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1.
Protein Sci ; 33(3): e4884, 2024 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-38145310

RESUMEN

Vibrio vulnificus (vv) is a multidrug-resistant human bacterial pathogen whose prevalence is expected to increase over the years. Transketolases (TK), transferases catalyzing two reactions of the nonoxidative branch of the pentose-phosphate pathway and therefore linked to several crucial metabolic pathways, are potential targets for new drugs against this pathogen. Here, the vvTK is crystallized and its structure is solved at 2.1 Å. A crown of 6 histidyl residues is observed in the active site and expected to participate in the thiamine pyrophosphate (cofactor) activation. Docking of fructose-6-phosphate and ferricyanide used in the activity assay, suggests that both substrates can bind vvTK simultaneously. This is confirmed by steady-state kinetics showing a sequential mechanism, on the contrary to the natural transferase reaction which follows a substituted mechanism. Inhibition by the I38-49 inhibitor (2-(4-ethoxyphenyl)-1-(pyrimidin-2-yl)-1H-pyrrolo[2,3-b]pyridine) reveals for the first time a cooperative behavior of a TK and docking experiments suggest a previously undescribed binding site at the interface between the pyrophosphate and pyridinium domains.


Asunto(s)
Transcetolasa , Vibrio vulnificus , Humanos , Transcetolasa/química , Transcetolasa/metabolismo , Vibrio vulnificus/metabolismo , Cinética , Conducta Cooperativa , Tiamina Pirofosfato/metabolismo , Transferasas/metabolismo
2.
Acta Crystallogr D Struct Biol ; 79(Pt 4): 290-303, 2023 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-36974963

RESUMEN

Phosphoketolase and transketolase are thiamine diphosphate-dependent enzymes and play a central role in the primary metabolism of bifidobacteria: the bifid shunt. The enzymes both catalyze phosphorolytic cleavage of xylulose 5-phosphate or fructose 6-phosphate in the first reaction step, but possess different substrate specificity in the second reaction step, where phosphoketolase and transketolase utilize inorganic phosphate (Pi) and D-ribose 5-phosphate, respectively, as the acceptor substrate. Structures of Bifidobacterium longum phosphoketolase holoenzyme and its complex with a putative inhibitor, phosphoenolpyruvate, were determined at 2.5 Šresolution by serial femtosecond crystallography using an X-ray free-electron laser. In the complex structure, phosphoenolpyruvate was present at the entrance to the active-site pocket and plugged the channel to thiamine diphosphate. The phosphate-group position of phosphoenolpyruvate coincided well with those of xylulose 5-phosphate and fructose 6-phosphate in the structures of their complexes with transketolase. The most striking structural change was observed in a loop consisting of Gln546-Asp547-His548-Asn549 (the QN-loop) at the entrance to the active-site pocket. Contrary to the conformation of the QN-loop that partially covers the entrance to the active-site pocket (`closed form') in the known crystal structures, including the phosphoketolase holoenzyme and its complexes with reaction intermediates, the QN-loop in the current ambient structures showed a more compact conformation with a widened entrance to the active-site pocket (`open form'). In the phosphoketolase reaction, the `open form' QN-loop may play a role in providing the binding site for xylulose 5-phosphate or fructose 6-phosphate in the first step, and the `closed form' QN-loop may help confer specificity for Pi in the second step.


Asunto(s)
Bifidobacterium longum , Tiamina Pirofosfato , Tiamina Pirofosfato/química , Tiamina Pirofosfato/metabolismo , Bifidobacterium longum/metabolismo , Cristalografía por Rayos X , Transcetolasa/química , Transcetolasa/metabolismo , Fosfoenolpiruvato , Temperatura , Xilulosa , Dominio Catalítico , Fructosa
3.
Appl Microbiol Biotechnol ; 107(1): 233-245, 2023 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-36441206

