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1.
Microb Cell Fact ; 20(1): 15, 2021 Jan 19.
Artículo en Inglés | MEDLINE | ID: mdl-33468127

RESUMEN

Genetic modification of Rhodococcus jostii RHA1 was carried out in order to optimise the production of pyridine-2,4-dicarboxylic acid and pyridine-2,5-dicarboxylic acid bioproducts from lignin or lignocellulose breakdown, via insertion of either the Sphingobium SYK-6 ligAB genes or Paenibacillus praA gene respectively. Insertion of inducible plasmid pTipQC2 expression vector containing either ligAB or praA genes into a ΔpcaHG R. jostii RHA1 gene deletion strain gave 2-threefold higher titres of PDCA production from lignocellulose (200-287 mg/L), compared to plasmid expression in wild-type R. jostii RHA1. The ligAB genes were inserted in place of the chromosomal pcaHG genes encoding protocatechuate 3,4-dioxygenase, under the control of inducible Picl or PnitA promoters, or a constitutive Ptpc5 promoter, producing 2,4-PDCA products using either wheat straw lignocellulose or commercial soda lignin as carbon source. Insertion of Amycolatopsis sp. 75iv2 dyp2 gene on a pTipQC2 expression plasmid led to enhanced titres of 2,4-PDCA products, due to enhanced rate of lignin degradation. Growth in minimal media containing wheat straw lignocellulose led to the production of 2,4-PDCA in 330 mg/L titre in 40 h, with > tenfold enhanced productivity, compared with plasmid-based expression of ligAB genes in wild-type R. jostii RHA1. Production of 2,4-PDCA was also observed using several different polymeric lignins as carbon sources, and a titre of 240 mg/L was observed using a commercially available soda lignin as feedstock.


Asunto(s)
Ácidos Dicarboxílicos/metabolismo , Lignina/metabolismo , Ingeniería Metabólica/métodos , Piridinas/metabolismo , Rhodococcus/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Carbono/metabolismo , Eliminación de Gen , Regulación Bacteriana de la Expresión Génica , Redes y Vías Metabólicas/genética , Familia de Multigenes/genética , Regiones Promotoras Genéticas/genética , Protocatecuato-3,4-Dioxigenasa/genética , Protocatecuato-3,4-Dioxigenasa/metabolismo , Rhodococcus/genética
2.
J Vis Exp ; (153)2019 11 08.
Artículo en Inglés | MEDLINE | ID: mdl-31762446

RESUMEN

Single molecule (SM) microscopy is used in the study of dynamic molecular interactions of fluorophore labeled biomolecules in real time. However, fluorophores are prone to loss of signal via photobleaching by dissolved oxygen (O2). To prevent photobleaching and extend the fluorophore lifetime, oxygen scavenging systems (OSS) are employed to reduce O2. Commercially available OSS may be contaminated by nucleases that damage or degrade nucleic acids, confounding interpretation of experimental results. Here we detail a protocol for the expression and purification of highly active Pseudomonas putida protocatechuate-3,4-dioxygenase (PCD) with no detectable nuclease contamination. PCD can efficiently remove reactive O2 species by conversion of the substrate protocatechuic acid (PCA) to 3-carboxy-cis,cis-muconic acid. This method can be used in any aqueous system where O2 plays a detrimental role in data acquisition. This method is effective in producing highly active, nuclease free PCD in comparison with commercially available PCD.


Asunto(s)
Oxígeno/metabolismo , Protocatecuato-3,4-Dioxigenasa/aislamiento & purificación , Protocatecuato-3,4-Dioxigenasa/metabolismo , Fotoblanqueo , Pseudomonas putida/enzimología , Especificidad por Sustrato
3.
BMC Res Notes ; 10(1): 606, 2017 Nov 21.
Artículo en Inglés | MEDLINE | ID: mdl-29162131

RESUMEN

OBJECTIVE: Oxygen scavenging systems are routinely used during single-molecule imaging experiments to improve fluorescent dye stability. Previous work has shown nuclease contamination in the commonly used oxygen scavenging systems. This study evaluates the potential for nuclease contamination in these oxygen scavenging systems. RESULTS: Linear and plasmid DNA was incubated with two different oxygen scavenging systems (1) protocatechuic acid (PCA)-protocatechuate-3,4-dioxygenase (PCD) and (2) glucose-coupled glucose oxidase/catalase (GODCAT). No nucleic acid degradation was observed on single and double-stranded linear DNA and plasmid DNA, indicating the absence of nuclease contamination in these oxygen scavenging systems.


