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Showing 61 - 70 of 110297 pathways
PathBank ID Pathway Chemical Compounds Proteins

SMP0000793

Pw000770 View Pathway
Metabolite

Lipoic Acid Metabolism

Escherichia coli
Lipoic acid metabolism starts with caprylic acid being introduced into the cytoplasm, however, no transporter has been identified yet. i) Once caprylic acid is in the cytoplasm, it can react with a holo-acp through an ATP-driven 2-acylglycerophosphoethanolamine acyltransferase/acyl-ACP synthetase resulting in pyrophosphate, AMP, and octanoyl-[acp]. The latter compound can also be obtained from palmitate biosynthesis. ii) Octanoyl-acp then interacts with a lipoyl-carrier protein L-lysine through an octanoyltransferase resulting in a hydrogen ion, a holo-acyl-acp, and an N6-(octanoyl)lysine. iii) N6-(octanoyl)lysine reacts with an S-adenosylmethionine, a sulfurated[sulfur carrier], and a reduced ferredoxin through a lipoate-protein ligase A, resulting in a 5-deoxyadenosine, an L-methionine, an unsulfurated [sulfur carrier], oxidized ferredoxin, and protein N6-(octanoyl)lysine. Caprylic acid can also interact with ATP and a lipoyl-carrier protein-L-lysine through a lipoate-protein ligase A resulting in an AMP, pyrophosphate, hydrogen ion, and protein N6-(octanoyl)lysine. The latter compound reacts with an S-adenosylmethionine, a sulfurated[sulfur carrier] and a reduced ferredoxin through a lipoate-protein ligase A, resulting in a 5-deoxyadenosine, an L-methionine, an unsulfurated [sulfur carrier], oxidized ferredoxin, and a protein N6-(octanoyl)lysine. R-Lipoic acid can be absorbed from the environment, as seen in studies by Morris TW. In this pathway, the lipoyl-protein ligase LplA utilizes pre-existing lipoate that has been imported from outside the cell, and thus catalyzes a salvage pathway. Lipoic acid interacts with ATP and hydrogen ion through a lipoyl-protein ligase A, resulting in a pyrophosphate and a lipoyl-AMP (lipoyl-adenylate). This compound then interacts with a lipoyl-carrier protein-L-lysine through a lipoate-protein ligase A resulting in an AMP, a hydrogen ion, and a protein N6-(lipoyl) lysine. It has been suggested that the conversion of octanoylated-domains into lipoylated ones described in this pathway may be a type of a repair pathway, activated only if the other lipoate biosynthetic pathways are malfunctioning.

Metabolic

SMP0063472

Pw064434 View Pathway
Metabolite

Vitamin B6 Metabolism

Arabidopsis thaliana
Vitamin B6 is a water-soluble vitamin essential for all living organisms. It is an important cofactor for enzymatic reactions in over one hundred different cellular reactions and processes. Vitamin B6 exists in different natural forms called vitamers, which are produced by plants, bacteria, and fungi, but not by animals and humans. These vitamers include: pyridoxal (PL), pyridoxine (PN) and pyridoxamine (PM) and their phosphorylated vitamers, PLP, PNP and PMP respectively. Vitamin B6 metabolic pathway was mainly characterized in E. coli, however most organisms, including plants, utilize an alternate pathway. In plants, the various vitamers can be produced via different specific pathways. In A. thaliana, this biosynthetic pathway involves few subpathways, which include: glycolysis, pentose phosphate pathway (PPP), and glyoxylate and dicarboxylate metabolism. Glyceraldehyde 3-phosphate produced by glycolysis and ribulose 5-phosphate produced by PPP are synthesized to pyridoxal 5-phosphate by a synthase. Pyridoxal 5-phosphate is then dephosphorylated to pyridoxal. Pyridoxal, a form of vitamin B6, could act as a precursor for butanoate metabolsim. Moreover, from PPP, 2-Oxo-3-hydroxy-4-phosphobutanoate is produced, this is synthesized to O-phospho-4-hydroxy-L-threonine and then to 4-hydroxy-L-threonine. Pyridoxine could also be produced after a multistep reaction from 4-hydroxy-L-threonine, which is then synthesized to pyridoxal. Glycoaldehyde produced from glyoxylate and dicarboxylate metabolism is converted to pyridoxine. Pyridoxine could also undergo phosphorylation where it is converted to pyridoxine phosphate which is then synthesized to pyridoxal 5-phosphate where the later is dephosphorylated to pyridoxal. Pyridoxal could also be synthesized to pyridoxamine, this that is phosphorylated to pyridoxamin 5-phosphate, which is then synthesized to pyridoxal 5-phosphate.