RESUMEN

Transketolase is a key enzyme in the pentose phosphate pathway in all organisms, recognizing sugar phosphates as substrates. Transketolase with a cofactor of thiamine pyrophosphate catalyzes the transfer of a 2-carbon unit from D-xylulose-5-phosphate to D-ribose-5-phosphate (5-carbon aldose), giving D-sedoheptulose-7-phosphate (7-carbon ketose). Transketolases can also recognize non-phosphorylated monosaccharides as substrates, and catalyze the formation of non-phosphorylated 7-carbon ketose (heptulose), which has attracted pharmaceutical attention as an inhibitor of sugar metabolism. Here, we report the structural and biochemical characterizations of transketolase from Thermus thermophilus HB8 (TtTK), a well-characterized thermophilic Gram-negative bacterium. TtTK showed marked thermostability with maximum enzyme activity at 85 °C, and efficiently catalyzed the formation of heptuloses from lithium hydroxypyruvate and four aldopentoses: D-ribose, L-lyxose, L-arabinose, and D-xylose. The X-ray structure showed that TtTK tightly forms a homodimer with more interactions between subunits compared with transketolase from other organisms, contributing to its thermal stability. A modeling study based on X-ray structures suggested that D-ribose and L-lyxose could bind to the catalytic site of TtTK to form favorable hydrogen bonds with the enzyme, explaining the high conversion rates of 41% (D-ribose) and 43% (L-lyxose) to heptulose. These results demonstrate the potential of TtTK as an enzyme producing a rare sugar of heptulose. KEY POINTS: • Transketolase catalyzes the formation of a 7-carbon sugar phosphate • Structural and biochemical characterizations of thermophilic transketolase were done • The enzyme could produce non-phosphorylated 7-carbon ketoses from sugars.


Asunto(s)
Thermus thermophilus , Transcetolasa , Transcetolasa/química , Transcetolasa/metabolismo , Ribosa , Monosacáridos , Fosfatos , Cetosas , Carbono
4.
Sheng Wu Gong Cheng Xue Bao ; 38(12): 4615-4629, 2022 Dec 25.
Artículo en Chino | MEDLINE | ID: mdl-36593197

RESUMEN

Transketolase (EC 2.2.1.1, TK) is a thiamine diphosphate-dependent enzyme that catalyzes the transfer of a two-carbon hydroxyacetyl unit with reversible C-C bond cleavage and formation. It is widely used in the production of chemicals, drug precursors, and asymmetric synthesis by cascade enzyme catalysis. In this paper, the activity of transketolase TKTA from Escherichia coli K12 on non-phosphorylated substrates was enhanced through site-directed saturation mutation and combined mutation. On this basis, the synthesis of tartaric semialdehyde was explored. The results showed that the optimal reaction temperature and pH of TKTA_M (R358I/H461S/R520Q) were 32 ℃ and 7.0, respectively. The specific activity on d-glyceraldehyde was (6.57±0.14) U/mg, which was 9.25 times higher than that of the wild type ((0.71±0.02) U/mg). Based on the characterization of TKTA_M, tartaric acid semialdehyde was synthesized with 50 mmol/L 5-keto-d-gluconate and 50 mmol/L non-phosphorylated ethanolaldehyde. The final yield of tartaric acid semialdehyde was 3.71 g with a molar conversion rate of 55.34%. Hence, the results may facilitate the preparation of l-(+)-tartaric acid from biomass, and provide an example for transketolase-catalyzed non-phosphorylated substrates.


Asunto(s)
Proteínas de Escherichia coli , Escherichia coli , Escherichia coli/genética , Transcetolasa/genética , Transcetolasa/química , Tartratos , Proteínas de Escherichia coli/genética
5.
Chinese Journal of Biotechnology ; (12): 4615-4629, 2022.
Artículo en Chino | WPRIM (Pacífico Occidental) | ID: wpr-970335

RESUMEN

Transketolase (EC 2.2.1.1, TK) is a thiamine diphosphate-dependent enzyme that catalyzes the transfer of a two-carbon hydroxyacetyl unit with reversible C-C bond cleavage and formation. It is widely used in the production of chemicals, drug precursors, and asymmetric synthesis by cascade enzyme catalysis. In this paper, the activity of transketolase TKTA from Escherichia coli K12 on non-phosphorylated substrates was enhanced through site-directed saturation mutation and combined mutation. On this basis, the synthesis of tartaric semialdehyde was explored. The results showed that the optimal reaction temperature and pH of TKTA_M (R358I/H461S/R520Q) were 32 ℃ and 7.0, respectively. The specific activity on d-glyceraldehyde was (6.57±0.14) U/mg, which was 9.25 times higher than that of the wild type ((0.71±0.02) U/mg). Based on the characterization of TKTA_M, tartaric acid semialdehyde was synthesized with 50 mmol/L 5-keto-d-gluconate and 50 mmol/L non-phosphorylated ethanolaldehyde. The final yield of tartaric acid semialdehyde was 3.71 g with a molar conversion rate of 55.34%. Hence, the results may facilitate the preparation of l-(+)-tartaric acid from biomass, and provide an example for transketolase-catalyzed non-phosphorylated substrates.


