Reaction Process: BioCyc:TRYPANO_GLYCINE-DEG1-PWY
glycine degradation III related metabolites
find 8 related metabolites which is associated with chemical reaction(pathway) glycine degradation III
H+ + NAD+ + gly + tetrahydrofolate ⟶ 5,10-methylenetetrahydrofolate + CO2 + NADH + ammonia
Glycine
Glycine (Gly), is an alpha-amino acid. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon). Amino acids are organic compounds that contain amino (–NH2) and carboxyl (–COOH) functional groups, along with a side chain (R group) specific to each amino acid. Glycine is one of 20 proteinogenic amino acids, i.e., the amino acids used in the biosynthesis of proteins. Glycine is found in all organisms ranging from bacteria to plants to animals. It is classified as an aliphatic, non-polar amino acid and is the simplest of all amino acids. In humans, glycine is a nonessential amino acid, although experimental animals show reduced growth on low-glycine diets. The average adult human ingests 3 to 5 grams of glycine daily. Glycine is a colorless, sweet-tasting crystalline solid. It is the only achiral proteinogenic amino acid. Glycine was discovered in 1820 by the French chemist Henri Braconnot when he hydrolyzed gelatin by boiling it with sulfuric acid. The name comes from the Greek word glucus or "sweet tasting". Glycine is biosynthesized in the body from the amino acid serine, which is in turn derived from 3-phosphoglycerate. In the liver of vertebrates, glycine synthesis is catalyzed by glycine synthase (also called glycine cleavage enzyme). In addition to being synthesized from serine, glycine can also be derived from threonine, choline or hydroxyproline via inter-organ metabolism of the liver and kidneys. Glycine is degraded via three pathways. The predominant pathway in animals and plants is the reverse of the glycine synthase pathway. In this context, the enzyme system involved glycine metabolism is called the glycine cleavage system. The glycine cleavage system catalyzes the oxidative conversion of glycine into carbon dioxide and ammonia, with the remaining one-carbon unit transferred to folate as methylenetetrahydrofolate. It is the main catabolic pathway for glycine and it also contributes to one-carbon metabolism. Patients with a deficiency of this enzyme system have increased glycine in plasma, urine, and cerebrospinal fluid (CSF) with an increased CSF:plasma glycine ratio (PMID: 16151895). Glycine levels are effectively measured in plasma in both normal patients and those with inborn errors of glycine metabolism (http://www.dcnutrition.com/AminoAcids/). Nonketotic hyperglycinaemia (OMIM: 606899) is an autosomal recessive condition caused by deficient enzyme activity of the glycine cleavage enzyme system (EC 2.1.1.10). The glycine cleavage enzyme system comprises four proteins: P-, T-, H- and L-proteins (EC 1.4.4.2, EC 2.1.2.10, and EC 1.8.1.4 for P-, T-, and L-proteins). Mutations have been described in the GLDC (OMIM: 238300), AMT (OMIM: 238310), and GCSH (OMIM: 238330) genes encoding the P-, T-, and H-proteins respectively. Glycine is involved in the bodys production of DNA, hemoglobin, and collagen, and in the release of energy. The principal function of glycine is as a precursor to proteins. Most proteins incorporate only small quantities of glycine, a notable exception being collagen, which contains about 35\\\\\\% glycine. In higher eukaryotes, delta-aminolevulinic acid, the key precursor to porphyrins (needed for hemoglobin and cytochromes), is biosynthesized from glycine and succinyl-CoA by the enzyme ALA synthase. Glycine provides the central C2N subunit of all purines, which are key constituents of DNA and RNA. Glycine is an inhibitory neurotransmitter in the central nervous system, especially in the spinal cord, brainstem, and retina. When glycine receptors are activated, chloride enters the neuron via ionotropic receptors, causing an inhibitory postsynaptic potential (IPSP). Glycine. CAS Common Chemistry. CAS, a division of the American Chemical Society, n.d. https://commonchemistry.cas.org/detail?cas_rn=56-40-6 (retrieved 2024-07-02) (CAS RN: 56-40-6). Licensed under the Attribution-Noncommercial 4.0 International License (CC BY-NC 4.0). Glycine is an inhibitory neurotransmitter in the CNS and also acts as a co-agonist along with glutamate, facilitating an excitatory potential at the glutaminergic N-methyl-D-aspartic acid (NMDA) receptors. Glycine is an inhibitory neurotransmitter in the CNS and also acts as a co-agonist along with glutamate, facilitating an excitatory potential at the glutaminergic N-methyl-D-aspartic acid (NMDA) receptors. Glycine is orally active. Glycine can be used to study cell protection, cancer, neurological diseases, and angiogenesis[1][2][3][4][5][6]. Glycine is an inhibitory neurotransmitter in the CNS and also acts as a co-agonist along with glutamate, facilitating an excitatory potential at the glutaminergic N-methyl-D-aspartic acid (NMDA) receptors.