Asunto(s)
Desoxirribonucleasas/análisis , Catalasa/metabolismo , Cromatografía en Gel , ADN/metabolismo , Glucosa Oxidasa/metabolismo , Hidroxibenzoatos/metabolismo , Indicadores y Reactivos , Oxígeno/metabolismo , Plásmidos/metabolismo , Protocatecuato-3,4-Dioxigenasa/metabolismo , Especies Reactivas de Oxígeno/metabolismo
4.
Appl Biochem Biotechnol ; 183(3): 1035-1048, 2017 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-28516418

RESUMEN

Protocatechuate 3,4-dioxygenase (P34O), which is isolated from Rhizobium sp. LMB-1, catalyzes the ring cleavage step in the metabolism of aromatic compounds, and has great potential for environmental bioremediation. However, its structure is very sensitive to different environmental factors, which weaken its activity. Immobilization of the enzyme can improve its stability, allow reusability, and reduce operation costs. In this work, the relative molecular mass of the native P34O enzyme was determined to be 500 kDa by gel filtration chromatography on Sephadex G-200, and the enzyme was immobilized onto (3-aminopropyl) triethoxysilane-modified Fe3O4 nanoparticles (NPs) by the glutaraldehyde method. The optimum pH of immobilized and free P34O was unaffected, but the optimum temperature of immobilized P34O increased from 60 to 70 °C, and the thermal stability of immobilized P34O was better than that of the free enzyme and showed higher enzymatic activity at 60 and 70 °C. In addition, with the exception of Fe3+, most metal ions and organic chemicals could not improve the activity of free and immobilized P34O. The kinetic parameters of the immobilized P34O were higher than those of the free enzyme, and immobilized P34O on Fe3O4 NPs could be reused ten times without a remarkable decrease in enzymatic activity.


Asunto(s)
Enzimas Inmovilizadas/química , Enzimas Inmovilizadas/metabolismo , Nanopartículas de Magnetita/química , Protocatecuato-3,4-Dioxigenasa/química , Protocatecuato-3,4-Dioxigenasa/metabolismo , Rhizobium/enzimología , Alcoholes/farmacología , Estabilidad de Enzimas , Concentración de Iones de Hidrógeno , Metales/farmacología , Peso Molecular , Temperatura
5.
Extremophiles ; 20(3): 311-21, 2016 May.
Artículo en Inglés | MEDLINE | ID: mdl-26995683

RESUMEN

A benzoate-degrading archaeal enrichment was developed using sediment samples from Rozel Point at Great Salt Lake, UT. The enrichment degraded benzoate as the sole carbon source at salinity ranging from 2.0 to 5.0 M NaCl with highest rate of degradation observed at 4.0 M. The enrichment was also tested for its ability to grow on other aromatic compounds such as 4-hydroxybenzoic acid (4-HBA), gentisic acid, protocatechuic acid (PCA), catechol, benzene and toluene as the sole sources of carbon and energy. Of these, the culture only utilized 4-HBA as the carbon source. To determine the initial steps in benzoate degradation pathway, a survey of ring-oxidizing and ring-cleaving genes was performed using degenerate PCR primers. Results showed the presence of 4-hydroxybenzoate 3-monooxygenase (4-HBMO) and protocatechuate 3, 4-dioxygenase (3,4-PCA) genes suggesting that the archaeal enrichment might degrade benzoate to 4-HBA that is further converted to PCA by 4-HBMO and, thus, formed PCA would undergo ring-cleavage by 3,4-PCA to form intermediates that enter the Krebs cycle. Small subunit rRNA gene-based diversity survey revealed that the enrichment consisted entirely of class Halobacteria members belonging to the genera Halopenitus, Halosarcina, Natronomonas, Halosimplex, Halorubrum, Salinarchaeum and Haloterrigena. Of these, Halopenitus was the dominant group accounting for almost 91 % of the total sequences suggesting their potential role in degrading oxygenated aromatic compounds at extreme salinity.


Asunto(s)
Archaea/metabolismo , Benzoatos/metabolismo , Microbiota , 4-Hidroxibenzoato-3-Monooxigenasa/genética , 4-Hidroxibenzoato-3-Monooxigenasa/metabolismo , Archaea/genética , Archaea/aislamiento & purificación , Proteínas Arqueales/genética , Proteínas Arqueales/metabolismo , Lagos/química , Lagos/microbiología , Parabenos/metabolismo , Protocatecuato-3,4-Dioxigenasa/genética , Protocatecuato-3,4-Dioxigenasa/metabolismo , ARN Ribosómico/genética , Salinidad , Tolerancia a la Sal
6.
J Environ Sci Health B ; 51(3): 182-91, 2016.
Artículo en Inglés | MEDLINE | ID: mdl-26669259

