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Showing 21 - 30 of 605359 pathways
PathBank ID Pathway Name and Description Pathway Class Chemical Compounds Proteins

SMP0000793

Pw000770 View Pathway

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.
Metabolite
Metabolic

SMP0001985

Pw001971 View Pathway

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.
Metabolite
Metabolic

SMP0002032

Pw002018 View Pathway

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.
Metabolite
Metabolic

SMP0001908

Pw001894 View Pathway

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.
Metabolite
Metabolic

SMP0001901

Pw001887 View Pathway

Purine Degradation

Escherichia coli
Pseudouridine is phosphorylated by interacting with atp and a psuK resulting in the release of an ADP, a hydrogen ion and a pseudouridine 5'-phosphate. The latter compound then reacts with water through a pseudouridine 5'-phosphate glycosidase resulting in the release of a uracil and D-ribofuranose 5-phosphate
Metabolite
Metabolic

SMP0002119

Pw002107 View Pathway

Lipoate Biosynthesis and Incorporation I

Escherichia coli
Lipoate is an essential cofactor for key enzymes of oxidative metabolism. Mechanism of lipoate biosynthesis is similar to biotin biosynthesis. Octanoyltransferase facilitates the tranfer of octanoate moiety from octanoate-ACP to particular lysyl residues in lipoate-dependent enzymes. This process regenerates the acyl-carrier in the process, and create an octanylated domains in lipoate-dependent enzymes. Lipoyl synthase combines with S-adenosyl-L-methionine to generate an active lipoylated domain by converting the octanoyl side chain to an active lipoyl. Lipoyl synthase also split S-Adenosyl methionine (AdoMet) into 5'-deoxyadenosyl radical (later becomes 5'-deoxyadenosine by abstracting a hydrogen from a C-H bond) and L-methionine. L-methionine will undergo S-Adenosyl-L-Methionine Biosynthesis.
Metabolite
Metabolic

SMP0012026

Pw012887 View Pathway

Choline Biosynthesis I

Arabidopsis thaliana
Choline is a nitrogen-containing, water-soluble nutrient that is incorporated into the headgroups of membrane phospholipids such as phosphatidylcholine. Two pathways exist for choline biosynthesis whereby serine becomes choline. Both of these pathways take place in the cytosol. This is the first pathway of choline biosynthesis. First, serine decarboxylase (SDC) uses a proton and a pyridoxal 5'-phosphate cofactor to catalyze the conversion of L-serine to ethanolamine, producing carbon dioxide as a byproduct. Second, ethanolamine kinase, localized to the cell membrane (coloured dark green in the image), uses ATP to catalyze the conversion of ethanolamine to O-phosphoethanolamine. Note that this is only the probable ethanolamine kinase in Arabidopsis thaliana and requires further research to confirm its function. Steps 3, 4, and 5 are catalyzed by phosphoethanolamine N-methyltransferase (PEAMT). These three sequential N-methylation steps convert phosphoethanolamine to phosphocholine and utilize S-adenosyl-L-methionine as a methyl donor. The intermediates are as follows: O-Phosphoethanolamine, N-methylethanolamine phosphate, and N-dimethylethanolamine phosphate. Sixth, phosphoethanolamine/phosphocholine phosphatase catalyzes the synthesis of choline from phosphocholine. It requires magnesium as a cofactor.
Metabolite
Metabolic

SMP0012046

Pw012907 View Pathway

Thio-Molybdenum Cofactor Biosynthesis

Arabidopsis thaliana
Thio-molybdenum cofactor biosynthesis is a pathway that begins in the mitochondrial matrix and ends in the cytosol by which GTP becomes thio-molybdenum cofactor, the sulfo-form of molybdenum cofactor required by certain plant enzymes. First, the enzyme GTP 3',8-cyclase, located in the mitochondrial matrix, catalyzes the conversion of GTP, S-adenosylmethionine, and a reduced electron acceptor to 3′,8-cH2GTP, L-methionine, 5'-deoxyadenosine, an oxidized electron acceptor, and a hydrogen ion with the help of a [4Fe-4S] cluster cofactor. Second, cyclic pyranopterin monophosphate (cPMP) synthase catalyzes the conversion of 3′,8-cH2GTP to cPMP and pyrophosphate. Next, ABC transporter of the mitochondrion 3 (ATM3) exports cPMP from the mitochondrial matrix into the cytosol where it is acted upon by molybdopterin (MPT) synthase. MPT synthase is a heterotetramer composed of 2 large and 2 small subunits. The two small subunits are thiocarboxylated by molydopterin synthase sulfurtransferase, and each transfers a sulfur to cPMP to generate the dithiolene in molybdopterin and releasing hydrogen ion in the process. The following enzyme in the pathway, molybdenum insertase is a two-domain protein that catalyzes the fourth and fifth reactions. The smaller C-terminal Cnx1G domain functions as a molybdopterin molybdotransferase and activates molybdopterin for molybdenum insertion. The product of this reaction, molybdopterin adenine dinucleotide (MPT-AMP), is then transferred to the larger N-terminal Cnx1E domain which exhibits molybdopterin adenylyltransferase activity and inserts molybdenum into the dithiolene of molybdopterin, creating molybdenum cofactor (Moco). Molybdenum insertase requires a divalent cation (e.g. magnesium) as a cofactor. Lastly, molybdenum cofactor sulfurtransferase uses L-cysteine and a reduced electron acceptor to convert molybdenum cofactor into thio-molybdenum cofactor, producing L-alanine, oxidized electron acceptor, and water as byproducts. It requires pyridoxal 5'-phosphate as a cofactor.
Metabolite
Metabolic

