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Showing 1 - 10 of 109292 pathways
PathBank ID Pathway Chemical Compounds Proteins

SMP0121212

Pw122506 View Pathway
Metabolite

Camalexin Biosynthesis

Arabidopsis thaliana
Camalexin is a compound produced by Arabadopsis thaliana, used in plant defense. Its accumulation is induced by contact with parasites, and it inhibits the growth of those parasites. Synthesis of camalexin starts with L-tryptophan, which reacts using tryptophan N-monooxygenases 1 and 2 to form N-hydroxy-L-tryptophan. This then reacts using the same enzyme to form N,N-dihydroxy-L-tryptophan, which spontaneously forms (E)-indol-3-ylacetaldoxime. (E)-indol-3-ylacetaldoxime reversibly reacts with a indoleacetaldoxime dehydratase enzyme to form (Z)-indol-3-ylacetaldoxime, its isomer. The isomer then loses a water molecule via indoleacetaldoxime dehydratase again, forming 3-indoleacetonitrile. Another reaction with indoleacetaldoxime dehydratase forms 2-hydroxy-2-(1H-indol-3-yl0acetonitrile, which then reacts one final time with the indoleacetaldoxime dehydratase enzyme to lose a water molecule and form dehydro(indole-3-yl)acetonitrile. At this point, a glutatione molecule is added using glutatione S-transferase F6 to form (glutation-S-yl)(1H-indol-3-yl)acetonitrile. A water molecule is added by gamma-glutamyl peptidases 1 and 3, as well as glutathione hydrolase 3, forming L-glutamic acid as a side product, as well as (L-cysteinylglycin-S-yl)(1H-indol-3-yl)acetonitrile. An unknown enzyme then catalyzes a reaction that adds a water molecule and removes a glycine, forming 2-(cystein-S-yl)-2-(1H-indol-3-yl)-acetonitrile. Then, in a reaction using bifunctional dihydrocamalexate synthase/camalexin synthase, an oxygen molecule is added, a hydrogen ion, hydrogen cyanide molecule and water molecule are removed, and (R)-dihydrocamalexate is formed. Finally, the same enzyme catalyzes the formation of camalexin, the final product of this pathway.

Metabolic

SMP0121210

Pw122504 View Pathway
Metabolite

Terpenoid Backbone Biosynthesis

Arabidopsis thaliana
Terpenoids are a class of organic compounds made up of 5 carbon isoprene units. There are two pathways, melvalonate and MEP/DOXP, that synthesize the terpenoid backbone components. Both of these create isopentenyl pyrophosphate, which may then react using isopentenyl diphosphate isomerase in the chloroplast to form dimethylallylprophosphate. This molecule is also produced by the MEP/DOXP pathway. Isopentenyl pyrophosphate and dimethylallylprophosphate can react with geranylphosphate synthase in the mitochondrion to form geranyl-pyrophosphate, the main compound used in monoterpenoid biosynthesis. Geranyl-pyrophosphate may also react again with isopentenyl pyrophosphate using solanesyl diphosphate synthase 2 in the chloroplast to form solanesyl pyrophosphate, a potential end product of this pathway. Alternately, they can react with (2E,6E)-farnesyl diphosphate synthase, also in the mitochondrion, to form farnesyl phosphate. Farnesyl pyrophosphate may then be used as the main precursor in the sesquiterpenoid and triterpenoid biosynthesis pathways. It may also react with geranylgeranyl pyrophosphate 6 in the mitochondrion to form geranylgeranyl pyrophosphate. Geranylgeranyl pyrophosphate can react with isopentenyl pyrophosphate, catalyzed by solanesyl diphosphate syntahse 2, again in the chloroplast, to form solanesyl pyrophosphate. Aside this reaction, it can be converted by geranylgeranyl dehydrogenase in the chloroplast to form phytyl pyrophosphate, another end product of this pathway. Farnesyl pyrophosphate can additionally react using an undecaprenyl pyrophosphate synthetase family protein as a catalyst in order to form dehydrolichol pyrophosphate, or with the protein farnesyltransferase complex, which will add a protein-cysteine to the farnesyl pyrophosphate, which in turn loses its pyrophosphate group. The S-farnesyl protein then reacts with either CAAX prenyl protease 1 or 2 in the endoplasmic reticulum membrane to form protein C-terminal S-farnesyl-L-cysteine. This complex then reacts using protein-S-isoprenylcysteine O-methyltransferase B, still in the endoplasmic reticulum membrane, to form protein-C-terminal S-farnesyl-L-cysteine methyl ester. This reaction may be reversed by isoprenylcysteine alpha-carbonyl methylesterase, yet again in the endoplasmic reticulum membrane. Alternately, through an as of yet unknown reaction, the protein may be removed, as well as several other structure changes, leaving farnesylcysteine. In the lysosome, farnesylcysteine can be catalyzed by farnesylcysteine to remove the cysteine group, leaving behind farnesal. Then, a NAD-binding Rossman-fold superfamily protein can catalyze its transformation into farnesol. Finally, within the chloroplast, farnesol can be catalyzed by farnesol kinase to form farnesyl phosphate, the final product of this pathway.