RESUMEN

The process of benzoate degradation by strain Rhodococcus opacus 1CP after a five-year dormancy was investigated and its peculiarities were revealed. The strain was shown to be capable of growth on benzoate at a concentration of up to 10 g L(-1). The substrate specificity of benzoate dioxygenase (BDO) during the culture growth on a medium with a low (200-250 mg L(-1)) and high (4 g L(-1)) concentration of benzoate was assessed. BDO of R. opacus 1CP was shown to be an extremely narrow specificity enzyme. Out of 31 substituted benzoates, only with one, 3-chlorobenzoate, its activity was higher than 9% of that of benzoate. Two dioxygenases, catechol 1,2-dioxygenase (Cat 1,2-DO) and protocatechuate 3,4-dioxygenase (PCA 3,4-DO), were identified in a cell-free extract, purified and characterized. The substrate specificity of Cat 1,2-DO isolated from cells of strain 1CP after the dormancy was found to differ significantly from that of Cat 1,2-DO isolated earlier from cells of this strain grown on benzoate. By its substrate specificity, the described Cat 1,2-DO was close to the Cat 1,2-DO from strain 1CP grown on 4-methylbenzoate. Neither activity nor inhibition by protocatechuate was observed during the reaction of Cat 1,2-DO with catechol, and catechol had no inhibitory effect on the reaction of PCA 3,4-DO with protocatechuate.


Asunto(s)
Dioxigenasas/metabolismo , Rhodococcus/metabolismo , Benzoatos/metabolismo , Biodegradación Ambiental , Catecol 1,2-Dioxigenasa/metabolismo , Catecoles/metabolismo , Sistema Libre de Células , Clorobenzoatos/metabolismo , Hidroxibenzoatos/metabolismo , Protocatecuato-3,4-Dioxigenasa/metabolismo , Rhodococcus/fisiología , Especificidad por Sustrato
7.
Bioorg Chem ; 60: 102-9, 2015 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-25984987

RESUMEN

Bacterial lignin degradation could be used to generate aromatic chemicals from the renewable resource lignin, provided that the breakdown pathways can be manipulated. In this study, selective inhibitors of enzymatic steps in bacterial degradation pathways were developed and tested for their effects upon lignin degradation. Screening of a collection of hydroxamic acid metallo-oxygenase inhibitors against two catechol dioxygenase enzymes, protocatechuate 3,4-dioxygenase (3,4-PCD) and 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB), resulted in the identification of selective inhibitors D13 for 3,4-PCD (IC50 15µM) and D3 for MhpB (IC50 110µM). Application of D13 to Rhodococcus jostii RHA1 in minimal media containing ferulic acid led to the appearance of metabolic precursor protocatechuic acid at low concentration. Application of 1mM disulfiram, an inhibitor of mammalian aldehyde dehydrogenase, to R. jostii RHA1, gave rise to 4-carboxymuconolactone on the ß-ketoadipate pathway, whereas in Pseudomonas fluorescens Pf-5 disulfiram treatment gave rise to a metabolite found to be glycine betaine aldehyde.


Asunto(s)
Dioxigenasas/antagonistas & inhibidores , Inhibidores Enzimáticos/farmacología , Ácidos Hidroxámicos/farmacología , Lignina/metabolismo , Protocatecuato-3,4-Dioxigenasa/antagonistas & inhibidores , Pseudomonas fluorescens/enzimología , Rhodococcus/enzimología , Inhibidores del Acetaldehído Deshidrogenasa/farmacología , Dioxigenasas/metabolismo , Disulfiram/farmacología , Inhibidores Enzimáticos/química , Fermentación/efectos de los fármacos , Ácidos Hidroxámicos/química , Hidroxibenzoatos/metabolismo , Protocatecuato-3,4-Dioxigenasa/metabolismo , Pseudomonas fluorescens/efectos de los fármacos , Pseudomonas fluorescens/metabolismo , Rhodococcus/efectos de los fármacos , Rhodococcus/metabolismo , Ácidos Tricarboxílicos/metabolismo
8.
Proc Natl Acad Sci U S A ; 112(2): 388-93, 2015 Jan 13.
Artículo en Inglés | MEDLINE | ID: mdl-25548185

RESUMEN

Intradiol aromatic ring-cleaving dioxygenases use an active site, nonheme Fe(3+) to activate O2 and catecholic substrates for reaction. The inability of Fe(3+) to directly bind O2 presents a mechanistic conundrum. The reaction mechanism of protocatechuate 3,4-dioxygenase is investigated here using the alternative substrate 4-fluorocatechol. This substrate is found to slow the reaction at several steps throughout the mechanistic cycle, allowing the intermediates to be detected in solution studies. When the reaction was initiated in an enzyme crystal, it was found to halt at one of two intermediates depending on the pH of the surrounding solution. The X-ray crystal structure of the intermediate at pH 6.5 revealed the key alkylperoxo-Fe(3+) species, and the anhydride-Fe(3+) intermediate was found for a crystal reacted at pH 8.5. Intermediates of these types have not been structurally characterized for intradiol dioxygenases, and they validate four decades of spectroscopic, kinetic, and computational studies. In contrast to our similar in crystallo crystallographic studies of an Fe(2+)-containing extradiol dioxygenase, no evidence for a superoxo or peroxo intermediate preceding the alkylperoxo was found. This observation and the lack of spectroscopic evidence for an Fe(2+) intermediate that could bind O2 are consistent with concerted formation of the alkylperoxo followed by Criegee rearrangement to yield the anhydride and ultimately ring-opened product. Structural comparison of the alkylperoxo intermediates from the intra- and extradiol dioxygenases provides a rationale for site specificity of ring cleavage.


