cyclisation cascades. It does this by tightly controlling the final steps in cineole formation catalysed by bCinS to form a single hydroxylated monoterpene product.


Asunto(s)
Liasas Intramoleculares/metabolismo , Monoterpenos/metabolismo , Sitios de Unión , Dominio Catalítico , Ciclización , Monoterpenos Ciclohexánicos/química , Monoterpenos Ciclohexánicos/metabolismo , Eucaliptol/química , Eucaliptol/metabolismo , Hidroxilación , Liasas Intramoleculares/genética , Simulación de Dinámica Molecular , Monoterpenos/química , Mutagénesis Sitio-Dirigida , Estereoisomerismo , Streptomyces/enzimología , Agua/química , Agua/metabolismo
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