Metabolic

SMP0121209

Pw122503 View Pathway
Metabolite

Mevalonate Pathway

Arabidopsis thaliana
The mevalonate pathway, also known as the isoprenoid pathway, plays an essential role in creating the chemicals needed for many plants to function. This pathway, combined with the MEP/DOXP pathway give many plants their scents, such as cinnamon and ginger, and are responsible for the red colour in tomatoes. The pathway begins with acetyl-CoA, having come from the glycolysis pathway. Acetyl-CoA immediately becomes acetoacetyl-CoA through the enzyme acetyl-CoA acetyltransferase 1/2. Combined, acetoacetyl-CoA and acetyl-CoA react with hydroxymethylglutaryl-CoA synthase to create 3-hydroxy-3methylglutaryl-CoA. From here, this compound is catalyzed by 3-hydroxy-3-methylglutaryl-coenzyme A reductase 1 and becomes (R)-mevalonate. Mevalonate is paired with mevalonate kinase to produce mevalonic acid-5P. In turn, mevalonic acid-5P reacts with phosphomevalonate kinase, and entering the peroxisome and becoming (R)-mevalonic acid-5-pyrophosphate. Remaining in the peroxisome, diphosphomevalonate decarboxylase MVD1 is used alongside (R)-mevalonic acid-5-pyrophosphate to create isopentenyl pyrophosphate, bringing the pathway into the chloroplast. Dimethylallylpyrophosphate is produced after isopentenyl pyrophosphate and isopentenyl diphosphate delta-isomerase II team up to catalyze it. Dimethylallylpyrophosphate then joins forces with isopentenyl again, this time adding geranylgeranyl pyrophosphate synthase 6 and moving into the mitochondria to produce geranyl-PP. This is followed by monoterpenoid biosynthesis.

Metabolic

SMP0121208

Pw122502 View Pathway
Metabolite

MEP/DOXP Pathway

Arabidopsis thaliana
The DOXP/MEP pathway, also known as the non-mevalonate pathway, plays an essential role in creating the chemicals needed for many plants to function. This pathway, combined with the MEP/DOXP pathway give many plants their scents, such as cinnamon and ginger, and are responsible for the red colour in tomatoes. Terpenoids, also called isoprenoids, are a substantial yet varied class of organic chemicals that occur naturally. Plant terpenoids have aromatic qualities and are used for this and their role in traditional herbal remedies. The pathway begins with D-glyceraldehyde 3-phosphate, which is produced through glycolysis. Together with pyruvic acid and the enzyme 1-deoxy-D-xylulose 5-phosphate synthase 1, these are catalyzed into 1-deoxy-xylulose 5-phosphate. From there, 1-deoxy-xylulose 5-phosphate teams up with 1-deoxy-D-xylulose 5-phosphate reductoisomerase to create 2-c-methyl-D-erythritol 4-phosphate. Moving along in the chloroplast, after being produced through 2-c-methyl-D-erythritol 4-phosphate and the enzyme 2-c-methyl-D-erythritol 4-phosphate cytidyltransferase,4-cytidine 5'-diphospho)-2-C-methyl-D-erythritol is catalyzed by 4-diphosphocytidyl-2-c-methyl-D-erythritol kinase to create 2-phospho-4-(cytidine 5'-diphospho)-2-c-methyl-D-erythritol. After that, 2-c-methyl-D-erythritol 2,4-cyclodiphosphate synthase uses the newly produced 2-phospho-4-(cytidine 5'-diphospho)-2-c-methyl-D-erythritol to create 2-c-methyl-D-erythritol-2,4-cyclodiphosphate. This compound is then joined with 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase to become 1-hydroxy-2-methyl-2-butenyl 4-diphosphate. This compound gets busy soon after its inception, branching off into two separate reactions: first reacting with 4-hydroxy-3-methylbut-2-enyl diphosphate reductase to create isopentenyl pyrophosphate, then reacting with the same enzyme to create dimethylallylpyrophosphate. Dimethylallylpyrophosphate is then looped into another reaction with isopentenyl-diphosphate delta-isomerase II, recreating isopentenyl pyrophosphate. It also reacts with geranylgeranyl pyrophosphate synthase 6, bringing the pathway into the mitochondrion to create geranyl pyrophosphate. This is later followed by a monoterpenoid biosynthesis pathway.

