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1.
J Biol Chem ; 300(6): 107404, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38782204

RESUMO

Infectious diseases are a significant cause of death, and recent studies estimate that common bacterial infectious diseases were responsible for 13.6% of all global deaths in 2019. Among the most significant bacterial pathogens is Staphylococcus aureus, accounting for more than 1.1 million deaths worldwide in 2019. Vitamin biosynthesis has been proposed as a promising target for antibacterial therapy. Here, we investigated the biochemical, structural, and dynamic properties of the enzyme complex responsible for vitamin B6 (pyridoxal 5-phosphate, PLP) biosynthesis in S. aureus, which comprises enzymes SaPdx1 and SaPdx2. The crystal structure of the 24-mer complex of SaPdx1-SaPdx2 enzymes indicated that the S. aureus PLP synthase complex forms a highly dynamic assembly with transient interaction between the enzymes. Solution scattering data indicated that SaPdx2 typically binds to SaPdx1 at a substoichiometric ratio. We propose a structure-based view of the PLP synthesis mechanism initiated with the assembly of SaPLP synthase complex that proceeds in a highly dynamic interaction between Pdx1 and Pdx2. This interface interaction can be further explored as a potentially druggable site for the design of new antibiotics.


Assuntos
Proteínas de Bactérias , Fosfato de Piridoxal , Staphylococcus aureus , Staphylococcus aureus/enzimologia , Staphylococcus aureus/metabolismo , Fosfato de Piridoxal/metabolismo , Fosfato de Piridoxal/química , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/genética , Cristalografia por Raios X , Conformação Proteica , Ligação Proteica
2.
J Am Chem Soc ; 146(21): 14672-14684, 2024 May 29.
Artigo em Inglês | MEDLINE | ID: mdl-38743881

RESUMO

Pyridoxal 5'-phosphate (PLP)-dependent enzymes are the most versatile biocatalysts for synthesizing nonproteinogenic amino acids. α,α-Disubstituted quaternary amino acids, such as 1-aminocyclopentane-1-carboxylic acid (cycloleucine), are useful building blocks for pharmaceuticals. In this study, starting with the biosynthesis of fusarilin A, we discovered a family of PLP-dependent enzymes that can facilitate tandem carbon-carbon forming steps to catalyze an overall [3 + 2]-annulation. In the first step, the cycloleucine synthases use SAM as the latent electrophile and an in situ-generated enamine as the nucleophile for γ-substitution. Whereas previously characterized γ-replacement enzymes protonate the resulting α-carbon and release the acyclic amino acid, cycloleucine synthases can catalyze an additional, intramolecular aldol or Mannich reaction with the nucleophilic α-carbon to form the substituted cyclopentane. Overall, the net [3 + 2]-annulation reaction can lead to 2-hydroxy or 2-aminocycloleucine products. These studies further expand the biocatalytic scope of PLP-dependent enzymes.


Assuntos
Fosfato de Piridoxal , Fosfato de Piridoxal/metabolismo , Fosfato de Piridoxal/química , Biocatálise , Estrutura Molecular , Ciclopentanos/química , Ciclopentanos/metabolismo
3.
Arch Biochem Biophys ; 756: 110011, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38649133

RESUMO

Structure-function relationships are key to understanding enzyme mechanisms, controlling enzyme activities, and designing biocatalysts. Here, we investigate the functions of arginine residues in the active sites of pyridoxal-5'-phosphate (PLP)-dependent non-canonical d-amino acid transaminases, focusing on the analysis of a transaminase from Haliscomenobacter hydrossis. Our results show that the tandem of arginine residues R28* and R90, which form the conserved R-[RK] motif in non-canonical d-amino acid transaminases, not only facilitates effective substrate binding but also regulates the catalytic properties of PLP. Non-covalent interactions between residues R28*, R90, and Y147 strengthen the hydrogen bond between Y147 and PLP, thereby maintaining the reactivity of the cofactor. Next, the R90 residue contributes to the stability of the holoenzyme. Finally, the R90I substitution induces structural changes that lead to substrate promiscuity, as evidenced by the effective binding of substrates with and without the α-carboxylate group. This study sheds light on the structural determinants of the activity of non-canonical d-amino acid transaminases. Understanding the structural basis of the active site plasticity in the non-canonical transaminase from H. hydrossis, which is characterized by effective conversion of d-amino acids and α-keto acids, may help to tailor it for industrial applications.