SMP0012033

Pw012894 View Pathway

Abscisic Acid Glucose Ester Metabolism

Arabidopsis thaliana
Abscisic acid glucose ester metabolism is a pathway that begins in the chloroplast and enters the cytosol and endoplasmic reticulum body by which violaxanthin becomes abscisic acid glucose ester, synthesizing abscisic acid in the process. Abscisic acid glucose ester synthesis and reformation back to abscisic acid provides a mechanism for precisely controlling abscisic acid concentration (quickly removing and adding abscisic acid when required). First, neoxanthin synthase catalyzes the opening of the violaxanthin epoxide ring to form neoxanthin. Second, a yet unidentified neoxanthin isomerase is theorized to isomerize neoxanthin to 9'-cis-neoxanthin. Third, 9-cis-epoxycarotenoid dioxygenase (NCED) uses oxygen to cleave 9'-cis-neoxanthin to form xanthoxin and C25-allenic-apo-aldehyde. This enzyme requires Fe2+ as a cofactor. Next, a xanthoxin transporter is theorized to export xanthoxin from the chloroplast into the cytosol to continue abscisic acid biosynthesis, but it has yet to be discovered. Fourth, xanthoxin dehydrogenase, located in the cytosol, catalyzes the conversion of xanthoxin and NAD to abscisic aldehyde, NADH, and a proton with the help of a molybdenum cofactor (MoCo). Fifth, abscisic-aldehyde oxidase converts abscisic aldehyde, water, and oxygen into hydrogen peroxide, hydrogen ion, and abscisic acid. Sixth, abscisic acid glucosyltransferase uses UDP to convert abscisic acid into abscisic acid glucose ester. Abscisic acid glucose ester can then be converted back to abscisic acid via abscisic acid glucose ester beta-glucosidase located in the endoplasmic reticulum body (coloured dark green in the image). Consequently, it is theorized that ABA-GE transporters are required for this enzyme to access its substrates from the cytosol.
Metabolite
Metabolic

SMP0012059

Pw012921 View Pathway

D-Galactose Degradation (Leloir pathway)

Arabidopsis thaliana
The Leloir pathway is a metabolic pathway for the catabolism of D-galactose into D-glucopyranose 6-phosphate named after Luis Federico Leloir . Since galactose cannot be directly used for glycolysis, it needs to be converted into a different form. This pathway starts in the cytosol and finishes in the chloroplast. First, aldose 1-epimerase is a predicted enzyme (coloured orange in the image) that is theorized to catalyze the conversion of beta-D-galactose into alpha-D-galactose. This enzyme has not yet been elucidated for Arabidopsis thaliana. Second, galactokinase catalyzes the conversion of alpha-D-galactose into alpha-D-galactose 1-phosphate. Third, D-galactose-1-phosphate uridylyltransferase is a predicted enzyme theorized to catalyze the reaction whereby alpha-D-galactose 1-phosphate and UDP-glucose is converted into alpha-D-glucopyranose 1-phosphate and UDP-galactose. This enzyme has not yet been elucidated in Arabidopsis thaliana. UDP-glucose and UDP-galactose can be interconverted by the enzyme UDP-glucose 4-epimerase which requires NAD as a cofactor. Alpha-D-glucopyranose 1-phosphate must then be imported into the chloroplast, by a yet not discovered alpha-D-glucopyranose 1-phosphate transporter. Last, phosphoglucomutase uses magnesium ion as a cofactor to convert alpha-D-glucopyranose 1-phosphate into D-glucopyranose 6-phosphate.
Metabolite
Metabolic
Showing 21 - 30 of 167268 pathways