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1.
J Biol Chem ; 300(1): 105491, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-37995940

RESUMO

l-2-hydroxyglutarate dehydrogenase (L2HGDH) is a mitochondrial membrane-associated metabolic enzyme, which catalyzes the oxidation of l-2-hydroxyglutarate (l-2-HG) to 2-oxoglutarate (2-OG). Mutations in human L2HGDH lead to abnormal accumulation of l-2-HG, which causes a neurometabolic disorder named l-2-hydroxyglutaric aciduria (l-2-HGA). Here, we report the crystal structures of Drosophila melanogaster L2HGDH (dmL2HGDH) in FAD-bound form and in complex with FAD and 2-OG and show that dmL2HGDH exhibits high activity and substrate specificity for l-2-HG. dmL2HGDH consists of an FAD-binding domain and a substrate-binding domain, and the active site is located at the interface of the two domains with 2-OG binding to the re-face of the isoalloxazine moiety of FAD. Mutagenesis and activity assay confirmed the functional roles of key residues involved in the substrate binding and catalytic reaction and showed that most of the mutations of dmL2HGDH equivalent to l-2-HGA-associated mutations of human L2HGDH led to complete loss of the activity. The structural and biochemical data together reveal the molecular basis for the substrate specificity and catalytic mechanism of L2HGDH and provide insights into the functional roles of human L2HGDH mutations in the pathogeneses of l-2-HGA.


Assuntos
Oxirredutases do Álcool , Encefalopatias Metabólicas Congênitas , Drosophila melanogaster , Modelos Moleculares , Animais , Humanos , Oxirredutases do Álcool/química , Oxirredutases do Álcool/metabolismo , Encefalopatias Metabólicas Congênitas/enzimologia , Encefalopatias Metabólicas Congênitas/genética , Encefalopatias Metabólicas Congênitas/fisiopatologia , Drosophila melanogaster/enzimologia , Glutaratos/metabolismo , Mutação , Domínio Catalítico/genética , Especificidade por Substrato/genética , Estrutura Terciária de Proteína , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo
2.
Biochemistry ; 63(14): 1808-1823, 2024 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-38962820

RESUMO

Theoretical concepts linking the structure, function, and evolution of a protein, while often intuitive, necessitate validation through investigations in real-world systems. Our study empirically explores the evolutionary implications of multiple gene copies in an organism by shedding light on the structure-function modulations observed in Pseudomonas aeruginosa's second copy of ketopantoate reductase (PaKPR2). We demonstrated with two apo structures that the typical active site cleft of the protein transforms into a two-sided pocket where a molecular gate made up of two residues controls the substrate entry site, resulting in its inactivity toward the natural substrate ketopantoate. Strikingly, this structural modification made the protein active against several important α-keto-acid substrates with varied efficiency. Structural constraints at the binding site for this altered functional trait were analyzed with two binary complexes that show the conserved residue microenvironment faces restricted movements due to domain closure. Finally, its mechanistic highlights gathered from a ternary complex structure help in delineating the molecular perspectives behind its kinetic cooperativity toward these broad range of substrates. Detailed structural characteristics of the protein presented here also identified four key amino acid residues responsible for its versatile α-keto-acid reductase activity, which can be further modified to improve its functional properties through protein engineering.


Assuntos
Proteínas de Bactérias , Pseudomonas aeruginosa , Pseudomonas aeruginosa/enzimologia , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/metabolismo , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Evolução Molecular , Domínio Catalítico , Especificidade por Substrato , Modelos Moleculares , Oxirredutases do Álcool/química , Oxirredutases do Álcool/metabolismo , Oxirredutases do Álcool/genética , Cristalografia por Raios X , Conformação Proteica , Cinética
3.
J Biol Chem ; 299(7): 104898, 2023 07.
Artigo em Inglês | MEDLINE | ID: mdl-37295774

RESUMO

Vanillyl alcohol oxidases (VAOs) belong to the 4-phenol oxidases family and are found predominantly in lignin-degrading ascomycetes. Systematical investigation of the enzyme family at the sequence level resulted in discovery and characterization of the second recombinantly produced VAO member, DcVAO, from Diplodia corticola. Remarkably high activities for 2,6-substituted substrates like 4-allyl-2,6-dimethoxy-phenol (3.5 ± 0.02 U mg-1) or 4-(hydroxymethyl)-2,6-dimethoxyphenol (6.3 ± 0.5 U mg-1) were observed, which could be attributed to a Phe to Ala exchange in the catalytic center. In order to rationalize this rare substrate preference among VAOs, we resurrected and characterized three ancestral enzymes and performed mutagenesis analyses. The results indicate that a Cys/Glu exchange was required to retain activity for É£-hydroxylations and shifted the acceptance towards benzyl ethers (up to 4.0 ± 0.1 U mg-1). Our findings contribute to the understanding of the functionality of VAO enzyme group, and with DcVAO, we add a new enzyme to the repertoire of ether cleaving biocatalysts.