Assuntos
Arginina , Domínio Catalítico , Fosfato de Piridoxal , Transaminases , Transaminases/metabolismo , Transaminases/química , Arginina/química , Arginina/metabolismo , Fosfato de Piridoxal/metabolismo , Fosfato de Piridoxal/química , Especificidade por Substrato , Proteínas de Bactérias/química , Proteínas de Bactérias/metabolismo , Modelos Moleculares
4.
Phys Chem Chem Phys ; 26(23): 16579-16588, 2024 Jun 12.
Artigo em Inglês | MEDLINE | ID: mdl-38832404

RESUMO

The transsulfuration pathway plays a key role in mammals for maintaining the balance between cysteine and homocysteine, whose concentrations are critical in several biochemical processes. Human cystathionine ß-synthase is a heme-containing, pyridoxal 5'-phosphate (PLP)-dependent enzyme found in this pathway. The heme group does not participate directly in catalysis, but has a regulatory function, whereby CO or NO binding inhibits the PLP-dependent reactions. In this study, we explore the detailed structural changes responsible for inhibition using quantum chemical calculations to validate the experimentally observed bonding patterns associated with heme CO and NO binding and molecular dynamics simulations to explore the medium-range structural changes triggered by gas binding and propagating to the PLP active site, which is more than 20 Å distant from the heme group. Our results support a previously proposed mechanical signaling model, whereby the cysteine decoordination associated with gas ligand binding leads to breaking of a hydrogen bond with an arginine residue on a neighbouring helix. In turn, this leads to a shift in position of the helix, and hence also of the PLP cofactor, ultimately disrupting a key hydrogen bond that stabilizes the PLP in its catalytically active form.


Assuntos
Cistationina beta-Sintase , Simulação de Dinâmica Molecular , Fosfato de Piridoxal , Cistationina beta-Sintase/metabolismo , Cistationina beta-Sintase/química , Humanos , Fosfato de Piridoxal/metabolismo , Fosfato de Piridoxal/química , Gases/química , Gases/metabolismo , Óxido Nítrico/metabolismo , Óxido Nítrico/química , Ligação de Hidrogênio , Monóxido de Carbono/química , Monóxido de Carbono/metabolismo , Heme/química , Heme/metabolismo , Domínio Catalítico , Teoria Quântica , Cisteína/química , Cisteína/metabolismo
5.
Int J Mol Sci ; 25(9)2024 May 06.
Artigo em Inglês | MEDLINE | ID: mdl-38732264

RESUMO

Pyridoxal and pyridoxal 5'-phosphate are aldehyde forms of B6 vitamin that can easily be transformed into each other in the living organism. The presence of a phosphate group, however, provides the related compounds (e.g., hydrazones) with better solubility in water. In addition, the phosphate group may sometimes act as a binding center for metal ions. In particular, a phosphate group can be a strong ligand for a gold(III) ion, which is of interest for researchers for the anti-tumor and antimicrobial potential of gold(III). This paper aims to answer whether the phosphate group is involved in the complex formation between gold(III) and hydrazones derived from pyridoxal 5'-phosphate. The answer is negative, since the comparison of the stability constants determined for the gold(III) complexes with pyridoxal- and pyridoxal 5'-phosphate-derived hydrazones showed a negligible difference. In addition, quantum chemical calculations confirmed that the preferential coordination of two series of phosphorylated and non-phosphorylated hydrazones to gold(III) ion is similar. The preferential protonation modes for the gold(III) complexes were also determined using experimental and calculated data.


