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EcoSal Plus 2015The transition element molybdenum (Mo) is of primordial importance for biological systems, because it is required by enzymes catalyzing key reactions in the global... (Review)
Review
The transition element molybdenum (Mo) is of primordial importance for biological systems, because it is required by enzymes catalyzing key reactions in the global carbon, sulfur, and nitrogen metabolism. To gain biological activity, Mo has to be complexed by a special cofactor. With the exception of bacterial nitrogenase, all Mo-dependent enzymes contain a unique pyranopterin-based cofactor coordinating a Mo atom at their catalytic site. Various types of reactions are catalyzed by Mo-enzymes in prokaryotes including oxygen atom transfer, sulfur or proton transfer, hydroxylation, or even nonredox reactions. Mo-enzymes are widespread in prokaryotes and many of them were likely present in the Last Universal Common Ancestor. To date, more than 50--mostly bacterial--Mo-enzymes are described in nature. In a few eubacteria and in many archaea, Mo is replaced by tungsten bound to the same unique pyranopterin. How Mo-cofactor is synthesized in bacteria is reviewed as well as the way until its insertion into apo-Mo-enzymes.
Topics: Archaea; Bacteria; Biocatalysis; Coenzymes; Enzymes; Escherichia coli; Metalloproteins; Molybdenum; Molybdenum Cofactors; Nitrogenase; Pteridines; Pterins; Sulfur; Tungsten
PubMed: 26435257
DOI: 10.1128/ecosalplus.ESP-0006-2013 -
Biological Chemistry Aug 2017The biosynthesis of the molybdenum cofactor (Moco) is a highly conserved pathway in bacteria, archaea and eukaryotes. The molybdenum atom in Moco-containing enzymes is... (Review)
Review
The biosynthesis of the molybdenum cofactor (Moco) is a highly conserved pathway in bacteria, archaea and eukaryotes. The molybdenum atom in Moco-containing enzymes is coordinated to the dithiolene group of a tricyclic pyranopterin monophosphate cofactor. The biosynthesis of Moco can be divided into three conserved steps, with a fourth present only in bacteria and archaea: (1) formation of cyclic pyranopterin monophosphate, (2) formation of molybdopterin (MPT), (3) insertion of molybdenum into MPT to form Mo-MPT, and (4) additional modification of Mo-MPT in bacteria with the attachment of a GMP or CMP nucleotide, forming the dinucleotide variants of Moco. While the proteins involved in the catalytic reaction of each step of Moco biosynthesis are highly conserved among the Phyla, a surprising link to other cellular pathways has been identified by recent discoveries. In particular, the pathways for FeS cluster assembly and thio-modifications of tRNA are connected to Moco biosynthesis by sharing the same protein components. Further, proteins involved in Moco biosynthesis are not only shared with other pathways, but additionally have moonlighting roles. This review gives an overview of Moco biosynthesis in bacteria and humans and highlights the shared function and moonlighting roles of the participating proteins.
Topics: Animals; Archaeal Proteins; Bacterial Proteins; Coenzymes; Humans; Metalloproteins; Molybdenum Cofactors; Organophosphorus Compounds; Pteridines; Pterins
PubMed: 28284029
DOI: 10.1515/hsz-2017-0110 -
Free Radical Biology & Medicine Aug 2021Folates (vitamin B9) are essential components of our diet and our gut microbiota. They are omnipresent in our cells and blood. Folates are necessary for DNA synthesis,... (Review)
Review
Folates (vitamin B9) are essential components of our diet and our gut microbiota. They are omnipresent in our cells and blood. Folates are necessary for DNA synthesis, methylation, and other vital bioprocesses. Folic acid (FA), as the synthetic form of folates, is largely found in supplements and fortified foods. FA and folate drugs are also extensively used as therapeutics. Therefore, we are continuously exposed to the pterin derivatives, and their photo-degradation products, such as 6-formylpterin (6-FPT) and pterin-6-carboxylic acid. During ultraviolet radiation, these two photolytic products generate reactive oxygen species (ROS) responsible for the cellular oxidative stress. 6-FPT can exhibit variable pro/anti-oxidative roles depending on the cell type and its environment (acting as a cell protector in normal cells, or as an enhancer of drug-induced cell death in cancer cells). The ROS-modulating capacity of 6-FPT is well-known, whereas its intrinsic reactivity has been much less investigated. Here, we have reviewed the properties of 6-FPT and highlighted its capacity to form covalent adducts with the ROS-scavenging drug edaravone (used to treat stroke and amyotrophic lateral sclerosis) as well as its implication in immune surveillance. 6-FPT and its analogue acetyl-6-FPT function as small molecule antigens, recognized by the major histocompatibility complex-related class I-like molecule, MR1, for presentation to mucosal-associated invariant T (MAIT) cells. As modulators of the MR1/MAIT machinery, 6-FPT derivatives could play a significant immuno-regulatory role in different diseases. This brief review shed light on the multiple properties and cellular activities of 6-FPT, well beyond its primary ROS-generating activity.