Asunto(s)
Escherichia coli/genética , Transcetolasa/química , Tartratos , Proteínas de Escherichia coli/genética
6.
Sci Rep ; 11(1): 23584, 2021 12 08.
Artículo en Inglés | MEDLINE | ID: mdl-34880340

RESUMEN

Transketolase (TK) has been previously engineered, using semi-rational directed evolution and substrate walking, to accept increasingly aliphatic, cyclic, and then aromatic substrates. This has ultimately led to the poor water solubility of new substrates, as a potential bottleneck to further exploitation of this enzyme in biocatalysis. Here we used a range of biophysical studies to characterise the response of both E. coli apo- and holo-TK activity and structure to a range of polar organic co-solvents: acetonitrile (AcCN), n-butanol (nBuOH), ethyl acetate (EtOAc), isopropanol (iPrOH), and tetrahydrofuran (THF). The mechanism of enzyme deactivation was found to be predominantly via solvent-induced local unfolding. Holo-TK is thermodynamically more stable than apo-TK and yet for four of the five co-solvents it retained less activity than apo-TK after exposure to organic solvents, indicating that solvent tolerance was not simply correlated to global conformational stability. The co-solvent concentrations required for complete enzyme inactivation was inversely proportional to co-solvent log(P), while the unfolding rate was directly proportional, indicating that the solvents interact with and partially unfold the enzyme through hydrophobic contacts. Small amounts of aggregate formed in some cases, but this was not sufficient to explain the enzyme inactivation. TK was found to be tolerant to 15% (v/v) iPrOH, 10% (v/v) AcCN, or 6% (v/v) nBuOH over 3 h. This work indicates that future attempts to engineer the enzyme to better tolerate co-solvents should focus on increasing the stability of the protein to local unfolding, particularly in and around the cofactor-binding loops.


Asunto(s)
Proteínas de Escherichia coli/química , Escherichia coli/química , Escherichia coli/metabolismo , Solventes/química , Transcetolasa/química , Agua/química , Biocatálisis , Estabilidad de Enzimas/efectos de los fármacos
7.
FEBS J ; 288(6): 1935-1955, 2021 03.
Artículo en Inglés | MEDLINE | ID: mdl-32897608

RESUMEN

Site-specific saturation mutagenesis within enzyme active sites can radically alter reaction specificity, though often with a trade-off in stability. Extending saturation mutagenesis with a range of noncanonical amino acids (ncAA) potentially increases the ability to improve activity and stability simultaneously. Previously, an Escherichia coli transketolase variant (S385Y/D469T/R520Q) was evolved to accept aromatic aldehydes not converted by wild-type. The aromatic residue Y385 was critical to the new acceptor substrate binding, and so was explored here beyond the natural aromatic residues, to probe side chain structure and electronics effects on enzyme function and stability. A series of five variants introduced decreasing aromatic ring electron density at position 385 in the order para-aminophenylalanine (pAMF), tyrosine (Y), phenylalanine (F), para-cyanophenylalanine (pCNF) and para-nitrophenylalanine (pNTF), and simultaneously modified the hydrogen-bonding potential of the aromatic substituent from accepting to donating. The fine-tuning of residue 385 yielded variants with a 43-fold increase in specific activity for 50 mm 3-HBA and 100% increased kcat (pCNF), 290% improvement in Km (pNTF), 240% improvement in kcat /Km (pAMF) and decreased substrate inhibition relative to Y. Structural modelling suggested switching of the ring-substituted functional group, from donating to accepting, stabilised a helix-turn (D259-H261) through an intersubunit H-bond with G262, to give a 7.8 °C increase in the thermal transition mid-point, Tm , and improved packing of pAMF. This is one of the first examples in which both catalytic activity and stability are simultaneously improved via site-specific ncAA incorporation into an enzyme active site, and further demonstrates the benefits of expanding designer libraries to include ncAAs.


Asunto(s)
Aminoácidos/genética , Estabilidad de Enzimas/genética , Proteínas de Escherichia coli/genética , Escherichia coli/genética , Transcetolasa/genética , Sustitución de Aminoácidos , Aminoácidos/química , Aminoácidos/metabolismo , Sitios de Unión/genética , Biocatálisis , Dominio Catalítico , Escherichia coli/enzimología , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Cinética , Simulación del Acoplamiento Molecular , Mutagénesis Sitio-Dirigida , Desnaturalización Proteica , Especificidad por Sustrato , Temperatura , Transcetolasa/química , Transcetolasa/metabolismo
8.
Anal Biochem ; 613: 114022, 2021 01 15.
Artículo en Inglés | MEDLINE | ID: mdl-33217405