Nadide
[Spectral] NAD+ (exact mass = 663.10912) and 3,4-Dihydroxy-L-phenylalanine (exact mass = 197.06881) and Cytidine (exact mass = 243.08552) were not completely separated on HPLC under the present analytical conditions as described in AC$XXX. Additionally some of the peaks in this data contains dimers and other unidentified ions. [Spectral] NAD+ (exact mass = 663.10912) and NADP+ (exact mass = 743.07545) were not completely separated on HPLC under the present analytical conditions as described in AC$XXX. Additionally some of the peaks in this data contains dimers and other unidentified ions. COVID info from COVID-19 Disease Map Corona-virus Coronavirus SARS-CoV-2 COVID-19 SARS-CoV COVID19 SARS2 SARS
1,4-Dihydronicotinamide adenine dinucleotide
Nicotinamide adenine dinucleotide (NAD) is a coenzyme central to metabolism. Found in all living cells, NAD is called a dinucleotide because it consists of two nucleotides joined through their phosphate groups. One nucleotide contains an adenine nucleobase and the other nicotinamide. NAD exists in two forms: an oxidized and reduced form, abbreviated as NAD+ and NADH (H for hydrogen) respectively. NADH is the reduced form of NAD+, and NAD+ is the oxidized form of NADH. NAD (or nicotinamide adenine dinucleotide) is used extensively in glycolysis and the citric acid cycle of cellular respiration. The reducing potential stored in NADH can be either converted into ATP through the electron transport chain or used for anabolic metabolism. ATP "energy" is necessary for an organism to live. Green plants obtain ATP through photosynthesis, while other organisms obtain it via cellular respiration. NAD is a coenzyme composed of ribosylnicotinamide 5-diphosphate coupled to adenosine 5-phosphate by a pyrophosphate linkage. It is found widely in nature and is involved in numerous enzymatic reactions in which it serves as an electron carrier by being alternately oxidized (NAD+) and reduced (NADH). NADP is formed through the addition of a phosphate group to the 2 position of the adenosyl nucleotide through an ester linkage. NADH is the reduced form of NAD+, and NAD+ is the oxidized form of NADH, A coenzyme composed of ribosylnicotinamide 5-diphosphate coupled to adenosine 5-phosphate by pyrophosphate linkage. It is found widely in nature and is involved in numerous enzymatic reactions in which it serves as an electron carrier by being alternately oxidized (NAD+) and reduced (NADH). It forms NADP with the addition of a phosphate group to the 2 position of the adenosyl nucleotide through an ester linkage.(Dorland, 27th ed) [HMDB]. NADH is found in many foods, some of which are dill, ohelo berry, fox grape, and black-eyed pea. Acquisition and generation of the data is financially supported in part by CREST/JST. COVID info from COVID-19 Disease Map Corona-virus Coronavirus SARS-CoV-2 COVID-19 SARS-CoV COVID19 SARS2 SARS
Carbon dioxide
Carbon dioxide is a colorless, odorless gas that can be formed by the body and is necessary for the respiration cycle of plants and animals. Carbon dioxide is produced during respiration by all animals, fungi and microorganisms that depend on living and decaying plants for food, either directly or indirectly. It is, therefore, a major component of the carbon cycle. Additionally, carbon dioxide is used by plants during photosynthesis to make sugars which may either be consumed again in respiration or used as the raw material to produce polysaccharides such as starch and cellulose, proteins and the wide variety of other organic compounds required for plant growth and development. When inhaled at concentrations much higher than usual atmospheric levels, it can produce a sour taste in the mouth and a stinging sensation in the nose and throat. These effects result from the gas dissolving in the mucous membranes and saliva, forming a weak solution of carbonic acid. Carbon dioxide is used by the food industry, the oil industry, and the chemical industry. Carbon dioxide