Topics: Folic Acid; Histocompatibility Antigens Class I; Pterins; Ultraviolet Rays
PubMed: 33965562
DOI: 10.1016/j.freeradbiomed.2021.05.002 -
Accounts of Chemical Research Sep 2021Over the past decade, we have contributed to the chemistry of microbial natural products and synthetic ligands, related to riboflavin and uracils, that modulate immune...
Over the past decade, we have contributed to the chemistry of microbial natural products and synthetic ligands, related to riboflavin and uracils, that modulate immune cells called mucosal associated invariant T cells (MAIT cells). These highly abundant T lymphocytes were only discovered in 2003 and have become recognized for their importance in mammalian immunology. Unlike other T cells, MAIT cells are not activated by peptide or lipid antigens. In collaboration with immunology and structural biology research groups, we discovered that they are instead activated by unstable nitrogen-containing heterocycles synthesized by bacteria. The most potent naturally occurring activating compound (antigen) is -(2-oxopropylideneamino)-d-ribitylaminouracil (5-OP-RU). This compound is an imine (Schiff base) formed through condensation between an intermediate in the biosynthesis of riboflavin (vitamin B2) and a metabolic byproduct of mammalian and microbial glycolysis. Although it is very unstable in water due to intramolecular ring closure or hydrolysis, we were able to develop a non-enzymatic synthesis that yields a pure kinetically stable compound in a nonaqueous solvent. This compound has revolutionized the study of MAIT cell immunology due to its potent activation (EC = 2 pM) of MAIT cells and its development into immunological reagents for detecting and characterizing MAIT cells in tissues. MAIT cells are now linked to key physiological processes and disease, including antibacterial defense, tissue repair, regulation of graft--host disease, gastritis, inflammatory bowel diseases, and cancer. 5-OP-RU activates MAIT cells and, like a vaccine, has been shown to protect mice from bacterial infections and cancers. Mechanistic studies on the binding of 5-OP-RU to its dual protein targets, the major histocompatibility complex class I related protein (MR1) and the MAIT cell receptor (MAIT TCR), have involved synthetic chemistry, 2D H NMR spectroscopy, mass spectrometry, computer modeling and molecular dynamics simulations, biochemical, cellular, and immunological assays, and protein structural biology. These combined studies have revealed structural influences for 5-OP-RU in solution on protein binding and antigen presentation and potency; informed the development of potent (EC = 2 nM) and water stable analogues; led to fluorescent analogues for detecting and tracking binding proteins in and on cells; and enabled discovery of drugs and drug-like molecules that bind MR1 and modulate MAIT cell function. MAIT cells offer new opportunities for chemical synthesis to enhance the stability, potency, selectivity, and bioavailability of small molecule ligands for MR1 or MAIT TCR proteins, and to contribute to the understanding of T cell immunity and the development of prospective new immunomodulating medicines.