Metabolic

SMP0000034

Pw000148 View Pathway
Metabolite

Sphingolipid Metabolism

Homo sapiens
The sphingolipid metabolism pathway depicted here describes the synthesis of sphingolipids which include sphingomyelins, ceramides, phosphoceramides, glucosylceramides, galactosylceramides, sulfagalactosylceramides, lactosylceramides, and various other ceramides. The core of a sphingolipid is the long-chain amino alcohol called sphingosine. Amino acylation, with a long-chain fatty acid, at the 2-carbon position of sphingosine yields a ceramide. Sphingolipids are a component of all membranes but are particularly abundant in the myelin sheath. De novo sphingolipid synthesis begins at the cytoplasmic side of the ER (endoplasmic reticulum) with the formation of 3-keto-dihydrosphingosine (also known as 3-ketosphinganine) by the enzyme known as serine palmitoyltransferase (SPT). The preferred substrates for this reaction are palmitoyl-CoA and serine. Next, 3-keto-dihydrosphingosine is reduced to form dihydrosphingosine (also known as sphinganine) via the enzyme 3-ketodihydrosphingosine reductase (KDHR), which is also known as 3-ketosphinganine reductase. Dihydrosphingosine (sphinganine) is acylated by the action of several dihydroceramide synthases (CerS) to form dihydroceramide. Dihydroceramide is then desaturated in the original palmitic portion of the lipid via dihydroceramide desaturase 1 (DES1) to form ceramide. Following the conversion to ceramide, sphingosine is released via the action of ceramidase. Sphingosine can be re-converted into a ceramide by condensation with an acyl-CoA catalyzed by the various CerS enzymes. Ceramide may be phosphorylated by ceramide kinase to form ceramide-1-phosphate. Alternatively, it may be glycosylated by glucosylceramide synthase (to form a glucosylceramide) or galactosylceramide synthase (to form a galactosylceramide). Additionally, it can be converted to sphingomyelin by the addition of a phosphorylcholine headgroup by sphingomyelin synthase (SMS). Sphingomyelins are the only sphingolipids that are phospholipids. Diacylglycerol is also generated via this process. Alternately, ceramide may be broken down by a ceramidase to form sphingosine. Sphingosine may be phosphorylated to form sphingosine-1-phosphate, which may, in turn, be dephosphorylated to regenerate sphingosine. Sphingolipid catabolism allows the reversion of these metabolites to ceramide. The complex glycosphingolipids are hydrolyzed to glucosylceramide and galactosylceramide. These lipids are then hydrolyzed by beta-glucosidases and beta-galactosidases to regenerate ceramide. Similarly, sphingomyelins may be broken down by sphingomyelinase to create ceramides and phosphocholine. The only route by which sphingolipids are converted into non-sphingolipids is through sphingosine-1-phosphate lyase. This forms ethanolamine phosphate and hexadecenal.

Metabolic

SMP0000030

Pw000155 View Pathway
Metabolite

Oxidation of Branched-Chain Fatty Acids

Homo sapiens
In the majority of organisms, fatty acid degradation occurs mostly through the beta-oxidation cycle. In plants, this cycle only happens in the peroxisome, while in mammals this cycle happens in both the peroxisomes and mitochondria. Unfortunately, traditional fatty acid oxidation does not work for branched-chain fatty acids, or fatty acids that do not have an even number of carbons, like the fatty acid phytanic acid, found in animal milk. This acid can not be oxidized through beta-oxidation, as problems arise when water is added at the branched beta-carbon. To be able to oxidize this fatty acid, the carbon is oxidized by oxygen, which removes the initial carboxyl group, which shortens the chain. Now lacking a methyl group, this chain can be beta-oxidized. Now moving to the mitochondria, there are four reactions that occur, and are repeated for each molecule of the fatty acid. Each time the cycle of these reactions is completed, the chain is relieved of two carbons, which are oxidized and are taken away by NADH and FADH2, energy carriers that collect the carbons energy. After beta-oxidation in the cycle of reactions, an acetyl-CoA unit is released and is recycled into the cycle of reactions in the mitochondria, until the chain is fully broken down into acetyl-CoA, and can enter the TCA cycle. Once in the TCA cycle, it is converted to NADH and FADH2, which in turn help move along mitochondrial ATP production. Acetyl-CoA also helps produce ketone bodies that are further converted to energy in the heart and the brain.