Assuntos
Ouro , Hidrazonas , Piridoxal , Hidrazonas/química , Ouro/química , Piridoxal/química , Fosfato de Piridoxal/química , Complexos de Coordenação/química , Espectrofotometria Ultravioleta , Estrutura Molecular
6.
Angew Chem Int Ed Engl ; 63(13): e202317161, 2024 Mar 22.
Artigo em Inglês | MEDLINE | ID: mdl-38308582

RESUMO

Pyridoxal 5'-phosphate (PLP)-dependent enzymes that catalyze γ-replacement reactions are prevalent, yet their utilization of carbon nucleophile substrates is rare. The recent discovery of two PLP-dependent enzymes, CndF and Fub7, has unveiled unique C-C bond forming capabilities, enabling the biocatalytic synthesis of alkyl- substituted pipecolic acids from O-acetyl-L-homoserine and ß-keto acid or aldehyde derived enolates. This breakthrough presents fresh avenues for the biosynthesis of pipecolic acid derivatives. However, the catalytic mechanisms of these enzymes remain elusive, and a dearth of structural information hampers their extensive application. Here, we have broadened the catalytic scope of Fub7 by employing ketone-derived enolates as carbon nucleophiles, revealing Fub7's capacity for substrate-dependent regioselective α-alkylation of unsymmetrical ketones. Through an integrated approach combining X-ray crystallography, spectroscopy, mutagenesis, and computational docking studies, we offer a detailed mechanistic insight into Fub7 catalysis. Our findings elucidate the structural basis for its substrate specificity, stereoselectivity, and regioselectivity. Our work sets the stage ready for subsequent protein engineering effort aimed at expanding the synthetic utility of Fub7, potentially unlocking novel methods to access a broader array of noncanonical amino acids.


Assuntos
Aminoácidos , Fosfato de Piridoxal , Fosfato de Piridoxal/química , Fosfato de Piridoxal/metabolismo , Cristalografia por Raios X , Especificidade por Substrato , Carbono , Catálise
7.
Chembiochem ; 24(7): e202200669, 2023 04 03.
Artigo em Inglês | MEDLINE | ID: mdl-36652345

RESUMO

PLP-dependent enzymes represent an important class of highly "druggable" enzymes that perform a wide array of critical reactions to support all organisms. Inhibition of individual members of this family of enzymes has been validated as a therapeutic target for pathologies ranging from infection with Mycobacterium tuberculosis to epilepsy. Given the broad nature of the activities within this family of enzymes, we envisioned a universally acting probe to characterize existing and putative members of the family that also includes the necessary chemical moieties to enable activity-based protein profiling experiments. Hence, we developed a probe that contains an N-hydroxyalanine warhead that acts as a covalent inhibitor of PLP-dependent enzymes, a linear diazirine for UV crosslinking, and an alkyne moiety to enable enrichment of crosslinked proteins. Our molecule was used to study PLP-dependent enzymes in vitro as well as look at whole-cell lysates of M. tuberculosis and assess inhibitory activity. The probe was able to enrich and identify LysA, a PLP-dependent enzyme crucial for lysine biosynthesis, through mass spectrometry. Overall, our study shows the utility of this trifunctional first-generation probe. We anticipate further optimization of probes for PLP-dependent enzymes will enable the characterization of rationally designed covalent inhibitors of PLP-dependent enzymes, which will expedite the preclinical characterization of these important therapeutic targets.


Assuntos
Fosfato de Piridoxal , Fosfato de Piridoxal/química , Modelos Moleculares , Espectrometria de Massas
8.
Biotechnol Bioeng ; 120(1): 272-283, 2023 01.
Artigo em Inglês | MEDLINE | ID: mdl-36271696

RESUMO

Pyridoxal 5'-phosphate (pyridoxal phosphate, PLP) is an essential cofactor for multiple enzymatic reactions in industry. However, cofactor engineering based on PLP regeneration and related to the performance of enzymes in chemical production has rarely been discussed. First, we found that MG1655 strain was sensitive to nitrogen source and relied on different amino acids, thus the biomass was significantly reduced when PLP excess in the medium. Then, the six KEIO collection strains were applied to find out the prominent gene in deoxyxylulose-5-phosphate (DXP) pathway, where pdxB was superior in controlling cell growth. Therefore, the clustered regularly interspaced short palindromic repeats interference (CRISPRi) targeted on pdxB in MG1655 was employed to establish a novel direct enzymatic evaluation platform (DEEP) as a high-throughput tool and obtained the optimal modules for incorporating of PLP to enhance the biomass and activity of PLP-dependent enzymes simultaneously. As a result, the biomass has increased by 55% using PlacI promoter driven pyridoxine 5'-phosphate oxidase (PdxH) with a trace amount of precursor. When the strains incorporated DEEP and lysine decarboxylase (CadA), the cadaverine productivity was increased 32% due to the higher expression of CadA. DEEP is not only feasible for high-throughput screening of the best chassis for PLP engineering but also practical in fine-tuning the quantity and quality of enzymes.


