Reaction Process: Reactome:R-CEL-446193
Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein related metabolites
find 44 related metabolites which is associated with chemical reaction(pathway) Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
DOLP + UDP-GlcNAc ⟶ GlcNAcDOLDP + UMP
Isopentenyl pyrophosphate
Isopentenyl pyrophosphate, also known as delta3-isopentenyl diphosphate or ipp, is a member of the class of compounds known as isoprenoid phosphates. Isoprenoid phosphates are prenol lipids containing a phosphate group linked to an isoprene (2-methylbuta-1,3-diene) unit. Thus, isopentenyl pyrophosphate is considered to be an isoprenoid lipid molecule. Isopentenyl pyrophosphate is slightly soluble (in water) and a moderately acidic compound (based on its pKa). Isopentenyl pyrophosphate can be found in a number of food items such as american butterfish, conch, tea leaf willow, and butternut, which makes isopentenyl pyrophosphate a potential biomarker for the consumption of these food products. Isopentenyl pyrophosphate can be found primarily in human spleen tissue. Isopentenyl pyrophosphate exists in all living species, ranging from bacteria to humans. In humans, isopentenyl pyrophosphate is involved in several metabolic pathways, some of which include ibandronate action pathway, lovastatin action pathway, fluvastatin action pathway, and pravastatin action pathway. Isopentenyl pyrophosphate is also involved in several metabolic disorders, some of which include hypercholesterolemia, hyper-igd syndrome, lysosomal acid lipase deficiency (wolman disease), and wolman disease. Isopentenyl pyrophosphate (IPP, isopentenyl diphosphate, or IDP) is an isoprenoid precursor. IPP is an intermediate in the classical, HMG-CoA reductase pathway (commonly called the mevalonate pathway) and in the non-mevalonate MEP pathway of isoprenoid precursor biosynthesis. Isoprenoid precursors such as IPP, and its isomer DMAPP, are used by organisms in the biosynthesis of terpenes and terpenoids . Isopentenyl pyrophosphate, IPP or isopentenyl diphosphate, is an intermediate in the HMG-CoA reductase pathway used by organisms in the biosynthesis of terpenes and terpenoids. IPP is formed from Mevalonate-5-pyrophosphate, in a reaction catalyzed by the enzyme mevalonate-5-pyrophosphate decarboxylase. (wikipedia).
Farnesyl pyrophosphate
Farnesyl pyrophosphate is an intermediate in the HMG-CoA reductase pathway used by organisms in the biosynthesis of terpenes and terpenoids. -- Wikipedia [HMDB]. Farnesyl pyrophosphate is found in many foods, some of which are kumquat, macadamia nut, sweet bay, and agave. Farnesyl pyrophosphate is an intermediate in the HMG-CoA reductase pathway used by organisms in the biosynthesis of terpenes and terpenoids. -- Wikipedia.
Glucosamine 6-phosphate
C6H14NO8P (259.04570140000004)
Glucosamine 6-phosphate (CAS: 3616-42-0) is normally produced in endothelial cells via de novo glucosamine synthesis by the enzyme fructose-6-phosphate amidotransferase and the modulation of this pathway by hyperglycemia and glutamine. Glutamine-fructose-6-phosphate amidotransferase (GFAT) catalyzes the first committed step in the pathway for biosynthesis of hexosamines in mammals.It is a member of the N-terminal nucleophile class of amidotransferases, GFAT transfers the amino group from the L-glutamine amide to D-fructose 6-phosphate, producing glutamic acid and glucosamine 6-phosphate. As glucosamine inhibits endothelial nitric oxide synthesis it has important implications for impaired endothelium-dependent relaxation and vascular dysfunction in diabetes mellitus (PMID:11270676, 11842094). Glucosamine 6-phosphate is normally produced in endothelial cells via the de novo glucosamine synthesis by the enzyme fructose-6-phosphate amidotransferase and the modulation of this pathway by hyperglycemia and glutamine. glutamine-fructose-6-phosphate amidotransferase (GFAT) catalyzes the first committed step in the pathway for biosynthesis of hexosamines in mammals. A member of the N-terminal nucleophile class of amidotransferases, GFAT transfers the amino group from the L-glutamine amide to D-fructose 6-phosphate, producing glutamic acid and glucosamine 6-phosphate. As glucosamine inhibits endothelial nitric oxide synthesis it has important implications for impaired endothelium-dependent relaxation and vascular dysfunction in diabetes mellitus. (PMID 11270676, 11842094) [HMDB] Acquisition and generation of the data is financially supported in part by CREST/JST. KEIO_ID G021; [MS2] KO008968 KEIO_ID G021
