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1.
Angew Chem Int Ed Engl ; 62(2): e202211663, 2023 Jan 09.
Artículo en Inglés | MEDLINE | ID: mdl-36303469

RESUMEN

The influence of structural modifications on the catalytic activity of carbon materials is poorly understood. A collection of carbonaceous materials with different pore networks and high nitrogen content was characterized and used to catalyze four reactions to deduce structure-activity relationships. The CO2 cycloaddition and Knoevenagel reaction depend on Lewis basic sites (electron-rich nitrogen species). The absence of large conjugated carbon domains resulting from the introduction of large amounts of nitrogen in the carbon network is responsible for poor redox activity, as observed through the catalytic reduction of nitrobenzene with hydrazine and the catalytic oxidation of 3,3',5,5'-tetramethylbenzidine using hydroperoxide. The material with the highest activity towards Lewis acid catalysis (in the hydrolysis of (dimethoxymethyl)benzene to benzaldehyde) is the most effective for small molecule activation and presents the highest concentration of electron-poor nitrogen species.

2.
RNA Biol ; 18(11): 1858-1866, 2021 11.
Artículo en Inglés | MEDLINE | ID: mdl-33622172

RESUMEN

Nine distinct classes of self-cleaving ribozymes are known to date, of which the pistol ribozyme class was discovered only 5 years ago. Self-cleaving ribozymes are able to cleave their own phosphodiester backbone at a specific site with rates much higher than those of spontaneous RNA degradation. Our study focuses on a bioinformatically predicted pistol ribozyme from the bacterium Paenibacillus polymyxa. We provide a biochemical characterization of this ribozyme, which includes an investigation of the effect of various metal ions on ribozyme cleavage and a kinetic analysis of ribozyme activity under increasing Mg2+ concentrations and pH. Based on the obtained results, we discuss a possible catalytic role of divalent metal ions. Moreover, we investigated the ligation activity of the P. polymyxa pistol ribozyme - an aspect that has not been previously analysed for this ribozyme class. We determined that the P. polymyxa pistol ribozyme is almost fully cleaved at equilibrium with the ligation rate constant being nearly 30-fold lower than the cleavage rate constant. In summary, we have characterized an additional representative of this recently discovered ribozyme class isolated from P. polymyxa. We expect that our biochemical characterization of a pistol representative in a cultivatable, genetically tractable organism will support our future investigation of the biological roles of this ribozyme class in bacteria.


Asunto(s)
Biocatálisis , Paenibacillus polymyxa/metabolismo , ARN Catalítico/metabolismo , Dominio Catalítico , Biología Computacional , Cinética , Modelos Moleculares , Conformación de Ácido Nucleico , Paenibacillus polymyxa/genética , ARN Catalítico/química , ARN Catalítico/genética
3.
J Biol Chem ; 294(37): 13800-13810, 2019 09 13.
Artículo en Inglés | MEDLINE | ID: mdl-31350338

RESUMEN

The flavin transferase ApbE plays essential roles in bacterial physiology, covalently incorporating FMN cofactors into numerous respiratory enzymes that use the integrated cofactors as electron carriers. In this work we performed a detailed kinetic and structural characterization of Vibrio cholerae WT ApbE and mutants of the conserved residue His-257, to understand its role in substrate binding and in the catalytic mechanism of this family. Bi-substrate kinetic experiments revealed that ApbE follows a random Bi Bi sequential kinetic mechanism, in which a ternary complex is formed, indicating that both substrates must be bound to the enzyme for the reaction to proceed. Steady-state kinetic analyses show that the turnover rates of His-257 mutants are significantly smaller than those of WT ApbE, and have increased Km values for both substrates, indicating that the His-257 residue plays important roles in catalysis and in enzyme-substrate complex formation. Analyses of the pH dependence of ApbE activity indicate that the pKa of the catalytic residue (pKES1) increases by 2 pH units in the His-257 mutants, suggesting that this residue plays a role in substrate deprotonation. The crystal structures of WT ApbE and an H257G mutant were determined at 1.61 and 1.92 Å resolutions, revealing that His-257 is located in the catalytic site and that the substitution does not produce major conformational changes. We propose a reaction mechanism in which His-257 acts as a general base that deprotonates the acceptor residue, which subsequently performs a nucleophilic attack on FAD for flavin transfer.