Assuntos
Desidrogenases de Carboidrato , Proteínas de Escherichia coli , Cadaverina/metabolismo , Fosfato de Piridoxal/química , Fosfato de Piridoxal/genética , Fosfato de Piridoxal/metabolismo , Escherichia coli/genética , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Fosfatos/metabolismo , Proteínas de Escherichia coli/genética
9.
J Chem Inf Model ; 63(4): 1313-1322, 2023 02 27.
Artigo em Inglês | MEDLINE | ID: mdl-36745546

RESUMO

Aminodeoxychorismate lyase (ADCL) is a kind of pyridoxal-5'-phosphate (PLP)-dependent enzyme that catalyzes the conversion of 4-amino-4-deoxychorismate (ADC) to p-aminobenzoate (PABA), which is a key step for the biosynthesis of folate. To illuminate the reaction details at the atomistic level, an enzyme-substrate reactant model has been constructed, and QM/MM calculations have been performed. Our calculation results reveal that the overall catalytic cycle contains 11 elementary steps, which can be described by three stages, including the transamination reaction of PLP, the release of pyruvate and aromatization of ADC, and the recovery to the initial aldimine. During the reaction, a series of intramolecular proton transfer are involved, which are the key for the C-N bond formation and cleavage as well as the aromatization of the ADC ring. In addition to forming the Schiff base with the pocket residue Lys251 and substrate in the internal aldimine and the external aldimine, respectively, the coenzyme PLP also plays a critical role in the intramolecular proton transfer by employing its hydroxyl oxygen anion and phosphate group. These findings may provide useful information for further understanding the catalytic mechanism of other PLP-dependent enzymes.


Assuntos
Oxo-Ácido-Liases , Prótons , Fosfato de Piridoxal/química , Oxo-Ácido-Liases/química , Fosfatos
10.
Methods ; 206: 69-76, 2022 10.
Artigo em Inglês | MEDLINE | ID: mdl-36049704

RESUMO

The detection of albumin proteins with high accuracy by facile analytical approaches is important for the diagnosis of various diseases. This manuscript introduced an easy-to-prepare Schiff base L by condensing vitamin B6 cofactor pyridoxal 5'-phosphate (PLP) with 2-aminothiophenol for the fluorescence turn-on sensing of bovine serum albumin (BSA) and ovalbumin (OVA). The weakly emissive L showed a significant fluorescence enhancement at 485 and 490 nm in the presence of OVA and BSA with an estimated sensitivity limit of 1.7 µM and 0.3 µM, respectively. The formation of protein-ligand complex restricted the free intramolecular rotation of L is expected to show the selective fluorescence enhancement. The molecular docking and molecular dynamics simulations were performed to examine the binding affinity and modes between BSA/OVA and L. The practical utility of L as a fluorescent turn-on sensor was validated by quantifying BSA and OVA in various real biological samples of milk, serum, egg white and urine with good recovery percentages.


Assuntos
Soroalbumina Bovina , Vitamina B 6 , Ligantes , Simulação de Acoplamento Molecular , Ovalbumina , Fosfatos , Fosfato de Piridoxal/química , Fosfato de Piridoxal/metabolismo , Bases de Schiff/química , Soroalbumina Bovina/química , Espectrometria de Fluorescência , Vitamina B 6/química , Vitaminas
11.
Biochemistry (Mosc) ; 88(5): 600-609, 2023 May.
Artigo em Inglês | MEDLINE | ID: mdl-37331706