Metabolic

SMP0121207

Pw122501 View Pathway
Metabolite

Triterpenoid Biosynthesis

Arabidopsis thaliana
Triterpenoids have 30 carbons and six isoprene units. They are derived from (S)-2,3-epoxysqualene. They may contain rings or be acyclic, depending on the bonds formed by the loss of the diphosphate group. First, the terpenoid backbone is synthesized, producing farnesyl pyrophosphate. Two molecules of farnesyl pyrophosphate then join together to form presqualene diphosphate, catalyzed by squalene synthase 1. Then, the same enzyme removes the pyrophosphate group and replaces it with a hydrogen ion, forming squalene. Squalene then undergoes oxidation of one of its bonds via squlene monooxygenase 1, to form (S)-2,3-epoxysqualene. This may then proceed to the steroid biosynthesis pathway or may react with an isomerase or lyase to form a chair-chair-chair-boat triterpenoid. Similarly, squalene may interact with an isomerase or lyase to form a chair-chair-chair-chair triterpenoid. After the backbone is complete, (S)-2,3-epoxysqualene can interact with many enzymes in order to form the triterpenoids. It can interact with camelliol C synthase to form camelliol C, thalianol synthase to form thalianol, baruol synthase to form baruol, tirucalladienol synthase to form tirucalla-7,24-dien-3-beta-ol, amyrun synthase LUP2 to form lupeol, alpha- and beta-amyrin synthases to form alpha- and beta-amyrin respectively. It can also interact with lupan-3beta,20-diol synthase to add a water molecule to form lupan-3beta,20-diol, alpha- and beta-seco-amyrin synthases to form alpha- and beta-seco-amyrin respectively, marneral synthase to form marneral, and finally arabidiol synthase to add a water molecule and form arabidiol.

Metabolic

SMP0121205

Pw122499 View Pathway
Metabolite

Sesquiterpenoid Biosynthesis

Arabidopsis thaliana
Sesquiterpenoids have 15 carbons and three isoprene units. They are derived from farnesyl diphosphate. They may contain rings or be acyclic, depending on the bonds formed by the loss of the diphosphate group. First, the terpenoid backbone is synthesized, producing farnesyl pyrophosphate. Two molecules of farnesyl pyrophosphate then join together to form presqualene diphosphate, catalyzed by squalene synthase 1. Then, the same enzyme removes the pyrophosphate group and replaces it with a hydrogen ion, forming squalene. Squalene then undergoes oxidation of one of its bonds via squlene monooxygenase 1, to form (S)-2,3-epoxysqualene. This may then proceed to the steroid biosynthesis pathway or may react with an isomerase or lyase to form a chair-chair-chair-boat triterpenoid. Similarly, squalene may interact with an isomerase or lyase to form a chair-chair-chair-chair triterpenoid. After the backbone is complete, farnesyl pyrophosphate can have its pyrophosphate removed by different enzymes, leading to different conformations of sesquiterpenoids. If it interacts with (Z)-gamma-bisabolene synthase, it forms gamma-bisabolene. If it interacts wtih (+)-alpha-barbatene synthase, it forms (+)-alpha-barbatene, if it interacts wtih beta-chamigrene synthase it forms (+)-beta-chamigrene, and finally if it interacts with thujopsene synthase it forms (+)-thujopsene.