Fucose 1-phosphate
Fucose 1-phosphate (CAS: 16562-58-6) belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphate group linked to the carbohydrate unit. Fucose 1-phosphate is an intermediate in the reversible synthesis of GDP-L-fucose catalyzed by the enzyme guanosine triphosphate fucose pyrophosphorylase (GFPP, EC 2.7.7.30). The reversible reaction is magnesium-dependent, although the enzyme is partially active when cobalt or manganese is substituted. The reaction is unusual in that, of the four canonical nucleoside triphosphates, only guanosine can be utilized efficiently to form a nucleotide-sugar. Free cytosolic fucose is phosphorylated by L-fucokinase (EC 2.7.1.52) to form fucose-1-phosphate in the salvage pathway of GDP-L-fucose (PMID: 16185085, 14686921). Fucose-1-phosphate is an intermediate in the reversible synthesis of GDP-L-fucose, in a reaction catalyzed by the enzyme guanosine triphosphate fucose pyrophosphorylase (GFPP, E.C. 2.7.7.30) . The reversible reaction is magnesium-dependent, although the enzyme is partially active when cobalt or manganese is substituted. The reaction is unusual in that, of the four canonical nucleoside triphosphates, only guanosine can be utilized efficiently to form a nucleotide-sugar. Free cytosolic fucose is phosphorylated by L-fucokinase (EC 2.7.1.52) to form fucose-1-phosphate in the salvage pathway of GDP-L-fucose. (PMID: 16185085, 14686921) [HMDB]
Water
Water is a chemical substance that is essential to all known forms of life. It appears colorless to the naked eye in small quantities, though it is actually slightly blue in color. It covers 71\\% of Earths surface. Current estimates suggest that there are 1.4 billion cubic kilometers (330 million m3) of it available on Earth, and it exists in many forms. It appears mostly in the oceans (saltwater) and polar ice caps, but it is also present as clouds, rain water, rivers, freshwater aquifers, lakes, and sea ice. Water in these bodies perpetually moves through a cycle of evaporation, precipitation, and runoff to the sea. Clean water is essential to human life. In many parts of the world, it is in short supply. From a biological standpoint, water has many distinct properties that are critical for the proliferation of life that set it apart from other substances. It carries out this role by allowing organic compounds to react in ways that ultimately allow replication. All known forms of life depend on water. Water is vital both as a solvent in which many of the bodys solutes dissolve and as an essential part of many metabolic processes within the body. Metabolism is the sum total of anabolism and catabolism. In anabolism, water is removed from molecules (through energy requiring enzymatic chemical reactions) in order to grow larger molecules (e.g. starches, triglycerides and proteins for storage of fuels and information). In catabolism, water is used to break bonds in order to generate smaller molecules (e.g. glucose, fatty acids and amino acids to be used for fuels for energy use or other purposes). Water is thus essential and central to these metabolic processes. Water is also central to photosynthesis and respiration. Photosynthetic cells use the suns energy to split off waters hydrogen from oxygen. Hydrogen is combined with CO2 (absorbed from air or water) to form glucose and release oxygen. All living cells use such fuels and oxidize the hydrogen and carbon to capture the suns energy and reform water and CO2 in the process (cellular respiration). Water is also central to acid-base neutrality and enzyme function. An acid, a hydrogen ion (H+, that is, a proton) donor, can be neutralized by a base, a proton acceptor such as hydroxide ion (OH-) to form water. Water is considered to be neutral, with a pH (the negative