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Showing 31 - 40 of 605359 pathways
PathBank ID Pathway Name and Description Pathway Class Chemical Compounds Proteins

SMP0002319

Pw002397 View Pathway

Leloir Pathway

Saccharomyces cerevisiae
The pathway starts with the isomerization of Beta-D-galactose into Alpha-D-galactose through a galactose mutarotase. Alpha-D-galactose is then phosphorylated through an ATP dependent galactokinase resulting in the release of ADP, a hydrogen ion and alpha-D-galactose 1-phosphate. The latter compound reacts with UDP glucose which is the result of UTP reacting with alpha-D-glucose through a uridinephosphoglucose pyrophosphorylase. The reaction between alpha-D-galactose 1-phosphate and UDP glucose results in the release of glucose 1-phosphate and UDP-alpha-D-galactose. Glucose 1-phosphate can be further isomerized into glucose 6-phosphate, while UDP-alpha-D-galactose can be reverted into UDP glucose through a UDP-epimerase.
Metabolite
Metabolic

SMP0012038

Pw012899 View Pathway

Chlorophyll a Biosynthesis II

Arabidopsis thaliana
Chlorophyll a is the primary form of chlorophyll in plants. Chlorophylls are pigments that give plants their perceived green colour and are essential for photosynthesis, the process by which light energy is converted into chemical energy. Chlorophyll a, in particular, absorbs energy from wavelengths of violet-blue and orange-red light. Two pathways exist for chlorophyll a biosynthesis whereby geranylgeranyl diphosphate and 3,8-divinyl chlorophyllide a becomes chlorophyll a. Both of these pathways take place in the chloroplast. This is the second pathway of chlorophyll a biosynthesis. First, 3,8-divinyl protochlorophyllide a 8-vinyl-reductase converts 3,8-divinyl chlorophyllide into chlorophyllide a. Second, chlorophyll synthetase uses magnesium ion as a cofactor to convert chlorophyllide a and geranylgeranyl diphosphate into geranylgeranyl chlorophyll a. The next three reactions to synthesize chlorophyll a from geranylgeranyl chlorophyll a are catalyzed by the same enzyme, geranylgeranyl dehydrogenase. It converts geranylgeranyl chlorophyll a into dihydrogeranylgeranyl chlorophyll a, dihydrogeranylgeranyl chlorophyll a into tetrahydrogeranylgeranyl chlorophyll a, and tetrahydrogeranylgeranyl chlorophyll a into chlorophyll a.
Metabolite
Metabolic

SMP0012467

Pw013330 View Pathway

Butanoate Metabolism

Arabidopsis thaliana
Butanoate or butyrate is the traditional name for the conjugate base of butanoic acid (also known as butyric acid). Butanoate metabolism includes L-glutamate degradation into the signal molecule GABA followed by subsequent reactions to make further products. Glutamate decarboxylase is an enzyme in the cytosol that catalyzes the conversion of L-glutamate into 4-aminobutanoate (GABA). It requires pyridoxal 5'-phosphate as a cofactor. This is followed by GABA permease, belonging to the APC Family of transport proteins, transporting GABA from the cytosol into the mitochondria matrix. Next, gamma-aminobutyrate transaminase degrades gamma-amino butyric acid (GABA) into succinate semialdehyde and uses either pyruvate or glyoxylate as an amino-group acceptor. The pyruvate-dependent activity is reversible while the glyoxylate-dependent activity is irreversible. Afterwards, succinate-semialdehyde dehydrogenase oxidizes succinate semialdehyde into succinate. A predicted succinate semialdehyde transporter in the mitochondria inner membrane is theorized to export succinate semialdehyde from the mitochondrial matrix into the cytosol. There, glyoxylate/succinic semialdehyde reductase catalyzes the reversible conversion of succinate semialdehyde into 4-hydroxybutanoate. Butanoate metabolism in Arabidopsis thaliana also includes reactions involving acetyl-CoA and acetoacetyl-CoA. 3-hydroxybutyryl-CoA dehydrogenase is a predicted enzyme (coloured orange in the image) in the cytosol that is theorized to catalyze the reversible conversion of 3-hydroxybutanoyl-CoA into acetoacetyl-CoA. Acetyl-CoA acetyltransferase then catalyzes the reversible conversion of acetoacetyl-CoA into acetyl-CoA. Then, hydroxymethylglutaryl-CoA synthase condenses acetyl-CoA with acetoacetyl-CoA to form 3-hydroxy-3-methylglutaryl-CoA. This is followed by a predicted 3-hydroxy-3-methylglutaryl-CoA transporter localized to the mitochondria inner membrane that is theorized to import 3-hydroxy-3-methylglutaryl-CoA into the mitochondrial matrix from the cytosol. Once there, hydroxymethylglutaryl-CoA lyase catalyzes the synthesis of acetoacetate and acetyl-CoA from 3-hydroxy-3-methylglutaryl-CoA.
Metabolite
Metabolic