RESUMEN

In a recent paper, we showed the difference between the first stage of the one-substrate and the two-substrate transketolase reactions - the possibility of transfer of glycolaldehyde formed as a result of cleavage of the donor substrate from the thiazole ring of thiamine diphosphate to its aminopyrimidine ring through the tricycle formation stage, which is necessary for binding and splitting the second molecule of donor substrate [O.N. Solovjeva et al., The mechanism of a one-substrate transketolase reaction, Biosci. Rep. 40 (8) (2020) BSR20180246]. Here we show that under the action of the reducing agent a tricycle accumulates in a significant amount. Therefore, a significant decrease in the reaction rate of the one-substrate transketolase reaction compared to the two-substrate reaction is due to the stage of transferring the first glycolaldehyde molecule from the thiazole ring to the aminopyrimidine ring of thiamine diphosphate. Fragmentation of the four-carbon thiamine diphosphate derivatives showed that two glycolaldehyde molecules are bound to both coenzyme rings and the erythrulose molecule is bound to a thiazole ring. It was concluded that in the one-substrate reaction erythrulose is formed on the thiazole ring of thiamine diphosphate from two glycol aldehyde molecules linked to both thiamine diphosphate rings. The kinetic characteristics were determined for the two substrates, fructose 6-phosphate and glycolaldehyde.


Asunto(s)
Transcetolasa/química , Transcetolasa/metabolismo , Acetaldehído/análogos & derivados , Acetaldehído/química , Acetaldehído/metabolismo , Biocatálisis , Borohidruros/química , Coenzimas/metabolismo , Fructosafosfatos/química , Fructosafosfatos/metabolismo , Cinética , Saccharomyces cerevisiae/enzimología , Proteínas de Saccharomyces cerevisiae/química , Proteínas de Saccharomyces cerevisiae/metabolismo , Espectrometría de Masa por Ionización de Electrospray , Especificidad por Sustrato , Tetrosas/metabolismo , Tiamina Pirofosfato/química , Tiamina Pirofosfato/metabolismo
9.
Malar J ; 19(1): 442, 2020 Nov 30.
Artículo en Inglés | MEDLINE | ID: mdl-33256744

RESUMEN

BACKGROUND: Plasmodial transketolase (PTKT) enzyme is one of the novel pharmacological targets being explored as potential anti-malarial drug target due to its functional role and low sequence identity to the human enzyme. Despite this, features contributing to such have not been exploited for anti-malarial drug design. Additionally, there are no anti-malarial drugs targeting PTKTs whereas the broad activity of these inhibitors against PTKTs from other Plasmodium spp. is yet to be reported. This study characterises different PTKTs [Plasmodium falciparum (PfTKT), Plasmodium vivax (PvTKT), Plasmodium ovale (PoTKT), Plasmodium malariae (PmTKT) and Plasmodium knowlesi (PkTKT) and the human homolog (HsTKT)] to identify key sequence and structural based differences as well as the identification of selective potential inhibitors against PTKTs. METHODS: A sequence-based study was carried out using multiple sequence alignment, phylogenetic tree calculations and motif discovery analysis. Additionally, TKT models of PfTKT, PmTKT, PoTKT, PmTKT and PkTKT were modelled using the Saccharomyces cerevisiae TKT structure as template. Based on the modelled structures, molecular docking using 623 South African natural compounds was done. The stability, conformational changes and detailed interactions of selected compounds were accessed viz all-atom molecular dynamics (MD) simulations and binding free energy (BFE) calculations. RESULTS: Sequence alignment, evolutionary and motif analyses revealed key differences between plasmodial and the human TKTs. High quality homodimeric three-dimensional PTKTs structures were constructed. Molecular docking results identified three compounds (SANC00107, SANC00411 and SANC00620) which selectively bind in the active site of all PTKTs with the lowest (better) binding affinity ≤ - 8.5 kcal/mol. MD simulations of ligand-bound systems showed stable fluctuations upon ligand binding. In all systems, ligands bind stably throughout the simulation and form crucial interactions with key active site residues. Simulations of selected compounds in complex with human TKT showed that ligands exited their binding sites at different time steps. BFE of protein-ligand complexes showed key residues involved in binding. CONCLUSIONS: This study highlights significant differences between plasmodial and human TKTs and may provide valuable information for the development of novel anti-malarial inhibitors. Identified compounds may provide a starting point in the rational design of PTKT inhibitors and analogues based on these scaffolds.