Asunto(s)
Flavinas/metabolismo , Transferasas/metabolismo , Vibrio cholerae/metabolismo , Proteínas Bacterianas/metabolismo , Catálisis , Dominio Catalítico , Secuencia Conservada , Mononucleótido de Flavina/metabolismo , Flavina-Adenina Dinucleótido/metabolismo , Flavinas/genética , Histidina/metabolismo , Cinética , Oxidación-Reducción , Especificidad por Sustrato/genética , Transferasas/genética , Vibrio cholerae/genética
4.
J Biol Chem ; 294(46): 17463-17470, 2019 11 15.
Artículo en Inglés | MEDLINE | ID: mdl-31615898

RESUMEN

PlGoxA from Pseudoalteromonas luteoviolacea is a glycine oxidase that utilizes a protein-derived cysteine tryptophylquinone (CTQ) cofactor. A notable feature of its catalytic mechanism is that it forms a stable product-reduced CTQ adduct that is not hydrolyzed in the absence of O2 Asp-678 resides near the quinone moiety of PlGoxA, and an Asp is structurally conserved in this position in all tryptophylquinone enzymes. In those other enzymes, mutation of that Asp results in no or negligible CTQ formation. In this study, mutation of Asp-678 in PlGoxA did not abolish CTQ formation. This allowed, for the first time, studying the role of this residue in catalysis. D678A and D678N substitutions yielded enzyme variants with CTQ, which did not react with glycine, although glycine was present in the crystal structures in the active site. D678E PlGoxA was active but exhibited a much slower kcat This mutation altered the kinetic mechanism of the reductive half-reaction such that one could observe a previously undetected reactive intermediate, an initial substrate-oxidized CTQ adduct, which converted to the product-reduced CTQ adduct. These results indicate that Asp-678 is involved in the initial deprotonation of the amino group of glycine, enabling nucleophilic attack of CTQ, as well as the deprotonation of the substrate-oxidized CTQ adduct, which is coupled to CTQ reduction. The structures also suggest that Asp-678 is acting as a proton relay that directs these protons to a water channel that connects the active sites on the subunits of this homotetrameric enzyme.


Asunto(s)
Aminoácido Oxidorreductasas/química , Coenzimas/química , Dipéptidos/química , Indolquinonas/química , Pseudoalteromonas/enzimología , Aminoácido Oxidorreductasas/genética , Secuencia de Aminoácidos/genética , Catálisis , Dominio Catalítico/genética , Coenzimas/genética , Dipéptidos/genética , Glicina/química , Indolquinonas/genética , Cinética , Modelos Moleculares , Mutación , Pseudoalteromonas/química
5.
Chemphyschem ; 21(17): 1925-1933, 2020 09 02.
Artículo en Inglés | MEDLINE | ID: mdl-32644277

RESUMEN

In this paper we continue working on our theory of electrical double layers resulting exclusively from dissociation of a solid electrolyte, which we previously proposed as a medium for catalytic interaction between solid cellulose and solid acid catalysts of hydrolysis. Two theoretical unidimensional models of the inner grain volume are considered: an infinitely long cylindrical pore, and a gel electrolyte near a grain outer surface. Despite the model simplicity, the predictions for the cylindrical pore case are in semi-quantitative agreement with literature data on electroosmotic experiments, adequately explaining high proton selectivity of sulfonic membranes, and decline of such selectivity at high background acid concentration. The gel model predicts less concentrated diffuse layer in comparison to electrolytes with impenetrable skeleton (e. g., sulfonated carbons). This suggests limited suitability of gel electrolytes as catalysts if a substrate cannot diffuse into the gel bulk and the reaction is thereby spatially limited to the near-surface region, for example if a substrate is solid like aforementioned cellulose.