is used to produce carbonated soft drinks and soda water. Traditionally, the carbonation in beer and sparkling wine comes about through natural fermentation, but some manufacturers carbonate these drinks artificially. Leavening agent, propellant, aerating agent, preservative. Solvent for supercritical extraction e.g. of caffeine in manufacture of caffeine-free instant coffee. It is used in carbonation of beverages, in the frozen food industry and as a component of controlled atmosphere packaging (CAD) to inhibit bacterial growth. Especies effective against Gram-negative spoilage bacteria, e.g. Pseudomonas V - Various > V03 - All other therapeutic products > V03A - All other therapeutic products > V03AN - Medical gases
ammonia
An azane that consists of a single nitrogen atom covelently bonded to three hydrogen atoms. Ammonia, also known as nh3 or ammonia solution, is a member of the class of compounds known as homogeneous other non-metal compounds. Homogeneous other non-metal compounds are inorganic non-metallic compounds in which the largest atom belongs to the class of other nonmetals. Ammonia can be found in a number of food items such as rose hip, yardlong bean, cereals and cereal products, and ceylon cinnamon, which makes ammonia a potential biomarker for the consumption of these food products. Ammonia can be found primarily in blood, cellular cytoplasm, cerebrospinal fluid (CSF), and urine, as well as throughout all human tissues. Ammonia exists in all eukaryotes, ranging from yeast to humans. In humans, ammonia is involved in several metabolic pathways, some of which include glucose-alanine cycle, phenylalanine and tyrosine metabolism, homocysteine degradation, and d-arginine and d-ornithine metabolism. Ammonia is also involved in several metabolic disorders, some of which include ureidopropionase deficiency, hyperornithinemia-hyperammonemia-homocitrullinuria [hhh-syndrome], non ketotic hyperglycinemia, and beta-mercaptolactate-cysteine disulfiduria. Moreover, ammonia is found to be associated with 3-Hydroxy-3-methylglutaryl-CoA lyase deficiency, 3-Methyl-crotonyl-glycinuria, citrullinemia type I, and short bowel syndrome. Ammonia is a non-carcinogenic (not listed by IARC) potentially toxic compound. Ammonia or azane is a compound of nitrogen and hydrogen with the formula NH3. The simplest pnictogen hydride, ammonia is a colourless gas with a characteristic pungent smell. It is a common nitrogenous waste, particularly among aquatic organisms, and it contributes significantly to the nutritional needs of terrestrial organisms by serving as a precursor to food and fertilizers. Ammonia, either directly or indirectly, is also a building block for the synthesis of many pharmaceutical products and is used in many commercial cleaning products . Acute Exposure: EYES: irrigate opened eyes for several minutes under running water. INGESTION: do not induce vomiting. Rinse mouth with water (never give anything by mouth to an unconscious person). Seek immediate medical advice. SKIN: should be treated immediately by rinsing the affected parts in cold running water for at least 15 minutes, followed by thorough washing with soap and water. If necessary, the person should shower and change contaminated clothing and shoes, and then must seek medical attention. INHALATION: supply fresh air. If required provide artificial respiration. (z)-n-coumaroyl-5-hydroxyanthranilic acid is a member of the class of compounds known as avenanthramides. Avenanthramides are a group of phenolic alkaloids consisting of conjugate of three phenylpropanoids (ferulic, caffeic, or p-coumaric acid) and anthranilic acid (z)-n-coumaroyl-5-hydroxyanthranilic acid is practically insoluble (in water) and a weakly acidic compound (based on its pKa). (z)-n-coumaroyl-5-hydroxyanthranilic acid can be found in cereals and cereal products and oat, which makes (z)-n-coumaroyl-5-hydroxyanthranilic acid a potential biomarker for the consumption of these food products.