log of the hydrogen ion concentration) of 7. Acids have pH values less than 7 while bases have values greater than 7. Stomach acid (HCl) is useful to digestion. However, its corrosive effect on the esophagus during reflux can temporarily be neutralized by ingestion of a base such as aluminum hydroxide to produce the neutral molecules water and the salt aluminum chloride. Human biochemistry that involves enzymes usually performs optimally around a biologically neutral pH of 7.4. (Wikipedia). Water, also known as purified water or dihydrogen oxide, 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. Water can be found in a number of food items such as caraway, oxheart cabbage, alaska wild rhubarb, and japanese walnut, which makes water a potential biomarker for the consumption of these food products. Water can be found primarily in most biofluids, including ascites Fluid, blood, cerebrospinal fluid (CSF), and lymph, as well as throughout all human tissues. Water exists in all living species, ranging from bacteria to humans. In humans, water is involved in several metabolic pathways, some of which include cardiolipin biosynthesis CL(20:4(5Z,8Z,11Z,14Z)/18:0/20:4(5Z,8Z,11Z,14Z)/18:2(9Z,12Z)), cardiolipin biosynthesis cl(i-13:0/i-15:0/i-20:0/i-24:0), cardiolipin biosynthesis CL(18:0/18:0/20:4(5Z,8Z,11Z,14Z)/22:5(7Z,10Z,13Z,16Z,19Z)), and cardiolipin biosynthesis cl(a-13:0/i-18:0/i-13:0/i-19:0). Water is also involved in several metabolic disorders, some of which include de novo triacylglycerol biosynthesis tg(i-21:0/i-13:0/21:0), de novo triacylglycerol biosynthesis tg(22:0/20:0/i-20:0), de novo triacylglycerol biosynthesis tg(a-21:0/i-20:0/i-14:0), and de novo triacylglycerol biosynthesis tg(i-21:0/a-17:0/i-12:0). Water is a drug which is used for diluting or dissolving drugs for intravenous, intramuscular or subcutaneous injection, according to instructions of the manufacturer of the drug to be administered [fda label]. Water plays an important role in the world economy. Approximately 70\\% of the freshwater used by humans goes to agriculture. Fishing in salt and fresh water bodies is a major source of food for many parts of the world. Much of long-distance trade of commodities (such as oil and natural gas) and manufactured products is transported by boats through seas, rivers, lakes, and canals. Large quantities of water, ice, and steam are used for cooling and heating, in industry and homes. Water is an excellent solvent for a wide variety of chemical substances; as such it is widely used in industrial processes, and in cooking and washing. Water is also central to many sports and other forms of entertainment, such as swimming, pleasure boating, boat racing, surfing, sport fishing, and diving .
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
(R)-5-Diphosphomevalonic acid
Mevalonate-diphosphate, also known as 5-diphosphomevalonic acid or mevelonic acid-5-diphosphoric acid, is a member of the class of compounds known as organic pyrophosphates. Organic pyrophosphates are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O. Thus, mevalonate-diphosphate is considered to be a fatty acid lipid molecule. Mevalonate-diphosphate is slightly soluble (in water) and a moderately acidic compound (based on its pKa). Mevalonate-diphosphate can be found in a number of food items such as kohlrabi, enokitake, avocado, and redcurrant, which makes mevalonate-diphosphate a potential biomarker for the consumption of these food products. Mevalonate-diphosphate exists in all eukaryotes, ranging from yeast to humans. In humans, mevalonate-diphosphate is involved in several metabolic pathways, some of which include zoledronate action pathway, lovastatin action pathway, pamidronate action pathway, and desmosterolosis. Mevalonate-diphosphate is also involved in several metabolic disorders, some of which include wolman disease, lysosomal acid lipase deficiency (wolman disease), cholesteryl ester storage disease, and CHILD syndrome. 5-Diphosphomevalonic acid (CAS: 1492-08-6) is a metabolic intermediate in the mevalonate pathway, catalyzed by the enzyme phosphomevalonate kinase from 5-phosphomevalonate (Wikipedia).