6.
Proc Natl Acad Sci U S A ; 114(26): E5103-E5112, 2017 06 27.
Artículo en Inglés | MEDLINE | ID: mdl-28607053

RESUMEN

The active site of multisubunit RNA polymerases (RNAPs) is highly conserved from humans to bacteria. This single site catalyzes both nucleotide addition required for RNA transcript synthesis and excision of incorrect nucleotides after misincorporation as a proofreading mechanism. Phosphoryl transfer and proofreading hydrolysis are controlled in part by a dynamic RNAP component called the trigger loop (TL), which cycles between an unfolded loop and an α-helical hairpin [trigger helices (TH)] required for rapid nucleotide addition. The precise roles of the TL/TH in RNA synthesis and hydrolysis remain unclear. An invariant histidine residue has been proposed to function in the TH form as a general acid in RNA synthesis and as a general base in RNA hydrolysis. The effects of conservative, nonionizable substitutions of the TL histidine (or a neighboring TL arginine conserved in bacteria) have not yet been rigorously tested. Here, we report that glutamine substitutions of these residues, which preserve polar interactions but are incapable of acid-base chemistry, had little effect on either phosphoryl transfer or proofreading hydrolysis by Escherichia coli RNAP. The TL substitutions did, however, affect the backtracking of RNAP necessary for proofreading and potentially the reactivity of the backtracked nucleotide. We describe a unifying model for the function of the RNAP TL, which reconciles available data and our results for representative RNAPs. This model explains diverse effects of the TL basic residues on catalysis through their effects on positioning reactants for phosphoryl transfer and easing barriers to transcript backtracking, rather than as acid-base catalysts.


Asunto(s)
ARN Polimerasas Dirigidas por ADN/química , Proteínas de Escherichia coli/química , Escherichia coli/enzimología , Modelos Químicos , Mutación Missense , Conformación de Ácido Nucleico , ARN/biosíntesis , Sustitución de Aminoácidos , ARN Polimerasas Dirigidas por ADN/genética , ARN Polimerasas Dirigidas por ADN/metabolismo , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , ARN/química , ARN/genética
7.
Macromol Rapid Commun ; 40(14): e1900148, 2019 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-31070820

RESUMEN

Multistep catalytic transformations using incompatible catalysts (Wolf-Lamb-type) in a one-pot reaction cascade require site isolation of different catalysts by compartmentalization. In this work, the use of different electrospun catalytic membranes in a modular way as individual compartments is shown for one-pot Wolf-Lamb-type reaction cascades. The data are presented for one-pot cascade reaction sequences catalyzed by acidic and basic membranes made by electrospinning polymeric acid (poly(styrene-co-styrene sulfonic acid-co-4-methacryloyl-oxybenzophen)) and basic (poly(styrene-co-4-vinylpyridine-co-4-methacryloyl-oxybenzophen)) catalysts, respectively. The two-step, one-pot system used is the acidic catalyzed deacetylation of dimethoxybenzylacetale to benzaldehyde, which reacts with ethyl cyanoformate to result in a high yield of product (over 90%) under base-catalyzed conditions. The reaction kinetics are further monitored and evaluated by using differential equations, showing the necessity of a parameter Δt to represent a retarded start for the second reaction step. The concept provides an easy and upscalable approach for use in Wolf-Lamb-type systems.