Topics: Animals; Antigens; Folic Acid; Humans; Molecular Structure; Mucosal-Associated Invariant T Cells; Protein Folding; Riboflavin; Structure-Activity Relationship
PubMed: 34415738
DOI: 10.1021/acs.accounts.1c00359 -
Biochemistry Jan 2018The radical SAM (S-adenosyl-l-methionine) superfamily is one of the largest group of enzymes with >113000 annotated sequences [Landgraf, B. J., et al. (2016) Annu. Rev.... (Review)
Review
The radical SAM (S-adenosyl-l-methionine) superfamily is one of the largest group of enzymes with >113000 annotated sequences [Landgraf, B. J., et al. (2016) Annu. Rev. Biochem. 85, 485-514]. Members of this superfamily catalyze the reductive cleavage of SAM using an oxygen sensitive 4Fe-4S cluster to transiently generate 5'-deoxyadenosyl radical that is subsequently used to initiate diverse free radical-mediated reactions. Because of the unique reactivity of free radicals, radical SAM enzymes frequently catalyze chemically challenging reactions critical for the biosynthesis of unique structures of cofactors and natural products. In this Perspective, I will discuss the impact of characterizing novel functions in radical SAM enzymes on our understanding of biosynthetic pathways and use two recent examples from my own group with a particular emphasis on two radical SAM enzymes that are responsible for carbon skeleton formation during the biosynthesis of a cofactor and natural products.
Topics: Biological Products; Carbon-Carbon Lyases; Coenzymes; Crystallography, X-Ray; Escherichia coli Proteins; Guanosine Triphosphate; Humans; Isomerases; Metalloproteins; Models, Molecular; Molecular Structure; Molybdenum Cofactors; Nuclear Proteins; Organophosphorus Compounds; Protein Conformation; Pteridines; Pterins; Recombinant Proteins; S-Adenosylmethionine
PubMed: 29072833
DOI: 10.1021/acs.biochem.7b00878 -
Metabolomics : Official Journal of the... Dec 2021Pteridines include folate-derived metabolites that have been putatively associated with certain cancers in clinical studies. However, their biological significance in...
INTRODUCTION
Pteridines include folate-derived metabolites that have been putatively associated with certain cancers in clinical studies. However, their biological significance in cancer metabolism and role in cancer development and progression remains poorly understood.
OBJECTIVES
The purpose of this study was to examine the effects of tumorigenicity on pteridine metabolism by studying a panel of 15 pteridine derivatives using a progressive breast cancer cell line model with and without folic acid dosing.
METHODS
The MCF10A progressive breast cancer model, including sequentially derived MCF10A (benign), MCF10AT (premalignant), and MCF10CA1a (malignant) cell lines were dosed with 0, 100, and 250 mg/L folic acid. Pteridines were analyzed in both intracellular and extracellular contexts using an improved high-performance liquid chromatography-tandem mass spectrometry method.
RESULTS
Pteridines were located predominately in the extracellular media. Folic acid dosing increased extracellular levels of pterin, 6-hydroxylumazine, xanthopterin, 6-hydroxymethylpterin, and 6-carboxypterin in a dose-dependent manner. In particular, pterin and 6-hydroxylumazine levels were positively correlated with tumorigenicity upon folate dosing.
CONCLUSIONS
Folic acid is a primary driver for pteridine metabolism in human breast cell. Higher folate levels contribute to increased formation and excretion of pteridine derivatives to the extracellular media. In breast cancer, this metabolic pathway becomes dysregulated, resulting in the excretion of certain pteridine derivatives and providing in vitro evidence for the observation of elevated pteridines in the urine of breast cancer patients. Finally, this study reports a novel use of the MCF10A progressive breast cancer model for metabolomics applications that may readily be applied to other metabolites of interest.
Topics: Breast Neoplasms; Chromatography, High Pressure Liquid; Female; Humans; Metabolomics; Pteridines
PubMed: 34919200
DOI: 10.1007/s11306-021-01861-9 -
Biochemistry Feb 2023Flavins are blue-light-absorbing chromophores with rich redox activity. Biologically, the most important are riboflavin (vitamin B), flavin mononucleotide, and flavin...