Tetrahydrofolic acid
Tetrahydrofolate is a soluble coenzyme (vitamin B9) that is synthesized de novo by plants and microorganisms, and absorbed from the diet by animals. It is composed of three distinct parts: a pterin ring, a p-ABA (p-aminobenzoic acid) and a polyglutamate chain with a number of residues varying between 1 and 8. Only the tetra-reduced form of the molecule serves as a coenzyme for C1 transfer reactions. In biological systems, the C1-units exist under various oxidation states and the different tetrahydrofolate derivatives constitute a family of related molecules named indistinctly under the generic term folate. (PMID 16042593). Folate is important for cells and tissues that rapidly divide. Cancer cells divide rapidly, and drugs that interfere with folate metabolism are used to treat cancer. Methotrexate is a drug often used to treat cancer because it inhibits the production of the active form, tetrahydrofolate. Unfortunately, methotrexate can be toxic, producing side effects such as inflammation in the digestive tract that make it difficult to eat normally. -- Wikipedia; Signs of folic acid deficiency are often subtle. Diarrhea, loss of appetite, and weight loss can occur. Additional signs are weakness, sore tongue, headaches, heart palpitations, irritability, and behavioral disorders. Women with folate deficiency who become pregnant are more likely to give birth to low birth weight and premature infants, and infants with neural tube defects. In adults, anemia is a sign of advanced folate deficiency. In infants and children, folate deficiency can slow growth rate. Some of these symptoms can also result from a variety of medical conditions other than folate deficiency. It is important to have a physician evaluate these symptoms so that appropriate medical care can be given. -- Wikipedia; Folinic acid is a form of folate that can help rescue or reverse the toxic effects of methotrexate. Folinic acid is not the same as folic acid. Folic acid supplements have little established role in cancer chemotherapy. There have been cases of severe adverse effects of accidental substitution of folic acid for folinic acid in patients receiving methotrexate cancer chemotherapy. It is important for anyone receiving methotrexate to follow medical advice on the use of folic or folinic acid supplements. -- Wikipedia. Low concentrations of folate, vitamin B12, or vitamin B6 may increase the level of homocysteine, an amino acid normally found in blood. There is evidence that an elevated homocysteine level is an independent risk factor for heart disease and stroke. The evidence suggests that high levels of homocysteine may damage coronary arteries or make it easier for blood clotting cells called platelets to clump together and form a clot. However, there is currently no evidence available to suggest that lowering homocysteine with vitamins will reduce your risk of heart disease. Clinical intervention trials are needed to determine whether supplementation with folic acid, vitamin B12 or vitamin B6 can lower your risk of developing coronary heart disease. -- Wikipedia. Tetrahydrofolate is a soluble coenzyme (vitamin B9) that is synthesized de novo by plants and microorganisms, and absorbed from the diet by animals. It is composed of three distinct parts: a pterin ring, a p-ABA (p-aminobenzoic acid) and a polyglutamate chain with a number of residues varying between 1 and 8. Only the tetra-reduced form of the molecule serves as a coenzyme for C1 transfer reactions. In biological systems, the C1-units exist under various oxidation states and the different tetrahydrofolate derivatives constitute a family of related molecules named indistinctly under the generic term folate. (PMID 16042593)
5,10-Methylene-THF
5,10-Methylene-THF is an intermediate in glycine, serine and threonine metabolism and one carbon metabolism. 5,10-CH2-THF can also be used as a coenzyme in the biosynthesis of thymidine. More specifically it is the C1-donor in the reactions catalyzed by thymidylate synthase and thymidylate synthase (FAD). It also acts as a coenzyme in the synthesis of serine from glycine via the enzyme serine hydroxymethyl transferase. 5,10-Methylene-THF is a substrate for Methylenetetrahydrofolate reductase. This enzyme converts 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate. This reaction is required for the multistep process that converts the amino acid homocysteine to methionine. The body uses methionine to make proteins and other important compounds. 5,10-CH2-THF is a substrate for many enzymes including Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase (mitochondrial), Aminomethyltransferase (mitochondrial), Serine hydroxymethyltransferase (mitochondrial), Methylenetetrahydrofolate reductase, C-1-tetrahydrofolate synthase (cytoplasmic), Serine hydroxymethyltransferase (cytosolic) and Thymidylate synthase. 5,10-Methylene-THF is an intermediate in the metabolism of Methane and the metabolism of Nitrogen. It is a substrate for Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase (mitochondrial), Aminomethyltransferase (mitochondrial), Serine hydroxymethyltransferase (mitochondrial), Methylenetetrahydrofolate reductase, C-1-tetrahydrofolate synthase (cytoplasmic), Serine hydroxymethyltransferase (cytosolic) and Thymidylate synthase. [HMDB] COVID info from COVID-19 Disease Map Corona-virus Coronavirus SARS-CoV-2 COVID-19 SARS-CoV COVID19 SARS2 SARS