Metabolic

SMP0121204

Pw122497 View Pathway
Metabolite

L-Homomethionine Biosynthesis

Arabidopsis thaliana
Homomethionine is a non-protein amino acid. Homomethionine is synthesized from methionine via chain elongation. Transamination of methionine first forms a 2-oxo acid. The 2-oxo acid is then extended by one methyl group by a condensation reaction, an isomerization reaction, and a oxidative decarboxylation reaction. The newly formed 2-oxo acid can be transaminated to homomethionine or undergo further cycles of condensation, isomerization and oxidative decarboxylation to form di, tri, tetra, penta, and hexahomomethionines. Mono, di, tri, tetra, penta, and hexahomomethionines are precursors for aliphatic glucosinolates biosynthesis in Arabidopsis. The cytosolic recycled methionine ( S-adenosyl-L-methionine cycle II), not the plastid-located de novo synthesized methionine, is believed to be the substrate for methionine chain elongation and glucosinolate biosynthesis [Schuster06]. This is based on two observations: first, the first enzyme in the chain elongation pathway, EC 2.6.1.88, methionine transaminase ( BCAT4), is cytosolic. Second, the gene expressions of BCAT4 and the two cytosolic methionine synthases, which are involved in the SAM cycle, are strongly co-regulated.

Metabolic

SMP0121131

Pw122411 View Pathway
Metabolite

2-Amino-3-Carboxymuconate Semialdehyde Degradation

Homo sapiens
This pathway is part of a major route of the degradation of L-tryptophan. It begins with 2-amino-3-carboxymuconate-6-semialdehyde which is generated from L-tryptophan degradation. The 2-amino-3-carboxymuconate-6-semialdehyde first is acted upon by a decarboxylase, forming 2-aminomuconic acid semialdehyde, which is then dehydrogenated by 2-aminomuconic semialdehyde dehydrogenase to form 2-aminomuconic acid. An unknown protein forms a 2-aminomuconate deaminase which forms (3E)-2-oxohex-3-enedioate, and a second unknown protein forms a 2-aminomuconate reductase, which forms oxoadipic acid from (3E)-2-oxohex-3-enedioate. Finally, within the mitochondria, oxoadipic acid is dehydrogenated and a coenzyme A is attached by the organelle’s oxoglutarate dehydrogenase complex, forming glutaryl-CoA. Glutaryl-CoA can then be further degraded.

Metabolic

SMP0121128

Pw122406 View Pathway
Metabolite

Pancreas Function - Delta Cell

Homo sapiens
Pancreatic delta cells produce somatostatin which functions to inhibit glucagon, insulin, and itself. Somatostatin is stored in granules in the delta cell and is released in response to an increase in blood sugar, calcium, and blood amino acids during absorption of a meal. In the process of somatostatin secretion, glucose must first undergo glycolysis in the mitochondrion to increase ATP in the cell. The inside of the alpha cell then becomes electrically positive due to the closure of potassium channels that were inhibited by ATP. From this closure, the potassium is no longer being shuttled out of the cell, thus depolarizing the cell due to the extra intracellular potassium. The resulting action potential from the increased membrane potential causes the voltage gate calcium channels to open, creating an influx of calcium into the cell. This triggers the exocytosis of somatostatin granules from the delta cell.

Physiological

SMP0121126

Pw122401 View Pathway
Metabolite

Aldosterone from Steroidogenesis

Homo sapiens
Aldosterone is a hormone produced in the zona glomerulosa of the adrenal cortex. It's function is to act on the distal convoluted tubule and the collecting duct of the nephron to make them more permeable to sodium to allow for its reuptake (in addition to allowing potassium wasting). As a result, water follows the sodium back into the body. The water retention contributes to an increased blood volume. Angiotensin II from the circulation binds to receptors on the zona glomerulosa cell membrane, activating the G protein and triggering a signaling cascade. The end result is the activation of the steroidogenic acute regulatory (StAR) protein that permits cholesterol uptake into the mitochondria. From there, cholesterol undergoes a series of reactions in both the mitochondrion and the smooth endoplasmic reticulum (steroidogenesis) where it finally becomes aldosterone.

Physiological
Showing 1 - 10 of 109292 pathways