Asunto(s)
Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Protocatecuato-3,4-Dioxigenasa/química , Protocatecuato-3,4-Dioxigenasa/metabolismo , Dominio Catalítico , Catecoles/metabolismo , Cristalografía por Rayos X , Concentración de Iones de Hidrógeno , Cinética , Modelos Moleculares , Pseudomonas putida/enzimología , Especificidad por Sustrato
9.
J Mol Microbiol Biotechnol ; 24(3): 150-60, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-24970342

RESUMEN

Protocatechuate 3,4-dioxygenases (P34Os) catalyze the reaction of the ring cleavage of aromatic acid derivatives. It is a key reaction in many xenobiotic metabolic pathways. P34Os characterize narrow substrate specificity. This property is an unfavorable feature in the biodegradation process because one type of pollution is rarely present in the environment. Thus, the following study aimed at the characterization of a P34O from Stenotrophomonas maltophilia KB2, being able to utilize a wide spectrum of aromatic carboxylic acids. A total of 3 mM vanillic acid and 4-hydroxybenzoate were completely degraded during 8 and 4.5 h, respectively. When cells of strain KB2 were grown on 9 mM 4-hydroxybenzoate, P34O was induced. Biochemical analysis revealed that the examined enzyme was similar to other known P34Os, but showed untypical wide substrate specificity. A high activity of P34O against 2,4- and 3,5-dihydroxybenzoate was observed. As these substrates do not possess ortho configuration hydroxyl groups, it is postulated that their cleavage could be connected with their monodentate binding of substrate to the active site. Since this enzyme characterizes untypical wide substrate specificity it makes it a useful tool in applications for environmental clean-up purposes.


Asunto(s)
Hidrocarburos Aromáticos/metabolismo , Protocatecuato-3,4-Dioxigenasa/aislamiento & purificación , Protocatecuato-3,4-Dioxigenasa/metabolismo , Stenotrophomonas maltophilia/enzimología , Biotransformación , Ácidos Carboxílicos/metabolismo , Análisis por Conglomerados , ADN Bacteriano/química , ADN Bacteriano/genética , Estabilidad de Enzimas , Concentración de Iones de Hidrógeno , Modelos Moleculares , Datos de Secuencia Molecular , Filogenia , Conformación Proteica , Protocatecuato-3,4-Dioxigenasa/química , Protocatecuato-3,4-Dioxigenasa/genética , Análisis de Secuencia de ADN , Homología de Secuencia de Aminoácido , Especificidad por Sustrato , Temperatura
10.
Biomed Res Int ; 2014: 138768, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-24693536

RESUMEN

Microbial intradiol dioxygenases have been shown to have a great potential for bioremediation; however, their structure is sensitive to various environmental and chemical agents. Immobilization techniques allow for the improvement of enzyme properties. This is the first report on use of glyoxyl agarose and calcium alginate as matrixes for the immobilization of protocatechuate 3,4-dioxygenase. Multipoint attachment of the enzyme to the carrier caused maintenance of its initial activity during the 21 days. Immobilization of dioxygenase in calcium alginate or on glyoxyl agarose resulted in decrease in the optimum temperature by 5 °C and 10 °C, respectively. Entrapment of the enzyme in alginate gel shifted its optimum pH towards high-alkaline pH while immobilization of the enzyme on glyoxyl agarose did not influence pH profile of the enzyme. Protocatechuate 3,4-dioygenase immobilized in calcium alginate showed increased activity towards 2,5-dihydroxybenzoate, caffeic acid, 2,3-dihydroxybenzoate, and 3,5-dihydroxybenzoate. Slightly lower activity of the enzyme was observed after its immobilization on glyoxyl agarose. Entrapment of the enzyme in alginate gel protected it against chelators and aliphatic alcohols while its immobilization on glyoxyl agarose enhanced enzyme resistance to inactivation by metal ions.


Asunto(s)
Alginatos/farmacología , Mezclas Complejas/química , Enzimas Inmovilizadas/metabolismo , Glioxilatos/farmacología , Hidrogeles/farmacología , Protocatecuato-3,4-Dioxigenasa/metabolismo , Sefarosa/farmacología , Stenotrophomonas maltophilia/enzimología , Biodegradación Ambiental/efectos de los fármacos , Quelantes/farmacología , Inhibidores Enzimáticos/farmacología , Estabilidad de Enzimas/efectos de los fármacos , Ácido Glucurónico/farmacología , Ácidos Hexurónicos/farmacología , Concentración de Iones de Hidrógeno , Metales/farmacología , Especificidad por Sustrato/efectos de los fármacos , Temperatura
11.
Dalton Trans ; 43(18): 6610-3, 2014 May 14.
Artículo en Inglés | MEDLINE | ID: mdl-24643434

RESUMEN

Three diamino, dihetero-phenol ligands were synthesized by sequential Mannich condensations. These ligands were combined with FeCl3 to produce three five-coordinate Fe(III) complexes that are structural models for the enzyme 3,4-PCD. The three Fe(III) complexes were characterized by elemental analysis, single crystal X-ray diffraction studies, UV-vis spectroscopy, and cyclic voltammetry. Combining the Fe(III) complexes with 3,5-di-t-butylcatechol and O2 resulted in oxidative cleavage similar to the function of 3,4-PCD.