Assuntos
Oxirredutases do Álcool , Ascomicetos , Biocatálise , Oxirredutases do Álcool/química , Oxirredutases do Álcool/genética , Oxirredutases do Álcool/metabolismo , Ascomicetos/enzimologia , Fenóis/química , Fenóis/metabolismo , Especificidade por Substrato , Hidroxilação , Éteres/química , Éteres/metabolismo
4.
Anal Chem ; 96(28): 11549-11556, 2024 Jul 16.
Artigo em Inglês | MEDLINE | ID: mdl-38958207

RESUMO

Human-borne acetone is a potent marker of lipid metabolism. Here, an enzyme immobilization method for secondary alcohol dehydrogenase (S-ADH), which is suitable for highly sensitive and selective biosensing of acetone, was developed, and then its applicability was demonstrated for spatiotemporal imaging of concentration distribution. After various investigations, S-ADH-immobilized meshes could be prepared with less than 5% variation by cross-linking S-ADH with glutaraldehyde on a cotton mesh at 40 °C for 15 min. Furthermore, high activity was obtained by adjusting the concentration of the coenzyme nicotinamide adenine dinucleotide (NADH) solution added to the S-ADH-immobilized mesh to 500 µM and the solvent to a potassium phosphate buffer solution at pH 6.5. The gas imaging system using the S-ADH-immobilized mesh was able to image the decrease in NADH fluorescence (ex 340 nm, fl 490 nm) caused by the catalytic reaction of S-ADH and the acetone distribution in the concentration range of 0.1-10 ppm-v, including the breath concentration of healthy people at rest. The exhaled breath of two healthy subjects at 6 h of fasting was quantified as 377 and 673 ppb-v, which were consistent with the values quantified by gas chromatography-mass spectrometry.


Assuntos
Acetona , Testes Respiratórios , Enzimas Imobilizadas , Acetona/análise , Acetona/química , Humanos , Enzimas Imobilizadas/química , Enzimas Imobilizadas/metabolismo , Técnicas Biossensoriais , Oxirredutases do Álcool/química , Oxirredutases do Álcool/metabolismo , Gases/química , Gases/análise , Expiração , NAD/análise , NAD/química , NAD/metabolismo
5.
Chembiochem ; 25(5): e202300811, 2024 03 01.
Artigo em Inglês | MEDLINE | ID: mdl-38269599

RESUMO

Artificial dye-coupled assays have been widely adopted as a rapid and convenient method to assess the activity of methanol dehydrogenases (MDH). Lanthanide(Ln)-dependent XoxF-MDHs are able to incorporate different lanthanides (Lns) in their active site. Dye-coupled assays showed that the earlier Lns exhibit a higher enzyme activity than the late Lns. Despite widespread use, there are limitations: oftentimes a pH of 9 and activators are required for the assay. Moreover, Ln-MDH variants are not obtained by isolation from the cells grown with the respective Ln, but by incubation of an apo-MDH with the Ln. Herein, we report the cultivation of Ln-dependent methanotroph Methylacidiphilum fumariolicum SolV with nine different Lns, the isolation of the respective MDHs and the assessment of the enzyme activity using the dye-coupled assay. We compare these results with a protein-coupled assay using its physiological electron acceptor cytochrome cGJ (cyt cGJ ). Depending on the assay, two distinct trends are observed among the Ln series. The specific enzyme activity of La-, Ce- and Pr-MDH, as measured by the protein-coupled assay, exceeds that measured by the dye-coupled assay. This suggests that early Lns also have a positive effect on the interaction between XoxF-MDH and its cyt cGJ thereby increasing functional efficiency.