RESUMO

O-acetylhomoserine sulfhydrylase is one of the key enzymes in biosynthesis of methionine in Clostridioides difficile. The mechanism of γ-substitution reaction of O-acetyl-L-homoserine catalyzed by this enzyme is the least studied among the pyridoxal-5'-phosphate-dependent enzymes involved in metabolism of cysteine and methionine. To clarify the role of active site residues Tyr52 and Tyr107, four mutant forms of the enzyme with replacements of these residues with phenylalanine and alanine were generated. Catalytic and spectral properties of the mutant forms were investigated. The rate of γ-substitution reaction catalyzed by the mutant forms with replaced Tyr52 residue decreased by more than three orders of magnitude compared to the wild-type enzyme. The Tyr107Phe and Tyr107Ala mutant forms practically did not catalyze this reaction. Replacements of the Tyr52 and Tyr107 residues led to the decrease in affinity of apoenzyme to coenzyme by three orders of magnitude and changes in the ionic state of the internal aldimine of the enzyme. The obtained results allowed us to assume that Tyr52 is involved in ensuring optimal position of the catalytic coenzyme-binding lysine residue at the stages of C-α-proton elimination and elimination of the side group of the substrate. Tyr107 could act as a general acid catalyst at the stage of acetate elimination.


Assuntos
Clostridioides difficile , Clostridioides difficile/metabolismo , Cisteína Sintase/química , Cisteína Sintase/metabolismo , Domínio Catalítico , Clostridioides/metabolismo , Tirosina , Fosfato de Piridoxal/química , Fosfato de Piridoxal/metabolismo , Metionina , Cinética
12.
J Biol Chem ; 297(3): 101046, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34358566

RESUMO

Bacteria require high-efficiency uptake systems to survive and proliferate in nutrient-limiting environments, such as those found in host organisms. ABC transporters in the bacterial plasma membrane provide a mechanism for transport of many substrates. In this study, we examine an operon containing a periplasmic binding protein in Actinobacillus for its potential role in nutrient acquisition. The electron density map of 1.76 Å resolution obtained from the crystal structure of the periplasmic binding protein was best fit with a molecular model containing a pyridoxal-5'-phosphate (P5P/pyridoxal phosphate/the active form of vitamin B6) ligand within the protein's binding site. The identity of the P5P bound to this periplasmic binding protein was verified by isothermal titration calorimetry, microscale thermophoresis, and mass spectrometry, leading us to name the protein P5PA and the operon P5PAB. To illustrate the functional utility of this uptake system, we introduced the P5PAB operon from Actinobacillus pleuropneumoniae into an Escherichia coli K-12 strain that was devoid of a key enzyme required for P5P synthesis. The growth of this strain at low levels of P5P supports the functional role of this operon in P5P uptake. This is the first report of a dedicated P5P bacterial uptake system, but through bioinformatics, we discovered homologs mainly within pathogenic representatives of the Pasteurellaceae family, suggesting that this operon exists more widely outside the Actinobacillus genus.


Assuntos
Transportadores de Cassetes de Ligação de ATP/metabolismo , Actinobacillus pleuropneumoniae/metabolismo , Proteínas de Bactérias/metabolismo , Vitamina B 6/metabolismo , Transportadores de Cassetes de Ligação de ATP/química , Transportadores de Cassetes de Ligação de ATP/genética , Actinobacillus pleuropneumoniae/química , Actinobacillus pleuropneumoniae/genética , Proteínas de Bactérias/química , Proteínas de Bactérias/genética , Sítios de Ligação , Transporte Biológico , Escherichia coli/genética , Escherichia coli/metabolismo , Modelos Moleculares , Óperon , Proteínas Periplásmicas de Ligação/química , Proteínas Periplásmicas de Ligação/genética , Proteínas Periplásmicas de Ligação/metabolismo , Fosfato de Piridoxal/química , Fosfato de Piridoxal/metabolismo , Vitamina B 6/química
13.
J Am Chem Soc ; 144(12): 5435-5440, 2022 03 30.
Artigo em Inglês | MEDLINE | ID: mdl-35293722