GDP-4-Dehydro-6-deoxy-D-mannose
C16H23N5O15P2 (587.0665868000001)
GDP-4-Dehydro-6-deoxy-D-mannose is an intermediate in the fucosylation of mammalian cells. The functional significance of these fucosylated glycans is unclear, although there is evidence that the sialyl Lex determinant participaates in leukocyte adhesion and trafficking processes. GDP-4-Dehydro-6-deoxy-D-mannose is generated by GDP-D-mannose-4,6-dehydratase (GMD). This compound is then converted by the FX protein (GDP-4-keto-6-D-deoxymannose epimerase/GDP-4-keto-6-L-galactose reductase) to GDP-L-fucose. (PMID: 11698403) [HMDB]. GDP-4-Dehydro-6-deoxy-D-mannose is found in many foods, some of which are bayberry, cherimoya, greenthread tea, and pulses. GDP-4-Dehydro-6-deoxy-D-mannose is an intermediate in the fucosylation of mammalian cells. The functional significance of these fucosylated glycans is unclear, although there is evidence that the sialyl Lex determinant participaates in leukocyte adhesion and trafficking processes. GDP-4-Dehydro-6-deoxy-D-mannose is generated by GDP-D-mannose-4,6-dehydratase (GMD). This compound is then converted by the FX protein (GDP-4-keto-6-D-deoxymannose epimerase/GDP-4-keto-6-L-galactose reductase) to GDP-L-fucose. (PMID: 11698403). COVID info from COVID-19 Disease Map Corona-virus Coronavirus SARS-CoV-2 COVID-19 SARS-CoV COVID19 SARS2 SARS
dolichyl beta-D-glucosyl phosphate
A polyprenyl glycosyl phosphate having dolichyl as the polyprenyl component and beta-D-glucose as the glycosyl component.
N-Acetyl-D-glucosaminyldiphosphodolichol
C33H59NO12P2 (723.3512314000001)
(2Z,6Z,10E,14E)-3,7,11,15,19-Pentamethylicosane-2,6,10,14,18-pentaene-1-ol
(6Z,10E,14E)-3,7,11,15,19-Pentamethylicosane-6,10,14,18-tetraene-1-ol
D-Mannose 1-phosphate
D-Mannose 1-phosphate (CAS: 27251-84-9) is a normal metabolite intermediate in fructose and mannose metabolism. It is a substrate of phosphomannomutase 1 (PMM, EC 5.4.2.8), an enzyme necessary for the synthesis of GDP-mannose (a substrate for dolichol-linked oligosaccharide synthesis). PMM converts mannose 6-phosphate into mannose-1-phosphate. A deficiency of phosphomannomutase in carbohydrate-deficient glycoprotein syndrome (CDGS) type I is associated with a decreased synthesis of mannose 1-phosphate. CDGS is a group of autosomal recessively transmitted disorders in which abnormally glycosylated proteins are formed (PMID: 9451026, 8549746, 12729595). α-d-mannose 1-phosphate is a member of the class of compounds known as monosaccharide phosphates. Monosaccharide phosphates are monosaccharides comprising a phosphated group linked to the carbohydrate unit. α-d-mannose 1-phosphate is soluble (in water) and a moderately acidic compound (based on its pKa). α-d-mannose 1-phosphate can be found in a number of food items such as lettuce, beech nut, red beetroot, and japanese pumpkin, which makes α-d-mannose 1-phosphate a potential biomarker for the consumption of these food products. Acquisition and generation of the data is financially supported in part by CREST/JST. KEIO_ID M080
Beta-1,4-D-Mannosylchitobiosyldiphosphodolichol
Beta-1,4-D-Mannosylchitobiosyldiphosphodolichol is a lipid-linked oligosaccharide. It is part of the N-glycan biosynthesis pathway. Beta-1,4-D-Mannosylchitobiosyldiphosphodolichol is formed by chitobiosyldiphosphodolichol beta-mannosyltransferase (EC 2.4.1.142) via the reaction: GDP-mannose + chitobiosyldiphosphodolichol = GDP + beta-(1->4)-D-mannosylchitobiosyldiphosphodolichol. It is also a reactant or product of glycolipid 3-alpha-mannosyltransferase or mannosyltransferase II. This enzyme transfers an alpha-D-mannosyl residue from GDP-mannose to a lipid-linked (dolichol) oligosaccharide, forming an alpha-(1->3)-D-mannosyl-D-mannose linkage. [HMDB] Beta-1,4-D-Mannosylchitobiosyldiphosphodolichol is a lipid-linked oligosaccharide. It is part of the N-glycan biosynthesis pathway. Beta-1,4-D-Mannosylchitobiosyldiphosphodolichol is formed by chitobiosyldiphosphodolichol beta-mannosyltransferase (EC 2.4.1.142) via the reaction: GDP-mannose + chitobiosyldiphosphodolichol = GDP + beta-(1->4)-D-mannosylchitobiosyldiphosphodolichol. It is also a reactant or product of glycolipid 3-alpha-mannosyltransferase or mannosyltransferase II. This enzyme transfers an alpha-D-mannosyl residue from GDP-mannose to a lipid-linked (dolichol) oligosaccharide, forming an alpha-(1->3)-D-mannosyl-D-mannose linkage.
