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Showing 71 - 80 of 111423 pathways
PathBank ID Pathway Chemical Compounds Proteins

SMP0001901

Pw001887 View Pathway
Metabolite

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

Metabolic

SMP0002119

Pw002107 View Pathway
Metabolite

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.

Metabolic

SMP0012446

Pw013309 View Pathway
Metabolite

Ascorbate Metabolism

Arabidopsis thaliana
Vitamin C (ascorbate) is a vitamin found in food and used as a dietary supplement. The vast majority of animals and plants are able to synthesize vitamin C, through a sequence of enzyme-driven steps, which convert monosaccharides to vitamin C. In plants, this is accomplished through the conversion of mannose or galactose to ascorbic acid starting in the cytosol and ending in the mitochondrial matrix . First, GDP-mannose 3,5-epimerase catalyzes the reversible epimerization of GDP-D-mannose into either GDP-L-gulose or GDP-L-galactose. It also can reversibly epimerize GDP-L-gulose into GDP-L-galactose and vice versa. It requires NAD as a cofactor. Second, GDP-L-galactose phosphorylase catalyzes the conversion of GDP-L-galactose into L-galactose 1-phosphate. Third, L-galactose 1-phosphate phosphatase catalyzes the conversion of L-galactose 1-phosphate into L-galactose. It requires magnesium ion as a cofactor. Fourth, L-galactose dehydrogenase catalyzes the conversion of L-galactose into L-galactono-1,4-lactone. L-galactono-1,4-lactone must then be imported into the mitochondrial matrix by a predicted innermitochondrial membrane transporter to complete ascorbate synthesis. L-galactono-1,4-lactone dehydrogenase, localized to the innermitochondrial membrane (coloured dark green in the image), catalyzes two reactions in ascorbate metabolism: the conversion of L-galactono-1,4-lactone into L-ascorbate and the subsequent conversion of L-ascorbate into L-dehydroascorbate. It requires FAD as a cofactor. Ascorbate can then be converted into monodehydroascorbate radical by the mitochondrial L-ascorbate peroxidase S (this plays a key role in hydrogen peroxide removal). Monodehydroascorbate reductase 5 then can convert monodehydroascorbate radical back into L-ascorbate.

Metabolic

SMP0012026

Pw012887 View Pathway
Metabolite

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.

Metabolic

SMP0012046

Pw012907 View Pathway
Metabolite

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.

Metabolic

SMP0012033

Pw012894 View Pathway
Metabolite

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.

Metabolic

SMP0012059

Pw012921 View Pathway
Metabolite

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.

Metabolic

SMP0002319

Pw002397 View Pathway
Metabolite

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.

Metabolic

SMP0012038

Pw012899 View Pathway
Metabolite

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.

Metabolic

SMP0012467

Pw013330 View Pathway
Metabolite

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.

Metabolic
Showing 71 - 80 of 111423 pathways