Asunto(s)
Catálisis , Polímeros/química , Poliestirenos/química , Membranas/química , Metacrilatos/química , Polímeros/síntesis química , Poliestirenos/síntesis química , Piridinas/síntesis química , Piridinas/química , Ácidos Sulfónicos/química
8.
Chemphyschem ; 19(4): 386-401, 2018 02 19.
Artículo en Inglés | MEDLINE | ID: mdl-29316166

RESUMEN

Chemo- and regioselectivity in a heterogeneously catalyzed cross aldol reaction were directed by tuning the nature of the sites, textural properties, and reaction conditions. Catalysts included sulfonic acid-functionalized resins or SBA-15 with varying particle size or pore diameter, H-BEA zeolites, and Sn-BEA zeotype; conditions were 25 °C to 170 °C in organic media. Benzaldehyde and 2-butanone yielded branched (reaction at -CH2 - of butanone) and linear (reaction at -CH3 ) addition and condensation products; and fission of the branched aldol led to ß-methyl styrene and acetic acid. Strong acids promoted the dehydration step, and regioselectivity originated from preferred formation of the branched aldol. Both, resins and functionalized SBA-15 materials yielded predominantly the branched condensation product, unless particle morphology or temperature moved the reaction into the diffusion-limited regime, in which case more fission products were formed, corresponding to Wheeler Type II selectivity. For H-form zeolites, fission of the branched aldol competed with dehydration of the linear aldol, possibly because weaker acidity or steric restrictions prevented dehydration of the branched aldol.

9.
Biochem Soc Trans ; 45(3): 683-691, 2017 06 15.
Artículo en Inglés | MEDLINE | ID: mdl-28620029

RESUMEN

Recent structural and mechanistic studies have shed considerable light on the catalytic mechanisms of nucleolytic ribozymes. The discovery of several new ribozymes in this class has now allowed comparisons to be made, and the beginnings of mechanistic groupings to emerge.


Asunto(s)
ARN Catalítico/metabolismo , Biocatálisis , Dominio Catalítico , Coenzimas , Eucariontes/enzimología , Humanos , Modelos Moleculares , Conformación de Ácido Nucleico , ARN Catalítico/química , ARN Catalítico/clasificación , Ribonucleasas/química , Ribonucleasas/clasificación , Ribonucleasas/metabolismo
10.
Angew Chem Int Ed Engl ; 56(33): 9820-9824, 2017 08 07.
Artículo en Inglés | MEDLINE | ID: mdl-28636790

RESUMEN

Although perovskites have been widely used in catalysis, tuning of their surface termination to control reaction selectivity has not been well established. In this study, we employed multiple surface-sensitive techniques to characterize the surface termination (one aspect of surface reconstruction) of SrTiO3 (STO) after thermal pretreatment (Sr enrichment) and chemical etching (Ti enrichment). We show, by using the conversion of 2-propanol as a probe reaction, that the surface termination of STO can be controlled to greatly tune catalytic acid/base properties and consequently the reaction selectivity over a wide range, which is not possible with single-metal oxides, either SrO or TiO2 . Density functional theory (DFT) calculations explain well the selectivity tuning and reaction mechanism on STO with different surface termination. Similar catalytic tunability was also observed on BaZrO3 , thus highlighting the generality of the findings of this study.

11.
Angew Chem Int Ed Engl ; 56(43): 13338-13341, 2017 10 16.
Artículo en Inglés | MEDLINE | ID: mdl-28872740

RESUMEN

An enantioselective direct Mannich-type reaction catalyzed by a sterically frustrated Lewis acid/Brønsted base complex is disclosed. Cooperative functioning of the chiral Lewis acid and achiral Brønsted base components gives rise to in situ enolate generation from monocarbonyl compounds. Subsequent reaction with hydrogen-bond-activated aldimines delivers ß-aminocarbonyl compounds with high enantiomeric purity.