Hydrogen Ion
Hydrogen ion, also known as proton or h+, is a member of the class of compounds known as other non-metal hydrides. Other non-metal hydrides are inorganic compounds in which the heaviest atom bonded to a hydrogen atom is belongs to the class of other non-metals. Hydrogen ion can be found in a number of food items such as lowbush blueberry, groundcherry, parsley, and tarragon, which makes hydrogen ion a potential biomarker for the consumption of these food products. Hydrogen ion exists in all living organisms, ranging from bacteria to humans. In humans, hydrogen ion is involved in several metabolic pathways, some of which include cardiolipin biosynthesis cl(i-13:0/a-25:0/a-21:0/i-15:0), cardiolipin biosynthesis cl(a-13:0/a-17:0/i-13:0/a-25:0), cardiolipin biosynthesis cl(i-12:0/i-13:0/a-17:0/a-15:0), and cardiolipin biosynthesis CL(16:1(9Z)/22:5(4Z,7Z,10Z,13Z,16Z)/18:1(11Z)/22:5(7Z,10Z,13Z,16Z,19Z)). Hydrogen ion is also involved in several metabolic disorders, some of which include de novo triacylglycerol biosynthesis TG(20:3(8Z,11Z,14Z)/22:6(4Z,7Z,10Z,13Z,16Z,19Z)/22:5(7Z,10Z,13Z,16Z,19Z)), de novo triacylglycerol biosynthesis TG(18:2(9Z,12Z)/20:0/20:4(5Z,8Z,11Z,14Z)), de novo triacylglycerol biosynthesis TG(18:4(6Z,9Z,12Z,15Z)/18:3(9Z,12Z,15Z)/18:4(6Z,9Z,12Z,15Z)), and de novo triacylglycerol biosynthesis TG(24:0/20:5(5Z,8Z,11Z,14Z,17Z)/24:0). A hydrogen ion is created when a hydrogen atom loses or gains an electron. A positively charged hydrogen ion (or proton) can readily combine with other particles and therefore is only seen isolated when it is in a gaseous state or a nearly particle-free space. Due to its extremely high charge density of approximately 2×1010 times that of a sodium ion, the bare hydrogen ion cannot exist freely in solution as it readily hydrates, i.e., bonds quickly. The hydrogen ion is recommended by IUPAC as a general term for all ions of hydrogen and its isotopes. Depending on the charge of the ion, two different classes can be distinguished: positively charged ions and negatively charged ions . Hydrogen ion is recommended by IUPAC as a general term for all ions of hydrogen and its isotopes. Depending on the charge of the ion, two different classes can be distinguished: positively charged ions and negatively charged ions. Under aqueous conditions found in biochemistry, hydrogen ions exist as the hydrated form hydronium, H3O+, but these are often still referred to as hydrogen ions or even protons by biochemists. [Wikipedia])
beta-L-Fucose
A L-fucopyranose with a beta-configuration at the anomeric position.
Coenzyme II
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UMP dianion
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3alpha,7alpha,12alpha-Trihydroxy-5beta-cholan-24-oate
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Uridine-diphosphate
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[Hydroxy(oxido)phosphoryl] phosphate
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[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-oxidophosphoryl]oxy-oxidophosphoryl] phosphate
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coenzyme A(4-)
C21H32N7O16P3S-4 (763.0839062)
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Adenosine-diphosphate
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acetyl-CoA(4-)
C23H34N7O17P3S-4 (805.0944704000001)
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UDP-N-acetyl-alpha-D-glucosamine
C17H25N3O17P2-2 (605.0659180000001)
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L-glutamate(1-)
An alpha-amino-acid anion that is the conjugate base of L-glutamic acid, having anionic carboxy groups and a cationic amino group
beta-D-fructofuranose 6-phosphate(2-)
C6H11O9P-2 (258.01406860000003)
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N-acetyl-D-glucosamine 6-phosphate(2-)
C8H14NO9P-2 (299.04061640000003)
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(alpha-D-Mannosyl)8-beta-D-mannosyl-diacetylchitobiosyldiphosphodolichol
(Gal)1(Glc)1(GlcNAc)2(Man)9(PP-Dol)1
C107H182N2O72P2 (2709.0116312)