RESUMO

Pyridoxal 5'-phosphate (PLP)-dependent enzymes are a group of versatile enzymes that catalyze various reactions, but only a small number of them react with O2. Here, we report an unprecedented PLP-dependent enzyme, NphE, that catalyzes both transamination and two-electron oxidation using O2 as an oxidant. Our intensive analysis reveals that NphE transfers the l-glutamate-derived amine to 1,3,6,8-tetrahydroxynaphthalene-derived mompain to form 8-amino-flaviolin (8-AF) via a highly conjugated quinonoid intermediate that is reactive with O2. During the NphE reaction, O2 is reduced to yield H2O2. An integrated technique involving NphE structure prediction by AlphaFold v2.0 and molecular dynamics simulation suggested the O2-accessible cavity. Our in vivo results demonstrated that 8-AF is a genuine biosynthetic intermediate for the 1,3,6,8-tetrahydroxynaphthalene-derived meroterpenoid naphterpin without an amino group, which was supported by site-directed mutagenesis. This study clearly establishes the NphE reaction product 8-AF as a common intermediate with a cryptic amino group for the biosynthesis of terpenoid-polyketide hybrid natural products.


Assuntos
Produtos Biológicos , Peróxido de Hidrogênio , Oxirredução , Estresse Oxidativo , Fosfato de Piridoxal/química
14.
J Am Chem Soc ; 144(12): 5629-5642, 2022 03 30.
Artigo em Inglês | MEDLINE | ID: mdl-35293728

RESUMO

Human ornithine aminotransferase (hOAT) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that contains a similar active site to that of γ-aminobutyric acid aminotransferase (GABA-AT). Recently, pharmacological inhibition of hOAT was recognized as a potential therapeutic approach for hepatocellular carcinoma. In this work, we first studied the inactivation mechanisms of hOAT by two well-known GABA-AT inactivators (CPP-115 and OV329). Inspired by the inactivation mechanistic difference between these two aminotransferases, a series of analogues were designed and synthesized, leading to the discovery of analogue 10b as a highly selective and potent hOAT inhibitor. Intact protein mass spectrometry, protein crystallography, and dialysis experiments indicated that 10b was converted to an irreversible tight-binding adduct (34) in the active site of hOAT, as was the unsaturated analogue (11). The comparison of kinetic studies between 10b and 11 suggested that the active intermediate (17b) was only generated in hOAT and not in GABA-AT. Molecular docking studies and pKa computational calculations highlighted the importance of chirality and the endocyclic double bond for inhibitory activity. The turnover mechanism of 10b was supported by mass spectrometric analysis of dissociable products and fluoride ion release experiments. Notably, the stopped-flow experiments were highly consistent with the proposed mechanism, suggesting a relatively slow hydrolysis rate for hOAT. The novel second-deprotonation mechanism of 10b contributes to its high potency and significantly enhanced selectivity for hOAT inhibition.


Assuntos
4-Aminobutirato Transaminase , Neoplasias Hepáticas , Ácidos Carboxílicos , Inibidores Enzimáticos/química , Humanos , Cinética , Simulação de Acoplamento Molecular , Ornitina-Oxo-Ácido Transaminase , Fenilacetatos , Fosfato de Piridoxal/química , Ácido gama-Aminobutírico
15.
Chembiochem ; 23(9): e202100555, 2022 05 04.
Artigo em Inglês | MEDLINE | ID: mdl-34762772

RESUMO

The catalytic mechanism of Pdx2 was studied with atomic detail employing the computational ONIOM hybrid QM/MM methodology. Pdx2 employs a Cys-His-Glu catalytic triad to deaminate glutamine to glutamate and ammonia - the source of the nitrogen of pyridoxal 5'-phosphate (PLP). This enzyme is, therefore, a rate-limiting step in the PLP biosynthetic pathway of Malaria and Tuberculosis pathogens that rely on this mechanism to obtain PLP. For this reason, Pdx2 is considered a novel and promising drug target to treat these diseases. The results obtained show that the catalytic mechanism of Pdx2 occurs in six steps that can be divided into four stages: (i) activation of Cys87 , (ii) deamination of glutamine with the formation of the glutamyl-thioester intermediate, (iii) hydrolysis of the formed intermediate, and (iv) enzymatic turnover. The kinetic data available in the literature (19.1-19.5 kcal mol-1 ) agree very well with the calculated free energy barrier of the hydrolytic step (18.2 kcal.mol-11 ), which is the rate-limiting step of the catalytic process when substrate is readily available in the active site. This catalytic mechanism differs from other known amidases in three main points: i) it requires the activation of the nucleophile Cys87 to a thiolate; ii) the hydrolysis occurs in a single step and therefore does not require the formation of a second tetrahedral reaction intermediate, as it is proposed, and iii) Glu198 does not have a direct role in the catalytic process. Together, these results can be used for the synthesis of new transition state analogue inhibitors capable of inhibiting Pdx2 and impair diseases like Malaria and Tuberculosis.