12.
J Biol Chem ; 290(8): 4887-4895, 2015 Feb 20.
Artículo en Inglés | MEDLINE | ID: mdl-25533455

RESUMEN

CAZy glycoside hydrolase family GH3 consists primarily of stereochemistry-retaining ß-glucosidases but also contains a subfamily of ß-N-acetylglucosaminidases. Enzymes from this subfamily were recently shown to use a histidine residue within a His-Asp dyad contained in a signature sequence as their catalytic acid/base residue. Reasons for their use of His rather than the Glu or Asp found in other glycosidases were not apparent. Through studies on a representative member, the Nag3 ß-N-acetylglucosaminidase from Cellulomonas fimi, we now show that these enzymes act preferentially as glycoside phosphorylases. Their need to accommodate an anionic nucleophile within the enzyme active site explains why histidine is used as an acid/base catalyst in place of the anionic glutamate seen in other GH3 family members. Kinetic and mechanistic studies reveal that these enzymes also employ a double-displacement mechanism involving a covalent glycosyl-enzyme intermediate, which was directly detected by mass spectrometry. Phosphate has no effect on the rates of formation of the glycosyl-enzyme intermediate, but it accelerates turnover of the N-acetylglucosaminyl-enzyme intermediate ∼3-fold, while accelerating turnover of the glucosyl-enzyme intermediate several hundredfold. These represent the first reported examples of retaining ß-glycoside phosphorylases, and the first instance of free ß-GlcNAc-1-phosphate in a biological context.


Asunto(s)
Proteínas Bacterianas/química , Cellulomonas/enzimología , Glutamatos/química , Glicósido Hidrolasas/química , Fosforilasas/química , Proteínas Bacterianas/metabolismo , Glutamatos/metabolismo , Glicósido Hidrolasas/metabolismo , Cinética , Fosforilasas/metabolismo , Especificidad por Sustrato
13.
Biochim Biophys Acta ; 1854(9): 1194-9, 2015 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-25688830

RESUMEN

The proposed mechanism for tryptophan synthase shows ßLys87 playing multiple catalytic roles: it bonds to the PLP cofactor, activates C4' for nucleophilic attack via a protonated Schiff base nitrogen, and abstracts and returns protons to PLP-bound substrates (i.e. acid-base catalysis). ε-¹5N-lysine TS was prepared to access the protonation state of ßLys87 using ¹5N solid-state nuclear magnetic resonance (SSNMR) spectroscopy for three quasi-stable intermediates along the reaction pathway. These experiments establish that the protonation state of the ε-amino group switches between protonated and neutral states as the ß-site undergoes conversion from one intermediate to the next during catalysis, corresponding to mechanistic steps where this lysine residue has been anticipated to play alternating acid and base catalytic roles that help steer reaction specificity in tryptophan synthase catalysis. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications. Guest Editors: Andrea Mozzarelli and Loredano Pollegioni.


Asunto(s)
Biocatálisis , Salmonella typhimurium/enzimología , Triptófano Sintasa/química , Sitios de Unión , Modelos Moleculares , Resonancia Magnética Nuclear Biomolecular , Triptófano Sintasa/metabolismo
14.
Biochim Biophys Acta ; 1854(9): 1167-74, 2015 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-25615531

RESUMEN

Pyridoxal-5'-phosphate (PLP) is a versatile cofactor that enzymes use to catalyze a wide variety of reactions of amino acids, including transamination, decarboxylation, racemization, ß- and γ-eliminations and substitutions, retro-aldol and Claisen reactions. These reactions depend on the ability of PLP to stabilize, to a varying degree, α-carbanionic intermediates. Furthermore, oxidative decarboxylations and rearrangements suggest that PLP can stabilize radical intermediates as well. The reaction mechanisms of two PLP-dependent enzymes are discussed, kynureninase and tyrosine phenol-lyase (TPL). Kynureninase catalyzes a retro-Claisen reaction of kynurenine to give anthranilate and alanine. The key step, hydration of the γ-carbonyl, is assisted by acid-base catalysis with the phosphate of the PLP, mediated by a conserved tyrosine, and an oxyanion hole. TPL catalyzes the reversible elimination of phenol, a poor leaving group, from l-tyrosine. In TPL, the Cß-Cγ bond cleavage is accelerated by ground state strain from the bending of the substrate ring out of the plane with the Cß-Cγ bond. This article is part of a Special Issue entitled: Cofactor-dependent proteins: evolution, chemical diversity and bio-applications.