Asunto(s)
Diaminas/química , Modelos Moleculares , Fenoles/química , Protocatecuato-3,4-Dioxigenasa/química , Cristalografía por Rayos X , Diaminas/metabolismo , Ligandos , Estructura Molecular , Fenoles/metabolismo , Unión Proteica , Protocatecuato-3,4-Dioxigenasa/metabolismo
12.
J Microbiol Biotechnol ; 24(4): 475-82, 2014 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-24375415

RESUMEN

The metabolic pathway of eugenol degradation by thermophilic Geobacillus sp. AY 946034 strain was analyzed based on the lack of data about eugenol degradation by thermophiles. TLC, GC-MS, and biotransformation with resting cells showed that eugenol was oxidized through coniferyl alcohol, and ferulic and vanillic acids to protocatechuic acid before the aromatic ring was cleaved. The cell-free extract of Geobacillus sp. AY 946034 strain grown on eugenol showed a high activity of eugenol hydroxylase, feruloyl-CoA synthetase, vanillate-O-demethylase, and protocatechuate 3,4-dioxygenase. The key enzyme, protocatechuate 3,4- dioxygenase, which plays a crucial role in the degradation of various aromatic compounds, was purified 135-fold to homogeneity with a 34% overall recovery from Geobacillus sp. AY 946034. The relative molecular mass of the native enzyme was about 450 ± 10 kDa and was composed of the non-identical subunits. The pH and temperature optima for enzyme activity were 8 and 60°C, respectively. The half-life of protocatechuate 3,4-dioxygenase at the optimum temperature was 50 min.


Asunto(s)
Eugenol/metabolismo , Geobacillus/metabolismo , Hidroxibenzoatos/metabolismo , Redes y Vías Metabólicas , Biotransformación , Cromatografía en Capa Delgada , Estabilidad de Enzimas , Cromatografía de Gases y Espectrometría de Masas , Concentración de Iones de Hidrógeno , Peso Molecular , Subunidades de Proteína/química , Protocatecuato-3,4-Dioxigenasa/química , Protocatecuato-3,4-Dioxigenasa/aislamiento & purificación , Protocatecuato-3,4-Dioxigenasa/metabolismo , Temperatura
13.
World J Microbiol Biotechnol ; 29(2): 267-73, 2013 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-23014843

RESUMEN

The aim of this paper was to describe the effect of various metal ions on the activity of protocatechuate 3,4-dioxygenase from Stenotrophomonas maltophilia KB2. We also compared activity of different dioxygenases isolated from this strain, in the presence of metal ions, after induction by various aromatic compounds. S. maltophilia KB2 degraded 13 mM 3,4-dihydroxybenzoate, 10 mM benzoic acid and 12 mM phenol within 24 h of incubation. In the presence of dihydroxybenzoate and benzoate, the activity of protocatechuate 3,4-dioxygenase and catechol 1,2-dioxygenase was observed. Although Fe(3+), Cu(2+), Zn(2+), Co(2+), Al(3+), Cd(2+), Ni(2+) and Mn(2+) ions caused 20-80 % inhibition of protocatechuate 3,4-dioxygenase activity, the above-mentioned metal ions (with the exception of Ni(2+)) inhibited catechol 1,2-dioxygenase to a lesser extent or even activate the enzyme. Retaining activity of at least one of three dioxygenases from strain KB2 in the presence of metal ions makes it an ideal bacterium for bioremediation of contaminated areas.


Asunto(s)
Proteínas Bacterianas/metabolismo , Metales/metabolismo , Protocatecuato-3,4-Dioxigenasa/metabolismo , Stenotrophomonas maltophilia/enzimología , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Ácido Benzoico/metabolismo , Biodegradación Ambiental , Dioxigenasas/genética , Dioxigenasas/metabolismo , Hidroxibenzoatos/metabolismo , Cinética , Protocatecuato-3,4-Dioxigenasa/química , Protocatecuato-3,4-Dioxigenasa/genética , Aguas del Alcantarillado/microbiología , Stenotrophomonas maltophilia/química , Stenotrophomonas maltophilia/genética , Stenotrophomonas maltophilia/metabolismo
14.
Dalton Trans ; 39(40): 9611-25, 2010 Oct 28.
Artículo en Inglés | MEDLINE | ID: mdl-20835480