Asunto(s)
Antimaláricos/química , Plasmodium/genética , Proteínas Protozoarias , Transcetolasa , Secuencia de Aminoácidos , Antimaláricos/farmacología , Dominio Catalítico , Ligandos , Simulación de Dinámica Molecular , Filogenia , Plasmodium/enzimología , Proteínas Protozoarias/antagonistas & inhibidores , Proteínas Protozoarias/química , Proteínas Protozoarias/genética , Proteínas Protozoarias/metabolismo , Alineación de Secuencia , Transcetolasa/antagonistas & inhibidores , Transcetolasa/química , Transcetolasa/genética , Transcetolasa/metabolismo
10.
FEBS J ; 287(9): 1758-1776, 2020 05.
Artículo en Inglés | MEDLINE | ID: mdl-31647171

RESUMEN

A narrow substrate range is a major limitation in exploiting enzymes more widely as catalysts in synthetic organic chemistry. For enzymes using two substrates, the simultaneous optimisation of both substrate specificities is also required for the rapid expansion of accepted substrates. Transketolase (TK) catalyses the reversible transfer of a C2 -ketol unit from a donor substrate to an aldehyde acceptor and suffers the limitation of narrow substrate scope for industrial applications. Herein, TK from Escherichia coli was engineered to accept both pyruvate, as a novel donor substrate, and unnatural acceptor aldehydes, including propanal, pentanal, hexanal and 3-formylbenzoic acid (FBA). Twenty single-mutant variants were first designed and characterised experimentally. Beneficial mutations were then recombined to construct a small library. Screening of this library identified the best variant with a 9.2-fold improvement in the yield towards pyruvate and propionaldehyde, relative to wild-type (WT). Pentanal and hexanal were used as acceptors to determine stereoselectivities of the reactions, which were found to be higher than 98% enantiomeric excess (ee) for the S configuration. Three variants were identified to be active for the reaction between pyruvate and 3-FBA. The best variant was able to convert 47% of substrate into product within 24 h, whereas no conversion was observed for WT. Docking experiments suggested a cooperation between the mutations responsible for donor and acceptor recognition, which would promote the activity towards both the acceptor and donor. The variants obtained have the potential to be used for developing catalytic pathways to a diverse range of high-value products.


Asunto(s)
Cetonas/metabolismo , Ingeniería de Proteínas , Transcetolasa/metabolismo , Biocatálisis , Escherichia coli/enzimología , Cetonas/química , Modelos Moleculares , Estructura Molecular , Especificidad por Sustrato , Transcetolasa/química , Transcetolasa/genética
11.
Biosci Rep ; 40(8)2020 08 28.
Artículo en Inglés | MEDLINE | ID: mdl-29500317

RESUMEN

Transketolase catalyzes the transfer of a glycolaldehyde residue from ketose (the donor substrate) to aldose (the acceptor substrate). In the absence of aldose, transketolase catalyzes a one-substrate reaction that involves only ketose. The mechanism of this reaction is unknown. Here, we show that hydroxypyruvate serves as a substrate for the one-substrate reaction and, as well as with the xylulose-5-phosphate, the reaction product is erythrulose rather than glycolaldehyde. The amount of erythrulose released into the medium is equimolar to a double amount of the transformed substrate. This could only be the case if the glycol aldehyde formed by conversion of the first ketose molecule (the product of the first half reaction) remains bound to the enzyme, waiting for condensation with the second molecule of glycol aldehyde. Using mass spectrometry of catalytic intermediates and their subsequent fragmentation, we show here that interaction of the holotransketolase with hydroxypyruvate results in the equiprobable binding of the active glycolaldehyde to the thiazole ring of thiamine diphosphate and to the amino group of its aminopyrimidine ring. We also show that these two loci can accommodate simultaneously two glycolaldehyde molecules. It explains well their condensation without release into the medium, which we have shown earlier.


Asunto(s)
Pentosafosfatos/metabolismo , Piruvatos/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/enzimología , Tetrosas/metabolismo , Transcetolasa/metabolismo , Sitios de Unión , Dominio Catalítico , Cinética , Simulación de Dinámica Molecular , Pentosafosfatos/química , Unión Proteica , Conformación Proteica , Piruvatos/química , Proteínas de Saccharomyces cerevisiae/química , Espectrometría de Masa por Ionización de Electrospray , Relación Estructura-Actividad , Especificidad por Sustrato , Espectrometría de Masas en Tándem , Tetrosas/química , Transcetolasa/química
12.
Nature ; 573(7775): 609-613, 2019 09.
Artículo en Inglés | MEDLINE | ID: mdl-31534226