SMP0012052

Pw012914 View Pathway

AMP Degradation (Hypoxanthine Route)

Arabidopsis thaliana
Purine nucleotides are eventually degraded to ammonia and carbon dioxide. This pathway follows the degradation of AMP to a urate intermediate in the cytosol via xanthine conversion from hypoxanthine. First, AMP deaminase catalyzes the conversion of AMP is into IMP. Second, the predicted enzyme 5′-nucleotidase (coloured orange in the image) is theorized to convert IMP into inosine. Third, ribonucleoside hydrolase converts inosine into hypoxanthine. Fourth, xanthine dehydrogenase is an enzyme that requires [2Fe-2S] cluster, FAD, and Moco as cofactors for catalyzing two subsequent reaction in the AMP degradation pathway: the conversion of hypoxanthine into xanthine and the conversion of xanthine into urate.
Metabolite
Metabolic

SMP0002094

Pw002082 View Pathway

Thioredoxin Pathway

Escherichia coli
Thioredoxins are a class of proteins that are used in redox reactions, and are found in all living organisms. In humans, they respond to reactive oxygen species, while in plants they are important for growth, photosynthesis, flowering and seed formation. In E. coli, thioredoxins catalyze a number of redox reactions, and are important in stress response, as well as other functions. In this pathway, oxidized thioredoxin is reduced by thioredoxin reductase, in order to form reduced thioredoxin. This reaction also uses NADPH as a cofactor. Reduced thioredoxin then, as part of a redox reaction, acts as the oxidizing agent and converts an oxidized electron acceptor into a reduced electron acceptor. This then produces oxidized thioredoxin, which can be further reduced and reused in other redox reactions.
Metabolite
Metabolic

SMP0014205

Pw015069 View Pathway

Phosphatidylcholine Biosynthesis

Arabidopsis thaliana
Phosphatidylcholines (PC) are a class of phospholipids that incorporate a phosphocholine headgroup into a diacylglycerol backbone. They are the most abundant phospholipid in eukaryotic cell membranes and has both structural and signalling roles. In eukaryotes, there exist two phosphatidylcholine biosynthesis pathways: the Kennedy pathway and the methylation pathway. The Kennedy pathway begins with the direct phosphorylation of free choline into phosphocholine followed by conversion into CDP-choline and subsequently phosphatidylcholine. It is the major synthesis route in animals. The methylation pathway involves the 3 successive methylations of phosphoethanolamine to form phosphocholine which is then funnelled into the Kennedy pathway to make phosphatidylcholine. In plants, phosphatidylcholine biosynthesis is implemented using a mix between the two pathways. An alternative of the methylation pathway uses phosphatidylethanolamine as a starting compound, but no enzyme has been found in Arabidopsis to catalyze the first methylation to form phosphatidyl-N-methylethanolamine. Many enzymes involved in this pathway are localized to the cell membrane but are not drawn as such for clarity. Instead, they are indicated with a dark green colour and appear to be free floating in the cytosol. The first reaction of the Kennedy pathway involves the membrane-localized enzyme choline/ethanolamine kinase catalyzing the conversion of choline into phosphocholine. Second, choline-phosphate cytidylyltransferase catalyzes the conversion of phosphocholine to CDP-choline. Last, choline/ethanolaminephosphotransferase, localized to the cell membrane, catalyzes phosphatidylcholine biosynthesis from CDP-choline. It requires either magnesium or manganese ions as cofactors. Note that phosphatidylcholine can be converted to either phosphocholine by a non-specific phospholipase or converted to choline by phospholipase D. Phosphocholine can also be converted to choline via phosphoethanolamine/phosphocholine phosphatase. The methylation pathway begins with serine decarboxylase catalyzing the biosynthesis of ethanolamine from serine. It requires pyridoxal 5'-phosphate as a cofactor. Next, choline/ethanolamine kinase, localized to the cell membrane, catalyzes the conversion of ethanolamine to phosphoethanolamine. Phosphoethanolamine N-methyltransferase (PEAMT), located in the cytosol, then catalyzes three sequential N-methylation steps to convert phosphoethanolamine to phosphocholine. PEAMT uses S-adenosyl-L-methionine as a methyl donor. Phosphocholine then enters the Kennedy pathway. Alternatively, in a subpathway parallel to the Kennedy pathway, phosphoethanolamine can be converted into phosphatidylethanolamine. Phosphatidylethanolamine is also synthesized from phosphatidylserine in the endoplasmic reticulum by phosphatidylserine decarboxylase. Note that phosphatidylethanolamine can be converted to either phosphoethanolamine by a non-specific phospholipase or converted to ethanolamine by phospholipase D. The two methylated intermediates N-methylethanolamine phosphate and N-dimethylethanolamine phosphate can also undergo reactions parallel to the Kennedy pathway to form the methylated intermediates of phosphatidylethanolamine (otherwise catalyzed by phosphatidyl-N-methylethanolamine N-methyltransferase, localized to the endoplasmic reticulum membrane, to form phosphatidylcholine).
Metabolite
Metabolic