Assuntos
Glutaminase , Malária , Catálise , Ácido Glutâmico , Glutaminase/química , Glutaminase/metabolismo , Glutamina/metabolismo , Humanos , Fosfato de Piridoxal/química
16.
Arch Biochem Biophys ; 731: 109429, 2022 11 30.
Artigo em Inglês | MEDLINE | ID: mdl-36265649

RESUMO

Tyrosine-430 of d-ornithine/d-lysine decarboxylase (DOKDC) is located in the active site, and was suggested to be responsible for the D-stereospecificity of the enzyme. We have prepared the Y430F mutant form of Salmonella enterica serovar typhimurium DOKDC and evaluated its catalytic activity with D- and l-lysine and ornithine. The kinetic results show that the Y430F mutant has measurable decarboxylase activity with both D- and l-lysine and ornithine, which wild type DOKDC does not. Spectroscopic experiments show that these amino acids bind to form external aldimine complexes with the pyridoxal-5'-phosphate with λmax = 425 nm. In addition, we have obtained crystal structures of Y430F DOKDC bound to HEPES, putrescine, d-ornithine, d-lysine, and d-arginine. The d-amino acids bind in the crystals to form equilibrium mixtures of gem-diamine and external aldimine complexes. Furthermore, the crystal structures reveal an unexpected allosteric product activator site for putrescine located on the 2-fold axis between the two active sites. Putrescine binds by donating hydrogen bonds from the ammonium groups to Asp-361 and Gln-358 in the specificity helix of both chains. Addition of 0.1-1 mM putrescine eliminates the lag in steady state kinetics and abolishes the sigmoid kinetics. The catalytic loop was modeled with AlphaFold2, and the model shows that Glu-181 can form additional hydrogen bonds with the bound putrescine, likely stabilizing the catalytic closed conformation.


Assuntos
Carboxiliases , Ornitina , Ornitina/química , Ornitina/metabolismo , Putrescina/química , Ornitina Descarboxilase/genética , Ornitina Descarboxilase/metabolismo , Lisina/metabolismo , Regulação Alostérica , Mutagênese Sítio-Dirigida , Carboxiliases/genética , Carboxiliases/metabolismo , Fosfato de Piridoxal/química , Fosfato de Piridoxal/metabolismo , Cinética , Salmonella/metabolismo
17.
Nat Chem Biol ; 16(8): 904-911, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32483377

RESUMO

Several nucleoside antibiotics are structurally characterized by a 5″-amino-5″-deoxyribose (ADR) appended via a glycosidic bond to a high-carbon sugar nucleoside (5'S,6'S)-5'-C-glycyluridine (GlyU). GlyU is further modified with an N-alkylamine linker, the biosynthetic origin of which has yet to be established. By using a combination of feeding experiments with isotopically labeled precursors and characterization of recombinant proteins from multiple pathways, the biosynthetic mechanism for N-alkylamine installation for ADR-GlyU-containing nucleoside antibiotics has been uncovered. The data reveal S-adenosyl-L-methionine (AdoMet) as the direct precursor of the N-alkylamine, but, unlike conventional AdoMet- or decarboxylated AdoMet-dependent alkyltransferases, the reaction is catalyzed by a pyridoxal-5'-phosphate-dependent aminobutyryltransferase (ABTase) using a stepwise γ-replacement mechanism that couples γ-elimination of AdoMet with aza-γ-addition onto the disaccharide alkyl acceptor. In addition to using a conceptually different strategy for AdoMet-dependent alkylation, the newly discovered ABTases require a phosphorylated disaccharide alkyl acceptor, revealing a cryptic intermediate in the biosynthetic pathway.