Asunto(s)
Hidrolasas/química , Fosfato de Piridoxal/fisiología , Tirosina Fenol-Liasa/química , Catálisis
15.
Bioorg Med Chem ; 24(6): 1346-55, 2016 Mar 15.
Artículo en Inglés | MEDLINE | ID: mdl-26899594

RESUMEN

A novel series of metal-free artificial ribonucleases (aRNases) was designed, synthesized and assessed in terms of ribonuclease activity and ability to inactivate influenza virus WSN/A33/H1N1 in vitro. The compounds were built of two short peptide fragments, which include Lys, Ser, Arg, Glu and imidazole residues in various combinations, connected by linkers of different hydrophobicity (1,12-diaminododecane or 4,9-dioxa-1,12-diaminododecane). These compounds efficiently cleaved different RNA substrates under physiological conditions at rates three to five times higher than that of artificial ribonucleases described earlier and displayed RNase A-like cleavage specificity. aRNases with the hydrophobic 1,12-diaminododecane linker displayed ribonuclease activity 3-40 times higher than aRNases with the 4,9-dioxa-1,12-diaminododecane linker. The assumed mechanism of RNA cleavage was typical for natural ribonucleases, that is, general acid-base catalysis via the formation of acid/base pairs by functional groups of amino acids present in the aRNases; the pH profile of cleavage confirmed this mechanism. The most active aRNases under study exhibited high antiviral activity and entirely inactivated influenza virus A/WSN/33/(H1N1) after a short incubation period of viral suspension under physiological conditions.


Asunto(s)
Antivirales/farmacología , Diseño de Fármacos , Interacciones Hidrofóbicas e Hidrofílicas , Orthomyxoviridae/efectos de los fármacos , Péptidos/química , División del ARN/efectos de los fármacos , Ribonucleasas/farmacología , Antivirales/síntesis química , Antivirales/química , Relación Dosis-Respuesta a Droga , Pruebas de Sensibilidad Microbiana , Estructura Molecular , Ribonucleasas/síntesis química , Ribonucleasas/química , Relación Estructura-Actividad
16.
Angew Chem Int Ed Engl ; 55(21): 6266-9, 2016 05 17.
Artículo en Inglés | MEDLINE | ID: mdl-27071502

RESUMEN

To quantify the properties of protic ionic liquids (PILs) as acid-base reaction media, potentiometric titrations were carried out in a neat PIL, ethylammonium nitrate (EAN). A linear relationship was found between the 14 pKa  values of 12 compounds in EAN and in water. In other words, the pKa  value in EAN was found to be roughly one unit greater than that in water regardless of the charge and hydrophobicity of the compounds. It is possible that this could be explained by the stronger acidity of HNO3 in EAN than that of H3 O(+) in water and not by the difference in the solvation state of the ions. The pH value in EAN ranges from -1 to 9 on the pH scale based on the pH value in water.

17.
Angew Chem Int Ed Engl ; 55(44): 13877-13881, 2016 10 24.
Artículo en Inglés | MEDLINE | ID: mdl-27690277

RESUMEN

Direct Mannich-type reactions that afford both α- and ß-amino esters by the reaction of a broad range of carbonyl compounds and aldimines are disclosed. The transformation is promoted by a sterically frustrated Lewis acid/Brønsted base pair, which is proposed to operate cooperatively: Within the catalyst complex, an enolate is generated that then reacts with a hydrogen-bond-activated imine. Noncovalent interactions between reactants and the catalyst provide selectivity and new opportunities for future catalyst design.