RESUMEN

The iron(iii) complexes of the bis(phenolate) ligands 1,4-bis(2-hydroxy-4-methyl-benzyl)-1,4-diazepane H(2)(L1), 1,4-bis(2-hydroxy-4-nitrobenzyl)-1,4-diazepane H(2)(L2), 1,4-bis(2-hydroxy-3,5-dimethylbenzyl)-1,4-diazepane H(2)(L3) and 1,4-bis(2-hydroxy-3,5-di-tert-butylbenzyl)-1,4-diazepane H(2)(L4) have been isolated and studied as structural and functional models for 3,4-PCD enzymes. The complexes [Fe(L1)Cl] 1, [Fe(L2)(H(2)O)Cl] 2, [Fe(L3)Cl] 3 and [Fe(L4)Cl] 4 have been characterized using ESI-MS, elemental analysis, and absorption spectral and electrochemical methods. The single crystal X-ray structure of 3 contains the FeN(2)O(2)Cl chromophore with a novel square pyramidal (τ, 0.20) coordination geometry. The Fe-O-C bond angle (135.5°) and Fe-O bond length (1.855 Å) are very close to the Fe-O-C bond angles (133, 148°) and Fe-O(tyrosinate) bond distances (1.81, 1.91 Å) in 3,4-PCD enzyme. All the complexes exhibit two intense absorption bands in the ranges 335-383 and 493-541 nm, which are assigned respectively to phenolate (pπ) → Fe(iii) (dσ*) and phenolate (pπ) → Fe(iii) (dπ*) LMCT transitions. The Fe(iii)/Fe(ii) redox potentials of 1, 3 and 4 (E(1/2), -0.882--1.010 V) are more negative than that of 2 (E(1/2), -0.577 V) due to the presence of two electron-withdrawing p-nitrophenolate moieties in the latter enhancing the Lewis acidity of the iron(iii) center. Upon adding H(2)DBC pretreated with two equivalents of Et(3)N to the iron(iii) complexes, two catecholate-to-iron(iii) LMCT bands (656, ε, 1030; 515 nm, ε, 1330 M(-1) cm(-1)) are observed for 2; however, interestingly, an intense catecholate-to-iron(iii) LMCT band (530-541 nm) is observed for 1, 3 and 4 apart from a high intensity band in the range 451-462 nm. The adducts [Fe(L)(DBC)](-) generated from 1-4in situ in DMF/Et(3)N solution react with dioxygen to afford almost exclusively the simple two-electron oxidation product 3,5-di-tert-butylbenzoquinone (DBQ), which is discerned from the appearance and increase in intensity of the electronic spectral band around 400 nm, and smaller amounts of cleavage products. Interestingly, in DMF/piperidine the amount of quinone product decreases and those of the cleavage products increase illustrating that the stronger base piperidine enhances the concentration of the catecholate adduct. The rates of both dioxygenation and quinone formation observed in DMF/Et(3)N solution vary in the order 1 > 3 > 4 < 2 suggesting that the ligand steric hindrance to molecular oxygen attack, the Lewis acidity of the iron(iii) center and the ability of the complexes to rearrange the Fe-O phenolate bonds to accommodate the catecholate substrate dictate the extent of interaction of the complexes with substrate and hence determine the rates of reactions. This is in line with the observation of DBSQ/H(2)DBC reduction wave for the adduct [Fe(L2)(DBC)](-) at a potential (E(1/2): -0.285 V) more positive than those for the adducts of 1, 3 and 4 (E(1/2): -0.522 to -0.645 V).


Asunto(s)
Catecol 1,2-Dioxigenasa/metabolismo , Complejos de Coordinación/química , Compuestos Férricos/química , Protocatecuato-3,4-Dioxigenasa/metabolismo , Quinonas/química , Catálisis , Dominio Catalítico , Catecol 1,2-Dioxigenasa/química , Catecoles/química , Cristalografía por Rayos X , Técnicas Electroquímicas , Ligandos , Modelos Moleculares , Conformación Molecular , Protocatecuato-3,4-Dioxigenasa/química
16.
Biophys J ; 94(5): 1826-35, 2008 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-17921203

RESUMEN

The application of single-molecule fluorescence techniques to complex biological systems places demands on the performance of single fluorophores. We present an enzymatic oxygen scavenging system for improved dye stability in single-molecule experiments. We compared the previously described protocatechuic acid/protocatechuate-3,4-dioxygenase system to the currently employed glucose oxidase/catalase system. Under standardized conditions, we observed lower dissolved oxygen concentrations with the protocatechuic acid/protocatechuate-3,4-dioxygenase system. Furthermore, we observed increased initial lifetimes of single Cy3, Cy5, and Alexa488 fluorophores. We further tested the effects of chemical additives in this system. We found that biological reducing agents increase both the frequency and duration of blinking events of Cy5, an effect that scales with reducing potential. We observed increased stability of Cy3 and Alexa488 in the presence of the antioxidants ascorbic acid and n-propyl gallate. This new O(2)-scavenging system should have wide application for single-molecule fluorescence experiments.