Assuntos
Elementos da Série dos Lantanídeos , Elementos da Série dos Lantanídeos/química , Oxirredutases do Álcool/química , Citocromos c/química , Malato Desidrogenase
6.
Appl Microbiol Biotechnol ; 108(1): 410, 2024 Jul 08.
Artigo em Inglês | MEDLINE | ID: mdl-38976076

RESUMO

We characterise a reversible bacterial zinc-containing benzyl alcohol dehydrogenase (BaDH) accepting either NAD+ or NADP+ as a redox cofactor. Remarkably, its redox cofactor specificity is pH-dependent with the phosphorylated cofactors favored at lower and the dephospho-forms at higher pH. BaDH also shows different steady-state kinetic behavior with the two cofactor forms. From a structural model, the pH-dependent shift may affect the charge of a histidine in the 2'-phosphate-binding pocket of the redox cofactor binding site. The enzyme is phylogenetically affiliated to a new subbranch of the Zn-containing alcohol dehydrogenases, which share this conserved residue. BaDH appears to have some specificity for its substrate, but also turns over many substituted benzyl alcohol and benzaldehyde variants, as well as compounds containing a conjugated C=C double bond with the aldehyde carbonyl group. However, compounds with an sp3-hybridised C next to the alcohol/aldehyde group are not or only weakly turned over. The enzyme appears to contain a Zn in its catalytic site and a mixture of Zn and Fe in its structural metal-binding site. Moreover, we demonstrate the use of BaDH in an enzyme cascade reaction with an acid-reducing tungsten enzyme to reduce benzoate to benzyl alcohol. KEY POINTS: •Zn-containing BaDH has activity with either NAD + or NADP+ at different pH optima. •BaDH converts a broad range of substrates. •BaDH is used in a cascade reaction for the reduction of benzoate to benzyl alcohol.


Assuntos
Oxirredutases do Álcool , Álcool Benzílico , Coenzimas , NADP , Oxirredução , Zinco , Concentração de Íons de Hidrogênio , NADP/metabolismo , Especificidade por Substrato , Álcool Benzílico/metabolismo , Álcool Benzílico/química , Cinética , Zinco/metabolismo , Coenzimas/metabolismo , Oxirredutases do Álcool/metabolismo , Oxirredutases do Álcool/química , Oxirredutases do Álcool/genética , NAD/metabolismo , Benzaldeídos/metabolismo , Benzaldeídos/química , Domínio Catalítico , Sítios de Ligação , Filogenia , Modelos Moleculares
7.
Mikrochim Acta ; 191(7): 399, 2024 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-38877162

RESUMO

Nicotine (3-(1-methyl-2-pyrrolidinyl)pyridine) is one of the most common addictive substances, causing the trace detection of nicotine to be very necessary. Herein, we designed and prepared a functionalized nanocomposite CS-PAA (NaYF4:19.5%Yb,0.5%Tm@NaYF4-PAA) using a simple method. The nicotine concentration was quantitatively detected through the inhibition of choline oxidase activity by nicotine and the luminescence intensity of CS-PAA being quenched by Fe3+. The mechanism of Fe3+ quenching CS-PAA emission was inferred by luminescence lifetime and UV-vis absorption spectra characterization. During the nicotine detection, both excitation (980 nm) and emission (802 nm) wavelengths of CS-PAA enable the avoidance of the interference of background fluorescence in complicated food objects, thus providing high selectivity and sensitivity with a linear range of 5-750 ng/mL and a limit of detection of 9.3 nM. The method exhibits an excellent recovery and relative standard deviation, indicating high accuracy and repeatability of the detection of nicotine.


Assuntos
Colina , Limite de Detecção , Nicotina , Nicotina/análise , Nicotina/química , Colina/química , Colina/análise , Nanocompostos/química , Medições Luminescentes/métodos , Oxirredutases do Álcool/química , Luminescência
8.
J Basic Microbiol ; 64(6): e2300751, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38644586