Flavins are blue-light-absorbing chromophores with rich redox activity. Biologically, the most important are riboflavin (vitamin B), flavin mononucleotide, and flavin adenine dinucleotide, the latter two of which are catalytic cofactors in enzymes. Flavins pivot between oxidized, one electron-, and two electron-reduced forms in different protonation states, depending on enzymatic requirements. Some flavoenzymes use light as a reagent for chemical bond formation, photoinduced electron transfer, or conformational changes required for light-sensitive signaling. Therefore, the photochemistry and photophysics of flavins have received wide attention. Fluorescence from oxidized flavin is often used to detect and track changes in flavin oxidation states. However, there have been conflicting reports over the past 45 years as to whether reduced flavin in solution has detectable fluorescence. Here, using single photon counting emission spectroscopy with rigorous sample preparation, we show definitively that reduced flavins are essentially nonfluorescent, having a quantum yield more than three orders of magnitude lower than oxidized flavin. This result will force a re-evaluation of experiments and models that assumed otherwise.
Topics: Flavins; Riboflavin; Oxidation-Reduction; Electron Transport; Flavin-Adenine Dinucleotide; Flavin Mononucleotide; Organic Chemicals
PubMed: 36689576
DOI: 10.1021/acs.biochem.2c00538 -
Accounts of Chemical Research Nov 2017Nitrogenase is known for its remarkable ability to catalyze the reduction of N to NH, and C substrates to short-chain hydrocarbon products, under ambient conditions. The...
Nitrogenase is known for its remarkable ability to catalyze the reduction of N to NH, and C substrates to short-chain hydrocarbon products, under ambient conditions. The best-studied Mo-nitrogenase utilizes a complex metallocofactor as the site of substrate binding and reduction. Designated the M-cluster, this [MoFeSC(R-homocitrate)] cluster can be viewed as [MoFeS] and [FeS] subclusters bridged by three μ-sulfides and one μ-interstitial carbide, with its Mo end further coordinated by an R-homocitrate moiety. The unique cofactor has attracted considerable attention ever since its discovery; however, the complexity of its structure has hindered mechanistic understanding and chemical synthesis of this cofactor. Motivated by the pressing questions related to the structure and function of the nitrogenase cofactor, one major thrust of our research has been to unravel the key biosynthetic steps of this metallocluster to cultivate a deeper understanding of these reactions and their effects on functionalizing the cofactor. In this Account, we will discuss our recent work that provides insights into how simple Fe and S atoms, along with a single C atom, a heterometallic Mo atom and an organic homocitrate entity, are assembled into one of the most complex metalloclusters known in Nature. Combined biochemical, spectroscopic and structural studies have led us to a working model of M-cluster assembly, which starts with the sequential synthesis of small [FeS] and [FeS] units by NifS/U, followed by the coupling and rearrangement of two [FeS] clusters on NifB concomitant with the insertion of an interstitial carbide and a "9th sulfur" that give rise to a [FeSC] core that is nearly indistinguishable in structure to the M-cluster except for the absence of Mo and homocitrate. This 8Fe core is then matured into an M-cluster on NifEN upon substitution of a Mo-homocitrate conjugate for one terminal Fe atom of the cluster prior to transfer of the M-cluster to its target binding site in the catalytic component of Mo-nitrogenase. Taking stock of the elemental inventory during the cofactor assembly process, the core Fe and S atoms are derived from modular fusion of FeS building blocks, going through 2Fe, 4Fe and 8Fe stages to generate an 8Fe core of the cofactor. However, such a flow of Fe/S along the biosynthetic pathway of the M-cluster is "intervened" by the insertion of C and Mo, which renders the cofactor unique in structure and reactivity. Insertion of C occurs through a novel, radical SAM-dependent mechanism, which involves SN2-type methyl transfer from SAM to a [FeS] cluster pair, hydrogen abstraction of the transferred methyl group by a SAM-derived 5'-dA· radical, and further deprotonation of the resultant methylene radical concomitant with radical chemistry-based coupling and rearrangement of the [FeS] cluster pair into an [FeSC] core. Insertion of Mo, on the other hand, employs an ATPase-dependent mechanism that parallels metal trafficking in the biosynthesis of molybdopterin and CO dehydrogenase cofactors. These findings provide a nice framework for further exploration of the "black box" of nitrogenase cofactor assembly and function.