Asunto(s)
Catalasa/metabolismo , Colorantes Fluorescentes/química , Depuradores de Radicales Libres/metabolismo , Glucosa Oxidasa/metabolismo , Nanotecnología/métodos , Oxígeno/metabolismo , Ácido Ascórbico/farmacología , Carbocianinas/química , Estabilidad de Enzimas , Hidroxibenzoatos/metabolismo , Microscopía Fluorescente , Fotoblanqueo , Galato de Propilo/farmacología , Protocatecuato-3,4-Dioxigenasa/metabolismo , Especies Reactivas de Oxígeno/metabolismo
17.
Pest Manag Sci ; 63(5): 459-67, 2007 May.
Artículo en Inglés | MEDLINE | ID: mdl-17427160

RESUMEN

Microorganisms degrading phenolic compounds play an important role in soil carbon cycling as well as in pesticide degradation. The pcaH gene encoding a key ring-cleaving enzyme of the beta-ketoadipate pathway was selected as a functional marker. Using a degenerate primer pair, pcaH fragments were cloned from two agricultural soils. Restriction fragment length polymorphism (RFLP) screening of 150 pcaH clones yielded 68 RFLP families. Comparison of 86 deduced amino acid sequences displayed 70% identity to known PcaH sequences. Phylogenetic analysis results in two major groups mainly related to PcaH sequences from Actinobacteria and Proteobacteria phyla. This confirms that the developed primer pair targets a wide diversity of pcaH sequences, thereby constituting a suitable molecular marker to estimate the response of the pca community to agricultural practices.


Asunto(s)
Actinobacteria/genética , Proteínas Bacterianas/genética , Plaguicidas/metabolismo , Proteobacteria/genética , Protocatecuato-3,4-Dioxigenasa/genética , Microbiología del Suelo , Actinobacteria/clasificación , Actinobacteria/metabolismo , Secuencia de Aminoácidos , Biodegradación Ambiental , Biodiversidad , Carbono/metabolismo , Cartilla de ADN , Marcadores Genéticos , Datos de Secuencia Molecular , Filogenia , Polimorfismo de Longitud del Fragmento de Restricción , Proteobacteria/clasificación , Proteobacteria/metabolismo , Protocatecuato-3,4-Dioxigenasa/metabolismo , Alineación de Secuencia , Análisis de Secuencia de Proteína
18.
J Am Chem Soc ; 129(7): 1944-58, 2007 Feb 21.
Artículo en Inglés | MEDLINE | ID: mdl-17256852

RESUMEN

Various mechanisms have been proposed for the initial O(2) attack in intradiol dioxygenases based on different electronic descriptions of the enzyme-substrate (ES) complex. We have examined the geometric and electronic structure of the high-spin ferric ES complex of protocatechuate 3,4-dioxygenase (3,4-PCD) with UV/visible absorption, circular dichroism (CD), magnetic CD (MCD), and variable-temperature variable-field (VTVH) MCD spectroscopies. The experimental data were coupled with DFT and INDO/S-CI calculations, and an experimentally calibrated bonding description was obtained. The broad absorption spectrum for the ES complex in the 6000-31000 cm(-1) region was resolved into at least five individual transitions, assigned as ligand-to-metal charge transfer (LMCT) from the protocatechuate (PCA) substrate and Tyr408. From our DFT calculations, all five LMCT transitions originate from the PCA and Tyr piop orbitals to the ferric dpi orbitals. The strong pi covalent donor interactions dominate the bonding in the ES complex. Using hypothetical Ga(3+)-catecholate/semiquinone complexes as references, 3,4-PCD-PCA was found to be best described as a highly covalent Fe(3+)-catecholate complex. The covalency is distributed unevenly among the four PCA valence orbitals, with the strongest interaction between the piop-sym and Fe dxz orbitals. This strong pi interaction, as reflected in the lowest energy PCA-to-Fe(3+) LMCT transition, is responsible for substrate activation for the O(2) reaction of intradiol dioxygenases. This involves a multi-electron-transfer (one beta and two alpha) mechanism, with Fe3+ acting as a buffer for the spin-forbidden two-electron redox process between PCA and O(2) in the formation of the peroxy-bridged ESO2 intermediate. The Fe ligand field overcomes the spin-forbidden nature of the triplet O(2) reaction, which potentially results in an intermediate spin state (S = 3/2) on the Fe(3+) center which is stabilized by a change in coordination along the reaction coordinate.