RESUMO

NAD+-dependent (2 R,3 R)­2,3­butanediol dehydrogenase (BDH) from Neisseria gonorrhoeae (NgBDH) is a representative member of the medium-chain dehydrogenase/reductase (MDR) superfamily. To date, little information is available on the substrate binding sites and catalytic residues of BDHs from this superfamily. In this work, according to molecular docking studies, we found that conserved residues Phe120 and Val161 form strong hydrophobic interactions with both (2 R,3 R)­2,3­butanediol (RR-BD) and meso-2,3­butanediol (meso-BD) and that mutations of these residues to alanine or threonine impair substrate binding. To further evaluate the roles of these two residues, Phe120 and Val161 were mutated to alanine or threonine. Kinetic analysis revealed that, relative to those of wild type, the apparent KM values of the Phe120Ala mutant for RR-BD and meso-BD increased 36- and 369-fold, respectively; the catalytic efficiencies of this mutant with RR-BD and meso-BD decreased approximately 586- and 3528-fold, respectively; and the apparent KM values of the Val161Ala mutant for RR-BD and meso-BD increased 4- and 37-fold, respectively, the catalytic efficiencies of this mutant with RR-BD and meso-BD decreased approximately 3- and 28-fold, respectively. Additionally, the Val161Thr mutant slightly decreased catalytic efficiencies (twofold with RR-BD; 7.3-fold with meso-BD) due to an increase in KM (sixfold for RR-BD; 24-fold for meso-BD) and a slight increase (2.8-fold with RR-BD; 3.3-fold with meso-BD) in kcat. These findings validate the critical roles of Phe120 and Val161 of NgBDH in substrate binding and catalysis. Overall, the current study provides a better understanding of the substrate binding and catalysis of BDHs within the MDR superfamily.


Assuntos
Oxirredutases do Álcool , Butileno Glicóis , Simulação de Acoplamento Molecular , Mutagênese Sítio-Dirigida , Neisseria gonorrhoeae , Fenilalanina , Neisseria gonorrhoeae/enzimologia , Neisseria gonorrhoeae/genética , Neisseria gonorrhoeae/metabolismo , Oxirredutases do Álcool/genética , Oxirredutases do Álcool/metabolismo , Oxirredutases do Álcool/química , Cinética , Butileno Glicóis/metabolismo , Fenilalanina/metabolismo , Fenilalanina/genética , Sítios de Ligação , Especificidade por Substrato , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/química , Valina/metabolismo , Valina/genética , Domínio Catalítico , Interações Hidrofóbicas e Hidrofílicas
9.
Int J Mol Sci ; 25(13)2024 Jul 05.
Artigo em Inglês | MEDLINE | ID: mdl-39000491

RESUMO

Derived from the denitrifying bacterium Aromatoleum aromaticum EbN1 (Azoarcus sp.), the enzyme S-1-(4-hydroxyphenyl)-ethanol dehydrogenase (S-HPED) belongs to the short-chain dehydrogenase/reductase family. Using research techniques like UV-Vis spectroscopy, dynamic light scattering, thermal-shift assay and HPLC, we investigated the catalytic and structural stability of S-HPED over a wide temperature range and within the pH range of 5.5 to 9.0 under storage and reaction conditions. The relationship between aggregation and inactivation of the enzyme in various pH environments was also examined and interpreted. At pH 9.0, where the enzyme exhibited no aggregation, we characterized thermally induced enzyme inactivation. Through isothermal and multitemperature analysis of inactivation data, we identified and confirmed the first-order inactivation mechanism under these pH conditions and determined the kinetic parameters of the inactivation process. Additionally, we report the positive impact of glucose as an enzyme stabilizer, which slows down the dynamics of S-HPED inactivation over a wide range of pH and temperature and limits enzyme aggregation. Besides characterizing the stability of S-HPED, the enzyme's catalytic activity and high stereospecificity for 10 prochiral carbonyl compounds were positively verified, thus expanding the spectrum of substrates reduced by S-HPED. Our research contributes to advancing knowledge about the biocatalytic potential of this catalyst.


Assuntos
Estabilidade Enzimática , Concentração de Íons de Hidrogênio , Cinética , Temperatura , Catálise , Oxirredutases do Álcool/química , Oxirredutases do Álcool/metabolismo
10.
Int J Mol Sci ; 25(13)2024 Jul 06.
Artigo em Inglês | MEDLINE | ID: mdl-39000549