Topics: Coenzymes; Metalloproteins; Molybdenum Cofactors; Nitrogenase; Pteridines
PubMed: 29064664
DOI: 10.1021/acs.accounts.7b00417 -
International Journal of Molecular... Dec 2022Pterins are an inseparable part of living organisms. Pterins participate in metabolic reactions mostly as tetrahydropterins. Dihydropterins are usually intermediates of... (Review)
Review
Pterins are an inseparable part of living organisms. Pterins participate in metabolic reactions mostly as tetrahydropterins. Dihydropterins are usually intermediates of these reactions, whereas oxidized pterins can be biomarkers of diseases. In this review, we analyze the available data on the quantum chemistry of unconjugated pterins as well as their photonics. This gives a comprehensive overview about the electronic structure of pterins and offers some benefits for biomedicine applications: (1) one can affect the enzymatic reactions of aromatic amino acid hydroxylases, NO synthases, and alkylglycerol monooxygenase through UV irradiation of Hpterins since UV provokes electron donor reactions of Hpterins; (2) the emission properties of Hpterins and oxidized pterins can be used in fluorescence diagnostics; (3) two-photon absorption (TPA) should be used in such pterin-related infrared therapy because single-photon absorption in the UV range is inefficient and scatters in vivo; (4) one can affect pathogen organisms through TPA excitation of Hpterin cofactors, such as the molybdenum cofactor, leading to its detachment from proteins and subsequent oxidation; (5) metal nanostructures can be used for the UV-vis, fluorescence, and Raman spectroscopy detection of pterin biomarkers. Therefore, we investigated both the biochemistry and physical chemistry of pterins and suggested some potential prospects for pterin-related biomedicine.
Topics: Molecular Structure; Pterins; Pteridines; Coenzymes; Metalloproteins; Oxidation-Reduction
PubMed: 36499560
DOI: 10.3390/ijms232315222 -
Advances in Experimental Medicine and... 2017Obesity activates both innate and adaptive immune responses in adipose tissue. Elevated levels of eosinophils with depression of monocyte and neutrophil indicate the... (Review)
Review
Obesity activates both innate and adaptive immune responses in adipose tissue. Elevated levels of eosinophils with depression of monocyte and neutrophil indicate the deficiencies in the immune system of morbidly obese individuals. Actually, adipose tissue macrophages are functional antigen-presenting cells that promote the proliferation of interferon-gamma (IFN-gamma)-producing CD4+ T cells in adipose tissue of obese subjects. Eventually, diet-induced obesity is associated with the loss of tissue homeostasis and development of type 1 inflammatory responses in visceral adipose tissue. Activity of inducible indoleamine 2,3-dioxygenase-1 (IDO-1) plays a major role under pro-inflammatory, IFN-gamma dominated settings. One of the two rate-limiting enzymes which can metabolize tryptophan to kynurenine is IDO-1. Tumor necrosis factor-alpha (TNF-alpha) correlates with IDO-1 in adipose compartments. Actually, IDO-1-mediated tryptophan catabolism due to chronic immune activation is the cause of reduced tryptophan plasma levels and be considered as the driving force for food intake in morbidly obese patients. Thus, decrease in plasma tryptophan levels and subsequent reduction in serotonin (5-HT) production provokes satiety dysregulation that leads to increased caloric uptake and obesity. However, after bariatric surgery, weight reduction does not lead to normalization of IDO-1 activity. Furthermore, there is a connection between arginine and tryptophan metabolic pathways in the generation of reactive nitrogen intermediates. Hence, abdominal obesity is associated with vascular endothelial dysfunction and reduced nitric oxide (NO) availability. IFN-gamma-induced activation of the inducible nitric oxide synthase (iNOS) and dissociation of endothelial adenosine monophosphate activated protein kinase (AMPK)- phosphoinositide 3-kinase (PI3K)-protein kinase B (Akt)- endothelial NO synthase (eNOS) pathway enhances oxidative stress production secondary to high-fat diet. Thus, reduced endothelial NO availability correlates with the increase in plasma non-esterified fatty acids and triglycerides levels. Additionally, in obese patients, folate-deficiency leads to hyperhomocysteinemia. Folic acid confers protection against hyperhomocysteinemia-induced oxidative stress.
Topics: Animals; Folic Acid; Humans; Inflammation; Kynurenine; Methionine; Obesity; Pteridines; Signal Transduction
PubMed: 28585214
DOI: 10.1007/978-3-319-48382-5_22