Metabolic

SMP0000465

Pw000016 View Pathway
Metabolite

Carnitine Synthesis

Homo sapiens
Carnitine is an ammonium compound that exists in two stereoisomers, of which only L-carnitine is biologically active. Carnitine can be obtained from dietary sources and also biosynthesized. It is necessary for fatty acid oxidation, transporting fatty acids from the cystosol to the mitochondria, where they are broken down via the citric acid cycle to release energy. Carnitine is synthesized from lysine residues in existing proteins. These residues are methylated using lysine methyltransferase enzymes and methyl groups from S-adenosylmethionine, then removed from the protein via hydrolysis. In the next step, the N6,N6,N6-trimethyl-L-lysine is converted to 3-hydroxy-N6,N6,N6-trimethyl-L-lysine t via the mitochondrial enzyme trimethyllysine dioxygenase. The 3-hydroxy-N6,N6,N6-trimethyl-L-lysine is then cleaved to 4-trimethylammoniobutanal and glycine, likely by an aldose identical to serine hydroxymethyltransferase. Next, 4-trimethylammoniobutanal is oxidized by the 4-trimethylaminobutyraldehyde dehydrogenase protein to 4-trimethylammoniobutanoic acid. Finally, 4-trimethylammoniobutanoic acid is transformed into L-carnitine via the enzyme gamma-butyrobetaine dioxygenase. The reactions in the carnitine synthesis pathway occur ubiquitously in the human body with the exception of the last step, as the gamma-butyrobetaine dioxygenase enzyme is found only in the liver and kidney (and at very low levels in the brain). The produced carnitine is then carried to other tissue via a number of transport systems.

Metabolic

SMP0000070

Pw000035 View Pathway
Metabolite

Riboflavin Metabolism

Homo sapiens
Riboflavin (vitamin B2) is an important part of the enzyme cofactors FAD (flavin-adenine dinucleotide) and FMN (flavin mononucleotide). The name "riboflavin" actually comes from "ribose" and "flavin". Like the other B vitamins, riboflavin is needed for the breaking down and processing of ketone bodies, lipids, carbohydrates, and proteins. Riboflavin is found in many different foods, such as meats and vegetables.As the digestion process occurs, many different flavoproteins that come from food are broken down and riboflavin is reabsorbed. The reverse reaction is mediated by acid phosphatase 6. FMN can be turned into to FAD via FAD synthetase, while the reverse reaction is mediated by nucleotide pyrophosphatase. FAD and FMN are essential hydrogen carriers and are involved in over 100 redox reactions that take part in energy metabolism.

Metabolic

SMP0000716

Pw000693 View Pathway
Metabolite

Thyroid Hormone Synthesis

Homo sapiens
Thyroid hormone synthesis is a process that occurs in the thyroid gland in humans that results in the production of thyroid hormones which regulate many different processes in the body, such as metabolism, temperature regulation and growth/development. Thyroid hormone synthesis begins in the nucleus of a thyroid follicular cell, as thyroglobulin synthesis occurs here and is transported to the endoplasmic reticulum. From there, thyroglobulin transported through endocytosis into the intracellular space, and then transported through exocytosis to the follicle colloid. There, thyroglobulin is joined by iodide that has been transported from the blood, through the thyroid follicular cell and arrived in the the follicle colloid using pendrin, and hydrogen peroxide to be catalyzed by thyroid peroxidase, creating thyroglobulin + iodotyrosine. Then, iodide, hydrogen peroxide and thyroidperoxidase create thyroglobulin + 3,5-diiodo-L-tyrosine. Thyroglobulin+3,5-diiodo-L-tyrosine then joins with hydrogen peroxide and thyroid peroxidase to create thyroglobulin + 2-aminoacrylic acid and thyroglobulin+liothyronine. Thyroglobulin + liothyronine then goes through two processes, the first being its transportation into the cell and undergoing of proteolysis, which is followed by liothyronine being transported into the bloodstream. The second process is thyroglobulin + liothyronine being catalyzed by thyroid peroxidase and resulting in the production of thyroglobulin + thyroxine. Thyroglobulin + thyroxine is then transported back into the cell, undergoes proteolysis, and thyroxine alone is transported back out of the cell and into the bloodstream.