SMP0012064

Pw012926 View Pathway

Triacylglycerol Degradation

Arabidopsis thaliana
In higher plants, the primary seed storage reserve is triacylglycerol rather than carbohydrates. Thus, triacylglycerol degradation is an important pathway from which plants obtain energy for growth. First, triacylglycerol lipase, an enzyme localized to the oil body (storage vacuole) membrane, catalyzes the conversion of a triglyceride into a 1,2-diglyceride. Second, the predicted enzyme diglyceride lipase (coloured orange in the image) is theorized to catalyze the conversion of a 1,2-diglyceride iinto a 2-acylglycerol. Third, a 2-acylglycerol is spontaneously converted into a 1-monoglyceride. Fourth, acylhydrolase catalyzes the conversion of a 1-monoglyceride into glycerol. Fifth, glycerol kinase catalyzes the conversion of glycerol into glycerol 3-phosphate. Sixth, glycerol-3-phosphate dehydrogenase (coloured dark green in the image), localized to the mitochondrial inner membrane, catalyzes the conversion of glycerol 3-phosphate into glycerone phosphate.
Metabolite
Metabolic

SMP0001000

Pw000984 View Pathway

Secondary Metabolites: Histidine Biosynthesis

Escherichia coli
Histidine biosynthesis starts with a product of PRPP biosynthesis pathway, phosphoribosyl pyrophosphate which interacts with a hydrogen ion through an ATP phosphoribosyltransferase resulting in an pyrophosphate and a phosphoribosyl-ATP. The phosphoribosyl-ATP interacts with water through a phosphoribosyl-AMP cyclohydrolase / phosphoribosyl-ATP pyrophosphatase resulting in the release of pyrophosphate, hydrogen ion and a phosphoribosyl-AMP. The same enzyme proceeds to interact with phosphoribosyl-AMP and water resulting in a 1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide. The product is then isomerized by a N-(5'-phospho-L-ribosyl-formimino)-5-amino-1-(5'-phosphoribosyl)-4-imidazolecarboxamide isomerase resulting in a PhosphoribosylformiminoAICAR-phosphate, which reacts with L-glutamine through an imidazole glycerol phosphate synthase resulting in a L-glutamic acid, hydrogen ion, 5-aminoimidazole-4-carboxamide and a D-erythro-imidazole-glycerol-phosphate. D-erythro-imidazole-glycerol-phosphate reacts with a imidazoleglycerol-phosphate dehydratase / histidinol-phosphatase, dehydrating the compound and resulting in a imidazole acetol-phosphate. Next, imidazole acetol-phosphate reacts with L-glutamic acid through a histidinol-phosphate aminotransferase, releasing oxoglutaric acid and L-histidinol-phosphate. The latter compound interacts with water and a imidazoleglycerol-phosphate dehydratase / histidinol-phosphatase resulting in L-histidinol and phosphate. L-histidinol interacts with a NAD-driven histidinol dehydrogenase resulting in a Histidinal. Histidinal in turn reacts with water in a NAD driven histidinal dehydrogenase resulting in L-Histidine. L-Histidine then represses ATP phosphoribosyltransferase, regulation its own biosynthesis.
Metabolite
Metabolic