RESUMO

Synaptic ribbons are the eponymous specializations of continuously active ribbon synapses. They are primarily composed of the RIBEYE protein that consists of a unique amino-terminal A-domain and carboxy-terminal B-domain that is largely identical to the ubiquitously expressed transcriptional regulator protein CtBP2. Both RIBEYE A-domain and RIBEYE B-domain are essential for the assembly of the synaptic ribbon, as shown by previous analyses of RIBEYE knockout and knockin mice and related investigations. How exactly the synaptic ribbon is assembled from RIBEYE subunits is not yet clear. To achieve further insights into the architecture of the synaptic ribbon, we performed analytical post-embedding immunogold-electron microscopy with direct gold-labelled primary antibodies against RIBEYE A-domain and RIBEYE B-domain for improved ultrastructural resolution. With direct gold-labelled monoclonal antibodies against RIBEYE A-domain and RIBEYE B-domain, we found that both domains show a very similar localization within the synaptic ribbon of mouse photoreceptor synapses, with no obvious differential gradient between the centre and surface of the synaptic ribbon. These data favour a model of the architecture of the synaptic ribbon in which the RIBEYE A-domain and RIBEYE B-domain are located similar distances from the midline of the synaptic ribbon.


Assuntos
Anticorpos Monoclonais , Sinapses , Animais , Camundongos , Sinapses/ultraestrutura , Sinapses/metabolismo , Anticorpos Monoclonais/imunologia , Oxirredutases do Álcool/metabolismo , Oxirredutases do Álcool/química , Proteínas Correpressoras/metabolismo , Imuno-Histoquímica/métodos , Domínios Proteicos , Microscopia Imunoeletrônica/métodos , Proteínas do Tecido Nervoso/metabolismo , Proteínas do Tecido Nervoso/imunologia
11.
Angew Chem Int Ed Engl ; 63(30): e202405833, 2024 Jul 22.
Artigo em Inglês | MEDLINE | ID: mdl-38748747

RESUMO

Nitrogen heterocycles are commonly found in bioactive natural products and drugs. However, the biocatalytic tools for nitrogen heterocycle synthesis are limited. Herein, we report the discovery of vanillyl alcohol oxidases (VAOs) as efficient biocatalysts for the one-pot synthesis of 2-aryl thiazolines from various 4-hydroxybenzaldehydes and aminothiols. The wild-type biocatalyst features a broad scope of 4-hydroxybenzaldehydes. Though the scope of aminothiols is limited, it could be improved via semi-rational protein engineering, generating a variant to produce previously inaccessible cysteine-derived bioactive 2-aryl thiazolines using the wild-type VAO. Benefiting from the derivatizable functional groups in the enzymatic products, we further chemically modified these products to expand the chemical space, offering a new chemoenzymatic strategy for the green and efficient synthesis of structurally diverse 2-aryl-thiazoline derivatives to prompt their use in drug discovery and catalysis.


Assuntos
Tiazóis , Tiazóis/química , Tiazóis/síntese química , Benzaldeídos/química , Biocatálise , Estrutura Molecular , Oxirredutases do Álcool/metabolismo , Oxirredutases do Álcool/química , Álcoois Benzílicos
12.
Proc Natl Acad Sci U S A ; 117(3): 1485-1495, 2020 01 21.
Artigo em Inglês | MEDLINE | ID: mdl-31911473

RESUMO

Many large proteins suffer from slow or inefficient folding in vitro. It has long been known that this problem can be alleviated in vivo if proteins start folding cotranslationally. However, the molecular mechanisms underlying this improvement have not been well established. To address this question, we use an all-atom simulation-based algorithm to compute the folding properties of various large protein domains as a function of nascent chain length. We find that for certain proteins, there exists a narrow window of lengths that confers both thermodynamic stability and fast folding kinetics. Beyond these lengths, folding is drastically slowed by nonnative interactions involving C-terminal residues. Thus, cotranslational folding is predicted to be beneficial because it allows proteins to take advantage of this optimal window of lengths and thus avoid kinetic traps. Interestingly, many of these proteins' sequences contain conserved rare codons that may slow down synthesis at this optimal window, suggesting that synthesis rates may be evolutionarily tuned to optimize folding. Using kinetic modeling, we show that under certain conditions, such a slowdown indeed improves cotranslational folding efficiency by giving these nascent chains more time to fold. In contrast, other proteins are predicted not to benefit from cotranslational folding due to a lack of significant nonnative interactions, and indeed these proteins' sequences lack conserved C-terminal rare codons. Together, these results shed light on the factors that promote proper protein folding in the cell and how biomolecular self-assembly may be optimized evolutionarily.