RESUMEN

The underlying molecular mechanisms of cooperativity and allosteric regulation are well understood for many proteins, with haemoglobin and aspartate transcarbamoylase serving as prototypical examples1,2. The binding of effectors typically causes a structural transition of the protein that is propagated through signalling pathways to remote sites and involves marked changes on the tertiary and sometimes even the quaternary level1-5. However, the origin of these signals and the molecular mechanism of long-range signalling at an atomic level remain unclear5-8. The different spatial scales and timescales in signalling pathways render experimental observation challenging; in particular, the positions and movement of mobile protons cannot be visualized by current methods of structural analysis. Here we report the experimental observation of fluctuating low-barrier hydrogen bonds as switching elements in cooperativity pathways of multimeric enzymes. We have observed these low-barrier hydrogen bonds in ultra-high-resolution X-ray crystallographic structures of two multimeric enzymes, and have validated their assignment using computational calculations. Catalytic events at the active sites switch between low-barrier hydrogen bonds and ordinary hydrogen bonds in a circuit that consists of acidic side chains and water molecules, transmitting a signal through the collective repositioning of protons by behaving as an atomistic Newton's cradle. The resulting communication synchronizes catalysis in the oligomer. Our studies provide several lines of evidence and a working model for not only the existence of low-barrier hydrogen bonds in proteins, but also a connection to enzyme cooperativity. This finding suggests new principles of drug and enzyme design, in which sequences of residues can be purposefully included to enable long-range communication and thus the regulation of engineered biomolecules.


Asunto(s)
Modelos Moleculares , Transcetolasa/química , Transcetolasa/metabolismo , Dominio Catalítico , Cristalografía por Rayos X , Escherichia coli/química , Escherichia coli/enzimología , Humanos , Enlace de Hidrógeno , Lactobacillus plantarum/enzimología , Lactobacillus plantarum/genética , Simulación de Dinámica Molecular , Mutación , Estructura Terciaria de Proteína , Piruvato Oxidasa/química , Piruvato Oxidasa/genética , Piruvato Oxidasa/metabolismo , Transcetolasa/genética
13.
Chemphyschem ; 20(21): 2881-2886, 2019 11 05.
Artículo en Inglés | MEDLINE | ID: mdl-31489766

RESUMEN

We have computationally determined the catalytic mechanism of human transketolase (hTK) using a cluster model approach and density functional theory calculations. We were able to determine all the relevant structures, bringing solid evidences to the proposed experimental mechanism, and to add important detail to the structure of the transition states and the energy profile associated with catalysis. Furthermore, we have established the existence of a crucial intermediate of the catalytic cycle, in agreement with experiments. The calculated data brought new insights to hTK's catalytic mechanism, providing free-energy values for the chemical reaction, as well as adding atomistic detail to the experimental mechanism.


Asunto(s)
Biocatálisis , Transcetolasa/metabolismo , Teoría Funcional de la Densidad , Humanos , Modelos Moleculares , Estructura Molecular , Termodinámica , Transcetolasa/química
14.
Biochemistry ; 58(52): 5255-5258, 2019 12 31.
Artículo en Inglés | MEDLINE | ID: mdl-31424204

RESUMEN

The biosynthesis of the azinomycins involves the conversion of glutamic acid to an aziridino[1,2-a]pyrrolidine moiety, which together with the epoxide moiety imparts anticancer activity to these agents. The mechanism of azabicycle formation is complex and involves at least 14 enzymatic steps. Previous research has identified N-acetyl-glutamate 5-semialdehyde as a key intermediate, which originates from protection of the amino terminus of glutamic acid and subsequent reduction of the γ-carboxylate. This study reports on the seminal discovery of a thiamin-dependent transketolase responsible for the formation of 2-acetamido-5,6-dihydroxy-6-oxoheptanoic acid, which accounts for the two-carbon extension needed to complete the carbon framework of the azabicycle moiety.


Asunto(s)
Compuestos de Azabiciclo/química , Compuestos de Azabiciclo/metabolismo , Transcetolasa/metabolismo , Humanos , Modelos Moleculares , Conformación Proteica , Transcetolasa/química
15.
BMC Struct Biol ; 19(1): 2, 2019 01 15.
Artículo en Inglés | MEDLINE | ID: mdl-30646877