18.
Acta Crystallogr D Biol Crystallogr ; 70(Pt 9): 2256-63, 2014 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-25195740

RESUMEN

The hammerhead ribozyme catalyzes RNA cleavage via acid-base catalysis. Whether it does so by general acid-base catalysis, in which the RNA itself donates and abstracts protons in the transition state, as is typically assumed, or by specific acid-base catalysis, in which the RNA plays a structural role and proton transfer is mediated by active-site water molecules, is unknown. Previous biochemical and crystallographic experiments implicate an invariant purine in the active site, G12, as the general base. However, G12 may play a structural role consistent with specific base catalysis. To better understand the role of G12 in the mechanism of hammerhead catalysis, a 2.2 Šresolution crystal structure of a hammerhead ribozyme from Schistosoma mansoni with a purine substituted for G12 in the active site of the ribozyme was obtained. Comparison of this structure (PDB entry 3zd4), in which A12 is substituted for G, with three previously determined structures that now serve as important experimental controls, allows the identification of structural perturbations that are owing to the purine substitution itself. Kinetic measurements for G12 purine-substituted schistosomal hammerheads confirm a previously observed dependence of rate on the pK(a) of the substituted purine; in both cases inosine, which is similar to G in pK(a) and hydrogen-bonding properties, is unexpectedly inactive. Structural comparisons indicate that this may primarily be owing to the lack of the exocyclic 2-amino group in the G12A and G12I substitutions and its structural effect upon both the nucleotide base and phosphate of A9. The latter involves the perturbation of a previously identified and well characterized metal ion-binding site known to be catalytically important in both minimal and full-length hammerhead ribozyme sequences. The results permit it to be suggested that G12 plays an important role in stabilizing the active-site structure. This result, although not inconsistent with the potential role of G12 as a general base, indicates that an alternative hammerhead cleavage mechanism involving specific base catalysis may instead explain the observed rate dependence upon purine substitutions at G12. The crystallographic results, contrary to previous assumptions, therefore cannot be interpreted to favor the general base catalysis mecahnism over the specific base catalysis mechanism. Instead, both of these mutually exclusive mechanistic alternatives must be considered in light of the current structural and biochemical data.


Asunto(s)
Ácidos/química , Álcalis/química , Purinas/química , ARN Catalítico/química , Catálisis , Cristalografía , Enlace de Hidrógeno , Cinética , Modelos Moleculares , Conformación de Ácido Nucleico
19.
Arch Biochem Biophys ; 544: 69-74, 2014 Feb 15.
Artículo en Inglés | MEDLINE | ID: mdl-24200862

RESUMEN

The kynurenine pathway is the major pathway of l-tryptophan catabolism in eukaryotes and some bacteria. In this pathway, kynureninase catalyzes the hydrolysis of l-kynurenine (in bacteria) or 3-hydroxy-l-kynurenine (in eukaryotes) to give anthranilic acid or 3-hydroxyanthranilic acid, respectively, and l-alanine. Kynureninase is a member of the aminotransferase superfamily and contains pyridoxal-5'-phosphate (PLP) as cofactor. The enzyme is a dimer of two identical subunits, with the active site containing residues contributed from both subunits. The reaction of kynureninase is formally a retro-Claisen reaction, and thus requires extensive acid-base catalysis. The pH dependence of the reaction of Pseudomonas fluorescens kynureninase shows two pKa's, a base with 6.5 and an acid with 8.8, on kcat/Km, and one pKa of 6.8 on kcat. The effects of mutagenesis of Tyr-226 and (31)P NMR results suggest that the basic group with pKa of 6.5 is the phosphate group of the PLP, which accepts a proton from the amino acid substrate zwitterion to initiate transaldimination. The external aldimine of kynurenine and PLP is then deprotonated by the ε-amino group of Lys-227 to give a quinonoid intermediate, which is reprotonated at C-4' to give a ketimine. Addition of water to the γ-carbonyl, assisted by Lys-227, then gives a gem-diol, which undergoes Cß-Cγ cleavage to give the first product, anthranilic acid, and an enamine intermediate. The enamine is protonated at the ß-carbon, resulting in a pyruvate ketimine. Deprotonation at C-4' and reprotonation of the α-carbon gives the external aldimine of l-alanine, which releases the second product, l-alanine. The reaction specificity of kynureninases is determined in part by active site residues, Trp64, Gly281, and Thr282 in P. fluorescens, and the homologous His102, Ser332, and Asn333 in human kynureninase. Asn333 can form a hydrogen bond to the 3-OH of 3-hydroxykynurenine in the human enzyme. Halogenation of kynurenine at C-5 increases activity with both enzymes, but halogenation at C-3 only increases activity for human kynureninase. The effect of halogenation at C-5 may be due to hydrophobic or van der Waals effects, and the effect of halogenation at C-3 for the human enzyme may be due to halogen bonding.