Metabolic

SMP0001985

Pw001971 View Pathway
Metabolite

Flavin Biosynthesis

Escherichia coli
The process of flavin biosynthesis starts with GTP being metabolized by interacting with 3 molecules of water through a GTP cyclohydrolase resulting in a release of formic acid, a pyrophosphate, two hydrog ions and 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one or 2,5-Diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine. Either of these compounds interacts with a water molecule and a hydrogen ion through a fused diaminohydroxyphosphoribosylaminopyrimidine deaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase resulting in an ammonium and 5-amino-6-(5-phospho-D-ribosylamino)uracil. This compound then interacts with a hydrogen ion through a NADPH dependent fused diaminohydroxyphosphoribosylaminopyrimidine deaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase resulting in the release of a NADP and a 5-amino-6-(5-phospho-D-ribitylamino)uracil. This compound then interacts with a water molecule through a 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase resulting in a release of a phosphate, and a 5-amino-6-(D-ribitylamino)uracil. D-ribulose 5-phosphate interacts with a3,4-dihydroxy-2-butanone 4-phosphate synthase resulting in the release of formic acid, a hydrogen ion and 1-deoxy-L-glycero-tetrulose 4-phosphate. A 5-amino-6-(D-ribitylamino)uracil and 1-deoxy-L-glycero-tetrulose 4-phosphate interact through a 6,7-dimethyl-8-ribityllumazine synthase resulting in the release of 2 water molecules, a phosphate, a hydrogen ion and a 6,7-dimethyl-8-(1-D-ribityl)lumazine. The latter compound then interacts with a hydrogen ion through a riboflavin synthase resulting in the release of a riboflavin and a 5-amino-6-(d-ribitylamino)uracil. The riboflavin is then phosphorylated through an ATP dependent riboflavin kinase resulting in the release of a ADP, a hydrogen ion and a FLAVIN MONONUCLEOTIDE. The flavin mononucleotide interad with a hydrogen ion and an ATP through the riboflavin kinase resulting in the release of a pyrophosphate and Flavin Adenine dinucleotide. This compound is then exported into the periplasm through a FMN/FAD exporter.

Metabolic

SMP0002032

Pw002018 View Pathway
Metabolite

Glutathione Metabolism III

Escherichia coli
The biosynthesis of glutathione starts with the introduction of L-glutamic acid through either a glutamate:sodium symporter, glutamate / aspartate : H+ symporter GltP or a glutamate / aspartate ABC transporter. Once in the cytoplasm, L-glutamice acid reacts with L-cysteine through an ATP glutamate-cysteine ligase resulting in gamma-glutamylcysteine. This compound reacts which Glycine through an ATP driven glutathione synthetase thus catabolizing Glutathione. This compound is metabolized through a spontaneous reaction with an oxidized glutaredoxin resulting in a reduced glutaredoxin and an oxidized glutathione. This compound is reduced by a NADPH glutathione reductase resulting in a glutathione.

Metabolic

SMP0001908

Pw001894 View Pathway
Metabolite

Selenium Metabolism

Escherichia coli
The selenium metabolism begins with the introduction of selenate and selenite to the cytosol through a sulphate permease system. Once in the cell, selenate can be reduced to selenite through nitrate reductases A and Z. Selenite then interacts with glutathione and 2 hydrogen ions resulting in the release of 2 water molecules, a hydroxide molecule, a glutathione disulfide and a selenodiglutathione. The latter compound then reacts with NADPH+H resulting in the release of a NADP, a glutathione and a glutathioselenol. Glutathiolselenol can then be oxidize resulting in a a glutathiolselenol ion which can then interact with a water molecule resulting in a release of glutathion and selenium Glutathiolselenol can also react with NADPH and hydrogen ion resulting in a release of glutathione, NADP, a hydroxide molecule and a hydrogen selenide. This compound can react in a reversible reaction by being oxidized resulting in a hydrogen selenide ion . This compound can then be phosphorylated by interacting with an ATP and releasing a AMP, a phosphate and a selenophosphate.

Metabolic
Showing 61 - 70 of 110297 pathways