Assuntos
Proteínas de Escherichia coli/química , Proteínas Intrinsicamente Desordenadas/química , Dobramento de Proteína , Oxirredutases do Álcool/química , Oxirredutases do Álcool/genética , Oxirredutases do Álcool/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Proteínas Intrinsicamente Desordenadas/genética , Proteínas Intrinsicamente Desordenadas/metabolismo , Cinética , Simulação de Dinâmica Molecular , Fosfotransferases/química , Fosfotransferases/genética , Fosfotransferases/metabolismo , Biossíntese de Proteínas , Proteínas Metiltransferases/química , Proteínas Metiltransferases/genética , Proteínas Metiltransferases/metabolismo , Proteínas Repressoras/química , Proteínas Repressoras/genética , Proteínas Repressoras/metabolismo , Tetra-Hidrofolato Desidrogenase/química , Tetra-Hidrofolato Desidrogenase/genética , Tetra-Hidrofolato Desidrogenase/metabolismo
13.
J Biol Chem ; 296: 100351, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33524397

RESUMO

C-terminal binding proteins (CtBPs) are cotranscriptional factors that play key roles in cell fate. We have previously shown that NAD(H) promotes the assembly of similar tetramers from either human CtBP1 and CtBP2 and that CtBP2 tetramer destabilizing mutants are defective for oncogenic activity. To assist structure-based design efforts for compounds that disrupt CtBP tetramerization, it is essential to understand how NAD(H) triggers tetramer assembly. Here, we investigate the moieties within NAD(H) that are responsible for triggering tetramer formation. Using multiangle light scattering (MALS), we show that ADP is able to promote tetramer formation of both CtBP1 and CtBP2, whereas AMP promotes tetramer assembly of CtBP1, but not CtBP2. Other NAD(H) moieties that lack the adenosine phosphate, including adenosine and those incorporating nicotinamide, all fail to promote tetramer assembly. Our crystal structures of CtBP1 with AMP reveal participation of the adenosine phosphate in the tetrameric interface, pinpointing its central role in NAD(H)-linked assembly. CtBP1 and CtBP2 have overlapping but unique roles, suggesting that a detailed understanding of their unique structural properties might have utility in the design of paralog-specific inhibitors. We investigated the different responses to AMP through a series of site-directed mutants at 13 positions. These mutations reveal a central role for a hinge segment, which we term the 120s hinge that connects the substrate with coenzyme-binding domains and influences nucleotide binding and tetramer assembly. Our results provide insight into suitable pockets to explore in structure-based drug design to interfere with cotranscriptional activity of CtBP in cancer.


Assuntos
Oxirredutases do Álcool/metabolismo , Proteínas Correpressoras/metabolismo , Proteínas de Ligação a DNA/metabolismo , NADP/metabolismo , Oxirredutases do Álcool/química , Proteínas Correpressoras/química , Proteínas de Ligação a DNA/química , Humanos , Modelos Moleculares , NAD/metabolismo , Multimerização Proteica
14.
Chembiochem ; 23(5): e202100589, 2022 03 04.
Artigo em Inglês | MEDLINE | ID: mdl-34951083

RESUMO

(S)-3-Cyclopentyl-3-hydroxypropanenitrile is the key precursor for the synthesis of ruxolitinib. The bioreduction of 3-cyclopentyl-3-ketopropanenitrile (1 a) offers an attractive method to access this important compound. A carbonyl reductase (PhADH) from Paraburkholderia hospita catalyzed the reduction of 1 a giving the (S)-alcohol (1 b) with 85 % ee. Rational engineering of PhADH resulted in a double mutant H93C/A139L, which enhanced the enantioselectivity from 85 % to >98 %, as well as a 6.3-fold improvement in the specific activity. The bioreduction of 1 a was performed at 200 g/L (1.5 M) substrate concentration, leading to isolation of (S)-1 b in 91 % yield. Similarly, using this mutant enzyme, 3-cyclohexyl-3-ketopropanenitrile (2 a) and 3-phenyl-3-ketopropanenitrile (3 a) were reduced at high concentration affording the corresponding alcohols in >99 % ee, and 90 % and 92 % yield, respectively. The results showed that the variant H93C/A139L was a powerful biocatalyst for reduction of ß-substituted-ß-ketonitriles.