SMP0002430

Pw002537 View Pathway

Isoleucine Biosynthesis

Arabidopsis thaliana
Isoleucine biosynthesis begins with L-threonine from the threonine biosynthesis pathway. L-threonine interacts with a threonine dehydratase biosynthetic releasing water, a hydrogen ion and (2Z)-2-aminobut-2-enoate. This compound is isomerized into a 2-iminobutanoate which interacts with water and a hydrogen ion spontaneously, resulting in the release of ammonium and 2-ketobutyric acid. This compound reacts with pyruvic acid and hydrogen ion through an acetohydroxybutanoate synthase / acetolactate synthase 2 resulting in carbon dioxide and (S)-2-Aceto-2-hydroxybutanoic acid. The latter compound is reduced by an NADPH driven acetohydroxy acid isomeroreductase releasing NADP and acetohydroxy acid isomeroreductase. The latter compound is dehydrated by a dihydroxy acid dehydratase resulting in 3-methyl-2-oxovaleric acid.This compound reacts in a reversible reaction with L-glutamic acid through a Branched-chain-amino-acid aminotransferase resulting in oxoglutaric acid and L-isoleucine.
Metabolite
Metabolic

SMP0000815

Pw000794 View Pathway

Proline Metabolism

Escherichia coli
The creation of L-proline in E. coli starts with L-glutamic acid being phosphorylated through an ATP driven glutamate 5-kinase resulting in a L-glutamic acid 5-phosphate. This compound is then reduced through an NADPH driven gamma glutamyl phosphate reductase resulting in the release of a phosphate, an NADP and a L-glutamic gamma-semialdehyde. L-glutamic gamma-semialdehyde is dehydrated spontaneously, resulting in a release of water,hydrogen ion and 1-Pyrroline-5-carboxylic acid. The latter compound is reduced by an NADPH driven pyrroline-5-carboxylate reductase which is then reduced to L-proline. L-proline works as a repressor of the pyrroline-5-carboxylate reductase enzyme and glutamate 5-kinase. Three genetic loci, proA, proB and proC control the biosynthesis of L-proline in E. coli.The pathway begins with a reaction that is catalyzed by γ-glutamyl kinase, which is encoded by proB. Next, NADPH-dependent reduction of γ-glutamyl phosphate to glutamate-5-semialdehyde, occurs through catalyzation by glutamate-5-semialdehyde dehydrogenase, encoded by proA. Following this, both enzymes join together in a multimeric bi-functional enzyme complex called γ-glutamyl kinase-GP-reductase multienzyme complex. This formation is thought to protect the highly labile glutamyl phosphate from the antagonistic nucleophilic and aqueous environment found in the cell. Finally, NADPH-dependent pyrroline-5-carboxylate reductase encoded by proC catalyzes the reduction of pyrroline 5-carboxylate into L-proline. Proline is metabolized in E. coli by returning to the form of L-glutamate, which is then degraded to α-ketoglutarate,which serves as an intermediary of the TCA cycle. Interestingly enough, L-glutamate, the obligate intermediate of the proline degradation pathway, is not able to serve as an outright source of carbon and energy for E. coli, because the rate at which glutamate transport supplies exogenous glutamate is not adequate. The process by which proline is turned into L-glutamate starts with L-proline interacting with ubiquinone through a bifunctional protein putA resulting in an ubiquinol, a hydrogen ion and a 1-pyrroline-5-carboxylic acid. The latter compound is then hydrated spontaneously resulting in a L-glutamic gamma-semialdehyde. This compound is then processed by interacting with water through an NAD driven bifunctional protein putA resulting in a hydrogen ion, NADH and L-glutamic acid.
Metabolite
Metabolic
Showing 31 - 40 of 167268 pathways