Assuntos
Antibacterianos/química , Fosfato de Piridoxal/química , Alquilação/fisiologia , Antibacterianos/farmacologia , Fenômenos Bioquímicos , Metionina/metabolismo , Nucleosídeos/química , Fosfatos , Fosforilação , Proteínas Recombinantes/metabolismo , S-Adenosilmetionina/química
18.
Biosci Biotechnol Biochem ; 86(9): 1161-1172, 2022 Aug 24.
Artigo em Inglês | MEDLINE | ID: mdl-35751623

RESUMO

Enzymology, the study of enzyme structures and reaction mechanisms can be considered a classical discipline. However, enzymes cannot be freely designed to catalyze desired reactions yet, and enzymology is by no means a complete science. I have long studied the reaction mechanisms of enzymes related to amino acid metabolism, such as aminotransferases and racemases, which depend on pyridoxal 5'-phosphate, a coenzyme form of vitamin B6. During these studies, I have often been reminded that enzymatic reactions are extremely sophisticated processes based on chemical principles and enzyme structures, and have often been amazed at the evolutionary mechanisms that bestowed them with such structures. In this review, I described the reaction mechanism of various pyridoxal enzymes especially related to d-amino acids metabolism, whose roles in mammals have recently attracted attention. I hope to convey some of the significance and interest in enzymology through this review.


Assuntos
Fosfato de Piridoxal , Transaminases , Aminoácidos/metabolismo , Animais , Mamíferos/metabolismo , Fosfato de Piridoxal/química , Fosfato de Piridoxal/metabolismo , Racemases e Epimerases , Transaminases/química , Transaminases/metabolismo , Vitamina B 6
19.
Mikrochim Acta ; 189(2): 70, 2022 01 24.
Artigo em Inglês | MEDLINE | ID: mdl-35067757

RESUMO

A colorimetric assay based on polydiacetylenes (PDA) nano-liposomes is reported for facile and sensitive detection of alkaline phosphatase (ALP) activity. The critical basis of this method is that the interaction of pyridoxal phosphate (PLP) with nitrogenous group functionalized PDA nano-liposomes induces distinct blue-to-red color changes of PDA nano-liposomes. In the presence of ALP, as a nature substrate, PLP is enzymatically hydrolyzed to form pyridoxal, which cannot interact with PDA nano-liposomes. As a result, the concentration of PLP is reduced and the color change of PDA nano-liposomes is retarded, which is associated with ALP level. Under optimal conditions, the proposed method showed good linear relationship with ALP activity in the range 10-200 U/L with a limit of detection of 2.8 U/L. The detection process could be vividly observed with the naked eye. Additional attempts by using the method for the evaluation of inhibitor efficiency were also achieved with satisfying results. The method was further challenged with real human serum samples, showing consistent results when compared with a commercial standard assay kit. Such simple and easy-to-use approach may provide a new alternative for clinical and biological detection of ALP.


Assuntos
Fosfatase Alcalina/metabolismo , Colorimetria/métodos , Lipossomos/química , Nanoestruturas/química , Polímero Poliacetilênico/química , Fosfato de Piridoxal/química , Fosfatase Alcalina/química , Sensibilidade e Especificidade
20.
Molecules ; 27(21)2022 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-36364171

RESUMO

Today, complexes of gold(I) and gold(III) are recognized as promising drugs for the treatment of bacterial infectious diseases and oncological diseases, respectively. It is of interest to broaden the area of potential use of gold(III) compounds to the pathogenic microorganism as well. The first step towards the development of new antibacterial drugs based on Au3+ complexes is the study of their stability in an aqueous solution. The present contribution reports on the investigation of gold(III) complexation with five hydrazones derived from a well-known biologically active compound, pyridoxal 5'-phosphate (one of the aldehyde forms of the B6 vitamin). The complex formation in aqueous solutions was confirmed by mass spectrometry and fluorescent spectroscopy. The stoichiometric composition of the complexes formed and their stability constants were determined using a UV-Vis titration method. The complexes are quite stable at physiological values of pH, as the speciation diagrams show. The results of the paper are helpful for further studies of gold(III) complexes interaction with biomacromolecules.


Assuntos
Ouro , Hidrazonas , Hidrazonas/química , Ouro/química , Fosfato de Piridoxal/química , Água , Fosfatos/química
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