Assuntos
Oxirredutases do Álcool , Nitrilas , Oxirredutases do Álcool/química , Etanol , Pirazóis , Pirimidinas , Estereoisomerismo
15.
Chembiochem ; 23(3): e202100553, 2022 02 04.
Artigo em Inglês | MEDLINE | ID: mdl-34859558

RESUMO

Flavonoids are secondary metabolites ubiquitously found in plants. Their antioxidant properties make them highly interesting natural compounds for use in pharmacology. Therefore, unravelling the mechanisms of flavonoid biosynthesis is an important challenge. Among all the enzymes involved in this biosynthetic pathway, dihydroflavonol-4-reductase (DFR) plays a key role in the production of anthocyanins and proanthocyanidins. Here, we provide new information on the mechanism of action of this enzyme by using QM/MM-MD simulations applied to both dihydroquercetin (DHQ) and dihydrokaempferol (DHK) substrates. The consideration of these very similar compounds shed light on the major role played by the enzyme on the stabilization of the transition state but also on the activation of the substrate before the reaction through near-attack conformer effects.


Assuntos
Oxirredutases do Álcool/metabolismo , Flavonoides/biossíntese , Simulação de Dinâmica Molecular , Teoria Quântica , Quercetina/análogos & derivados , Oxirredutases do Álcool/química , Biocatálise , Flavonoides/química , Conformação Molecular , Quercetina/biossíntese , Quercetina/química , Especificidade por Substrato , Vitis/enzimologia
16.
Nat Chem Biol ; 16(5): 493-496, 2020 05.
Artigo em Inglês | MEDLINE | ID: mdl-32066969

RESUMO

Nonribosomal depsipeptides are natural products composed of amino and hydroxy acid residues. The hydroxy acid residues often derive from α-keto acids, reduced by ketoreductase domains in the depsipeptide synthetases. Biochemistry and structures reveal the mechanism of discrimination for α-keto acids and a remarkable architecture: flanking intact adenylation and ketoreductase domains are sequences separated by >1,100 residues that form a split 'pseudoAsub' domain, structurally important for the depsipeptide module's synthetic cycle.


Assuntos
Depsipeptídeos/biossíntese , Cetoácidos/química , Peptídeo Sintases/química , Peptídeo Sintases/metabolismo , Oxirredutases do Álcool/química , Bacillus/enzimologia , Proteínas de Bactérias/química , Cristalografia por Raios X , Depsipeptídeos/química , Cetoácidos/metabolismo , Lisina/metabolismo , Peptídeo Sintases/genética , Conformação Proteica , Domínios Proteicos
17.
PLoS Comput Biol ; 17(9): e1009446, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34555022

RESUMO

Only a small fraction of genes deposited to databases have been experimentally characterised. The majority of proteins have their function assigned automatically, which can result in erroneous annotations. The reliability of current annotations in public databases is largely unknown; experimental attempts to validate the accuracy within individual enzyme classes are lacking. In this study we performed an overview of functional annotations to the BRENDA enzyme database. We first applied a high-throughput experimental platform to verify functional annotations to an enzyme class of S-2-hydroxyacid oxidases (EC 1.1.3.15). We chose 122 representative sequences of the class and screened them for their predicted function. Based on the experimental results, predicted domain architecture and similarity to previously characterised S-2-hydroxyacid oxidases, we inferred that at least 78% of sequences in the enzyme class are misannotated. We experimentally confirmed four alternative activities among the misannotated sequences and showed that misannotation in the enzyme class increased over time. Finally, we performed a computational analysis of annotations to all enzyme classes in the BRENDA database, and showed that nearly 18% of all sequences are annotated to an enzyme class while sharing no similarity or domain architecture to experimentally characterised representatives. We showed that even well-studied enzyme classes of industrial relevance are affected by the problem of functional misannotation.


Assuntos
Oxirredutases do Álcool/classificação , Bases de Dados de Proteínas/estatística & dados numéricos , Anotação de Sequência Molecular/estatística & dados numéricos , Oxirredutases do Álcool/química , Oxirredutases do Álcool/genética , Animais , Biologia Computacional , Enzimas/química , Enzimas/classificação , Enzimas/genética , Humanos , Modelos Moleculares , Domínios Proteicos , Homologia de Sequência de Aminoácidos
18.
Phys Chem Chem Phys ; 24(25): 15397-15405, 2022 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-35704886