RESUMEN

BACKGROUND: Three transketolase genes have been identified in the human genome to date: transketolase (TKT), transketolase-like 1 (TKTL1) and transketolase-like 2 (TKTL2). Altered TKT functionality is strongly implicated in the development of diabetes and various cancers, thus offering possible therapeutic utility. It will be of great value to know whether TKTL1 and TKTL2 are, similarly, potential therapeutic targets. However, it remains unclear whether TKTL1 and TKTL2 are functional transketolases. RESULTS: Homology modelling of TKTL1 and TKTL2 using TKT as template, revealed that both TKTL1 and TKTL2 could assume a folded structure like TKT. TKTL1/2 presented a cleft of suitable dimensions between the homodimer surfaces that could accommodate the co-factor-substrate. An appropriate cavity and a hydrophobic nodule were also present in TKTL1/2, into which the diphosphate group fitted, and that was implicated in aminopyrimidine and thiazole ring binding in TKT, respectively. The presence of several identical residues at structurally equivalent positions in TKTL1/2 and TKT identified a network of interactions between the protein and co-factor-substrate, suggesting the functional fidelity of TKTL1/2 as transketolases. CONCLUSIONS: Our data support the hypothesis that TKTL1 and TKTL2 are functional transketolases and represent novel therapeutic targets for diabetes and cancer.


Asunto(s)
Transcetolasa/química , Transcetolasa/metabolismo , Humanos , Enlace de Hidrógeno , Modelos Moleculares , Simulación de Dinámica Molecular , Unión Proteica , Conformación Proteica , Pliegue de Proteína , Pirimidinas/metabolismo , Homología Estructural de Proteína , Tiazoles/metabolismo
16.
Curr Comput Aided Drug Des ; 15(4): 308-317, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-30345923

RESUMEN

BACKGROUND: Orthosiphon stamineus is a traditional medicinal plant in Southeast Asia countries with various well-known pharmacological activities such as antidiabetic, diuretics and antitumor activities. Transketolase is one of the proteins identified in the leaves of the plant and transketolase is believed able to lower blood sugar level in human through non-pancreatic mechanism. In order to understand the protein behavioral properties, 3D model of transketolase and analysis of protein structure are of obvious interest. METHODS: In the present study, 3D model of transketolase was constructed and its atomic characteristics revealed. Besides, molecular dynamic simulation of the protein at 310 K and 368 K deciphered transketolase may be a thermophilic protein as the structure does not distort even at elevated temperature. This study also used the protein at 310 K and 368 K resimulated back at 310 K environment. RESULTS: The results revealed that the protein is stable at all condition which suggest that it has high capacity to adapt at different environment not only at high temperature but also from high temperature condition to low temperature where the structure remains unchanged while retaining protein function. CONCLUSION: The thermostability properties of transketolase is beneficial for pharmaceutical industries as most of the drug making processes are at high temperature condition.


Asunto(s)
Orthosiphon/enzimología , Proteínas de Plantas/química , Transcetolasa/química , Secuencia de Aminoácidos , Estabilidad de Enzimas , Calor , Simulación de Dinámica Molecular , Orthosiphon/química , Conformación Proteica , Alineación de Secuencia
17.
Proc Natl Acad Sci U S A ; 115(52): E12192-E12200, 2018 12 26.
Artículo en Inglés | MEDLINE | ID: mdl-30530661

RESUMEN

The directed evolution of enzymes for improved activity or substrate specificity commonly leads to a trade-off in stability. We have identified an activity-stability trade-off and a loss in unfolding cooperativity for a variant (3M) of Escherichia coli transketolase (TK) engineered to accept aromatic substrates. Molecular dynamics simulations of 3M revealed increased flexibility in several interconnected active-site regions that also form part of the dimer interface. Mutating the newly flexible active-site residues to regain stability risked losing the new activity. We hypothesized that stabilizing mutations could be targeted to residues outside of the active site, whose dynamics were correlated with the newly flexible active-site residues. We previously stabilized WT TK by targeting mutations to highly flexible regions. These regions were much less flexible in 3M and would not have been selected a priori as targets using the same strategy based on flexibility alone. However, their dynamics were highly correlated with the newly flexible active-site regions of 3M. Introducing the previous mutations into 3M reestablished the WT level of stability and unfolding cooperativity, giving a 10.8-fold improved half-life at 55 °C, and increased midpoint and aggregation onset temperatures by 3 °C and 4.3 °C, respectively. Even the activity toward aromatic aldehydes increased up to threefold. Molecular dynamics simulations confirmed that the mutations rigidified the active-site via the correlated network. This work provides insights into the impact of rigidifying mutations within highly correlated dynamic networks that could also be useful for developing improved computational protein engineering strategies.