Asunto(s)
Hidroxibenzoatos/química , Hidroxibenzoatos/metabolismo , Proteínas de Hierro no Heme/química , Proteínas de Hierro no Heme/metabolismo , Protocatecuato-3,4-Dioxigenasa/química , Protocatecuato-3,4-Dioxigenasa/metabolismo , Benzoquinonas/química , Benzoquinonas/metabolismo , Sitios de Unión , Dicroismo Circular , Frío , Modelos Moleculares , Oxígeno/química , Oxígeno/metabolismo , Ácido Sórbico/análogos & derivados , Ácido Sórbico/química , Ácido Sórbico/metabolismo
19.
Inorg Chem ; 45(19): 7709-21, 2006 Sep 18.
Artículo en Inglés | MEDLINE | ID: mdl-16961363

RESUMEN

A unique distorted trigonal-bipyramidal geometry observed for the non-heme iron center in protocatechuate 3,4-dioxygenase (3,4-PCD) was carefully examined utilizing a sterically hindered iron salen complex, which well reproduces the endogenous His2Tyr2 donor set with water as an external ligand. X-ray crystal structures of a series of iron model complexes containing bis(3,5-dimesitylsalicylidene)-1,2-dimesitylethylenediamine indicate that a distorted trigonal-bipyramidal geometry is achieved upon binding of water as an external ligand. The extent of a structural change of the iron center from a preferred square-pyramidal to a distorted trigonal-bipyramidal geometry varies with the external ligand that is bound in the order Cl << EtO < H2O, which is consistent with the spectrochemical series. The distortion in the model system is not due to steric repulsions but electronic interactions between the external ligand and the iron center, as evidenced from the X-ray crystal structures of another series of iron model complexes with a less-hindered bis(3-xylylsalicylidene)-1,2-dimesitylethylenediamine ligand, as well as by density functional theory calculations. Further spectroscopic investigations indicate that a unique distorted trigonal-bipyramidal geometry is indeed maintained even in solution. The present model study provides a new viewpoint that a unique distorted trigonal-bipyramidal iron site might not be preorganized by a 3,4-PCD protein but could be electronically induced upon the binding of an external hydroxide ligand to the iron(III) center. The structural change induced by the external water ligand is also discussed in relation to the reaction mechanism of 3,4-PCD.


Asunto(s)
Etilenodiaminas/química , Compuestos Férricos/química , Protocatecuato-3,4-Dioxigenasa/química , Protocatecuato-3,4-Dioxigenasa/metabolismo , Agua/química , Sitios de Unión , Catecoles/química , Catecoles/metabolismo , Cristalografía por Rayos X , Electroquímica , Ligandos , Modelos Moleculares , Resonancia Magnética Nuclear Biomolecular , Estructura Terciaria de Proteína , Espectrometría Raman , Especificidad por Sustrato
20.
J Am Chem Soc ; 128(39): 12941-53, 2006 Oct 04.
Artículo en Inglés | MEDLINE | ID: mdl-17002391

RESUMEN

The mechanism of the catalytic reaction of protocatechuate 3,4-dioxygenase (3,4-PCD), a representative intradiol dioxygenase, was studied with the hybrid density functional method B3LYP. First, a smaller model involving only the iron first-shell ligands (His460, His462, and Tyr408) and the substrates (catechol and dioxygen) was used to probe various a priori plausible reaction mechanisms. Then, an extended model involving also the most important second-shell groups (Arg457, Gln477, and Tyr479) was used for the refinement of the preselected mechanisms. The computational results suggest that the chemical reactions constituting the catalytic cycle of intradiol dioxygenases involve: (1) binding of the substrate as a dianion, in agreement with experimental suggestions, (2) binding of dioxygen to the metal aided by an electron transfer from the substrate to O(2), (3) formation of a bridging peroxo intermediate and its conformational change, which opens the coordination site trans to His462, (4) binding of a neutral XOH ligand (H(2)O or Tyr447) at the open site, (5) proton transfer from XOH to the neighboring peroxo ligand yielding the hydroperoxo intermediate, (6) a Criegee rearrangement leading to the anhydride intermediate, and (7) hydrolysis of the anhydride to the final acyclic product. One of the most important results obtained is that the Criegee mechanism requires an in-plane orientation of the four atoms (two oxygen and two carbon atoms) mainly involved in the reaction. This orientation yields a good overlap between the two sigma orbitals involved, C-C sigma and O-O sigma, allowing an efficient electron flow between them. Another interesting result is that under some conditions, a homolytic O-O bond cleavage might compete with the Criegee rearrangement. The role of the second-shell residues and the substituent effects are also discussed.


Asunto(s)
Proteínas de Hierro no Heme/química , Proteínas de Hierro no Heme/metabolismo , Protocatecuato-3,4-Dioxigenasa/química , Protocatecuato-3,4-Dioxigenasa/metabolismo , Anhídridos/química , Anhídridos/metabolismo , Catecoles/química , Catecoles/metabolismo , Cristalografía por Rayos X , Hidrólisis , Modelos Moleculares , Oxígeno/química , Oxígeno/metabolismo , Conformación Proteica , Termodinámica
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