Asunto(s)
Hidrolasas/química , Hidrolasas/metabolismo , Secuencia de Aminoácidos , Animales , Humanos , Datos de Secuencia Molecular , Pseudomonas fluorescens/química , Pseudomonas fluorescens/enzimología , Pseudomonas fluorescens/metabolismo , Fosfato de Piridoxal/química , Fosfato de Piridoxal/metabolismo , Alineación de Secuencia , Especificidad por Sustrato
20.
Bioorg Chem ; 57: 198-205, 2014 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-25035301

RESUMEN

The carbon-carbon lyases, tryptophan indole lyase (TIL) and tyrosine phenol-lyase (TPL) are bacterial enzymes which catalyze the reversible elimination of indole and phenol from l-tryptophan and l-tyrosine, respectively. These PLP-dependent enzymes show high sequence homology (∼40% identity) and both form homotetrameric structures. Steady state kinetic studies with both enzymes show that an active site base is essential for activity, and α-deuterated substrates exhibit modest primary isotope effects on kcat and kcat/Km, suggesting that substrate deprotonation is partially rate-limiting. Pre-steady state kinetics with TPL and TIL show rapid formation of external aldimine intermediates, followed by deprotonation to give quinonoid intermediates absorbing at about 500nm. In the presence of phenol and indole analogues, 4-hydroxypyridine and benzimidazole, the quinonoid intermediates of TPL and TIL decay to aminoacrylate intermediates, with λmax at about 340nm. Surprisingly, there are significant kinetic isotope effects on both formation and subsequent decay of the quinonoid intermediates when α-deuterated substrates are used. The crystal structure of TPL with a bound competitive inhibitor, 4-hydroxyphenylpropionate, identified several essential catalytic residues: Tyr-71, Thr-124, Arg-381, and Phe-448. The active sites of TIL and TPL are highly conserved with the exceptions of these residues: Arg-381(TPL)/Ile-396 (TIL); Thr-124 (TPL)/Asp-137 (TIL), and Phe-448 (TPL)/His-463 (TIL). Mutagenesis of these residues results in dramatic decreases in catalytic activity without changing substrate specificity. The conserved tyrosine, Tyr-71 (TPL)/Tyr-74 (TIL) is essential for elimination activity with both enzymes, and likely plays a role as a proton donor to the leaving group. Mutation of Arg-381 and Thr-124 of TPL to alanine results in very low but measurable catalytic activity. Crystallography of Y71F and F448H TPL with 3-fluoro-l-tyrosine bound demonstrated that there are two quinonoid structures, relaxed and tense. In the relaxed structure, the substrate aromatic ring is in plane with the Cß-Cγ bond, but in the tense structure, the substrate aromatic ring is about 20° out of plane with the Cß-Cγ bond. In the tense structure, hydrogen bonds are formed between the substrate OH and the guanidinium of Arg-381 and the OH of Thr-124, and the phenyl rings of Phe-448 and 449 provide steric strain. Based on the effects of mutagenesis, the substrate strain is estimated to contribute about 10(8) to TPL catalysis. Thus, the mechanisms of TPL and TIL require both substrate strain and acid/base catalysis, and substrate strain is probably responsible for the very high substrate specificity of TPL and TIL.


Asunto(s)
Bacterias/enzimología , Triptofanasa/metabolismo , Tirosina Fenol-Liasa/metabolismo , Secuencia de Aminoácidos , Bacterias/química , Bacterias/metabolismo , Cristalografía , Modelos Moleculares , Datos de Secuencia Molecular , Alineación de Secuencia , Especificidad por Sustrato , Triptofanasa/química , Tirosina Fenol-Liasa/química
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