RESUMO

Pyrroloquinoline quinone (PQQ) is a redox cofactor in calcium- and lanthanide-dependent alcohol dehydrogenases that has been known and studied for over 40 years. Despite its long history, many questions regarding its fluorescence properties, speciation in solution and in the active site of alcohol dehydrogenase remain open. Here we investigate the effects of pH and temperature on the distribution of different PQQ species (H3PQQ to PQQ3- in addition to water adducts and in complex with lanthanides) with NMR and UV-Vis spectroscopy as well as time-resolved laser-induced fluorescence spectroscopy (TRLFS). Using a europium derivative from a new, recently-discovered class of lanthanide-dependent methanol dehydrogenase (MDH) enzymes, we utilized two techniques to monitor Ln binding to the active sites of these enzymes. Employing TRLFS, we were able to follow Eu(III) binding directly to the active site of MDH using its luminescence and could quantify three Eu(III) states: Eu(III) in the active site of MDH, but also in solution as PQQ-bound Eu(III) and in the aquo-ion form. Additionally, we used the antenna effect to study PQQ and simultaneously Eu(III) in the active site.


Assuntos
Elementos da Série dos Lantanídeos , Cofator PQQ , Oxirredutases do Álcool/química , Metanol/química , Cofator PQQ/química
19.
Biotechnol Appl Biochem ; 69(6): 2530-2539, 2022 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-34902878

RESUMO

A novel short-chain alcohol dehydrogenase from Tarenaya hassleriana labeled as putative tropinone reductase was heterologously expressed in Escherichia coli. Purified recombinant protein had molecular weight of approximately 30 kDa on 12% sodium dodecyl sulfate-polyacrylamide gel electrophoresis. T. hassleriana tropinone reductase-like enzyme (ThTRL) had not detected oxidative activity. The optimum pH for enzyme activity of ThTRL was weakly acidic (pH 5.0). 50°C was the optimum temperature for ThTRL. The highest catalytic efficiency and substrate affinity for recombinant ThTRL were observed with (+)-camphorquinone (kcat /Km  = 814.3 s-1  mM-1 , Km  = 44.25 µM). ThTRL exhibited a broad substrate specificity and reduced various carbonyl compounds, including small lipophilic aldehydes and ketones, terpene ketones, and their structural analogs.


Assuntos
Oxirredutases do Álcool , Escherichia coli , Especificidade por Substrato , Oxirredutases do Álcool/química , Proteínas Recombinantes/química , Escherichia coli/genética , Escherichia coli/metabolismo , Cetonas/metabolismo , Cinética , Peso Molecular
20.
Cell Mol Life Sci ; 78(24): 8187-8208, 2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-34738149

RESUMO

There is significant contemporary interest in the application of enzymes to replace or augment chemical reagents toward the development of more environmentally sound and sustainable processes. In particular, copper radical oxidases (CRO) from Auxiliary Activity Family 5 Subfamily 2 (AA5_2) are attractive, organic cofactor-free catalysts for the chemoselective oxidation of alcohols to the corresponding aldehydes. These enzymes were first defined by the archetypal galactose-6-oxidase (GalOx, EC 1.1.3.13) from the fungus Fusarium graminearum. The recent discovery of specific alcohol oxidases (EC 1.1.3.7) and aryl alcohol oxidases (EC 1.1.3.47) within AA5_2 has indicated a potentially broad substrate scope among fungal CROs. However, only relatively few AA5_2 members have been characterized to date. Guided by sequence similarity network and phylogenetic analysis, twelve AA5_2 homologs have been recombinantly produced and biochemically characterized in the present study. As defined by their predominant activities, these comprise four galactose 6-oxidases, two raffinose oxidases, four broad-specificity primary alcohol oxidases, and two non-carbohydrate alcohol oxidases. Of particular relevance to applications in biomass valorization, detailed product analysis revealed that two CROs produce the bioplastics monomer furan-2,5-dicarboxylic acid (FDCA) directly from 5-hydroxymethylfurfural (HMF). Furthermore, several CROs could desymmetrize glycerol (a by-product of the biodiesel industry) to D- or L-glyceraldehyde. This study furthers our understanding of CROs by doubling the number of characterized AA5_2 members, which may find future applications as biocatalysts in diverse processes.


Assuntos
Cobre/metabolismo , Radicais Livres/metabolismo , Proteínas Fúngicas/metabolismo , Fusarium/enzimologia , Metaloproteínas/metabolismo , Oxirredutases/metabolismo , Filogenia , Oxirredutases do Álcool/química , Oxirredutases do Álcool/metabolismo , Cobre/química , Radicais Livres/química , Proteínas Fúngicas/química , Metaloproteínas/química , Oxirredução , Oxirredutases/química , Conformação Proteica , Especificidade por Substrato
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