Asunto(s)
Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/metabolismo , Escherichia coli/enzimología , Transcetolasa/química , Transcetolasa/metabolismo , Aldehídos/química , Aldehídos/metabolismo , Dominio Catalítico , Estabilidad de Enzimas , Escherichia coli/química , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Cinética , Simulación de Dinámica Molecular , Conformación Proteica , Ingeniería de Proteínas , Especificidad por Sustrato , Transcetolasa/genética
18.
Chembiochem ; 19(22): 2395-2402, 2018 11 16.
Artículo en Inglés | MEDLINE | ID: mdl-30155962

RESUMEN

Transketolase (TK) catalyzes a reversible transfer of a two-carbon (C2 ) unit between phosphoketose donors and phosphoaldose acceptors, for which the group-transfer reaction that follows a one- or two-electron mechanism and the force that breaks the C2"-C3" bond of the ketose donors remain unresolved. Herein, we report ultrahigh-resolution crystal structures of a TK (TKps) from Pichia stipitis in previously undiscovered intermediate states and support a diradical mechanism for a reversible group-transfer reaction. In conjunction with MS, NMR spectroscopy, EPR and computational analyses, it is concluded that the enzyme-catalyzed non-Kekulé diradical cofactor brings about the C2"-C3" bond cleavage/formation for the C2 -unit transfer reaction, for which suppression of activation energy and activation and destabilization of enzymatic intermediates are facilitated.


Asunto(s)
Pichia/enzimología , Transcetolasa/química , Biocatálisis , Cristalografía por Rayos X , Escherichia coli/genética , Cinética , Modelos Moleculares , Oxidación-Reducción
19.
Enzyme Microb Technol ; 116: 16-22, 2018 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-29887012

RESUMEN

The use of biocatalysis for the synthesis of high value added chemical building blocks derived from biomass is becoming an increasingly important application for future sustainable technologies. The synthesis of a higher value chemical from l-arabinose, the predominant monosaccharide obtained from sugar beet pulp, is demonstrated here via a transketolase and transaminase coupled reaction. Thermostable transketolases derived from Deinococcus geothermalis and Deinococcus radiodurans catalysed the synthesis of l-gluco-heptulose from l-arabinose and ß-hydroxypyruvate at elevated temperatures with high conversions. ß-Hydroxypyruvate, a commercially expensive compound used in the transketolase reaction, was generated in situ from l-serine and α-ketoglutaric acid via a thermostable transaminase, also from Deinococcus geothermalis. The two steps were investigated and implemented in a one-pot system for the sustainable and efficient production of l-gluco-heptulose.


Asunto(s)
Arabinosa/química , Proteínas Bacterianas/química , Deinococcus/enzimología , Monosacáridos/química , Transaminasas/química , Transcetolasa/química , Arabinosa/metabolismo , Proteínas Bacterianas/metabolismo , Biocatálisis , Deinococcus/química , Estabilidad de Enzimas , Cinética , Estructura Molecular , Monosacáridos/metabolismo , Piruvatos/química , Piruvatos/metabolismo , Transaminasas/metabolismo , Transcetolasa/metabolismo
20.
J Agric Food Chem ; 66(6): 1498-1508, 2018 Feb 14.
Artículo en Inglés | MEDLINE | ID: mdl-29400466

RESUMEN

In the present study, we investigated the role of transketolase (TK) in the modulation of glycolaldehyde driven Maillard reactions. In vitro experiments with recombinant human TK reduced glycolaldehyde and glyoxal induced carbonyl stress and thereby suppressed the formation of advanced glycation endproducts up to 70% due to the enzyme-catalyzed conversion of glycolaldehyde to erythrulose. This was further substantiated by the use of 13C-labeled compounds. For the first time, glycolaldehyde and other sugars involved in the TK reaction were quantified in vivo and compared to nondiabetic uremic patients undergoing hemodialysis. Quantitation revealed amounts of glycolaldehyde up to 2 µM and highlighted its crucial role in the formation of AGEs in vivo. In this context, a LC-MS2 method for the comprehensive detection of sedoheptulose-7-phosphate, fructose-6-phosphate, ribose-5-phosphate, erythrose-4-phosphate, erythrulose, and glycolaldehyde in whole blood, plasma, and red blood cells was established and validated based on derivatization with 1-naphthylamine and sodium cyanoborohydride.


Asunto(s)
Acetaldehído/análogos & derivados , Glioxal/metabolismo , Transcetolasa/química , Transcetolasa/metabolismo , Acetaldehído/metabolismo , Biocatálisis , Fructosafosfatos/metabolismo , Humanos , Reacción de Maillard , Procesamiento Proteico-Postraduccional , Ribosamonofosfatos/metabolismo , Fosfatos de Azúcar/metabolismo
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