Browsing Pathways

2-O-α-Mannosyl-D-glycerate (MG; also named as Alpha-Mannosylglycerate) is an organic compound that will affect the osmosis in hyperthermophilic archaea and bacteria. In E.coli, 2-O-α-mannosyl-D-glycerate PTS permease (mngA) import MG into cell, and then phosphorylate MG to 2-O-(6-phospho-α-mannosyl)-D-glycerate by phosphocarrier protein HPr. 2-O-(6-phospho-α-mannosyl)-D-glycerate is converted to glyceric acid as well as mannose 6-phosphate by alpha-mannosidase mngB. Finally, glyceric acid is catalyzed to 2-Phospho-D-glyceric acid with ATP as energy source by Glycerate kinase 2. E.coli can't use MG as osmotic stress protection, but it can use MG as a carbon source.

Sedoheptulose bisphospate bypass pathway demonstrates a series of reaction that form D-Erythrose 4-phosphate for pentose phosphate pathway and glycerone phosphate for glycolysis and pyruvate dehydrogenase pathway. D-Sedoheptulose 7-phosphate is obtained from pentose phosphate pathway, which later converted to sedoheptulose 1,7-bisphosphate via 6-phosphofructokinase-1. Fructose-bisphosphate aldolase class 2 catalyzes sedoheptulose 1,7-bisphosphate to form D-Erythrose 4-phosphate and pyruvate dehydrogenase.

The process of phenylethylamine metabolism starts with 2-phenylethylamine interacting with an oxygen molecule and a water molecule in the periplasmic space through a phenylethylamine oxidase. This reaction results in the release of a hydrogen peroxide, ammonium and phenylacetaldehyde. Phenylacetaldehyde is introduced into the cytosol and degraded into phenylacetate by reaction with a phenylacetaldehyde dehydrogenase. This reaction involves phenylacetaldehyde interacting with NAD, and a water molecule and then resulting in the release of NADH, and 2 hydrogen ion. Phenylacetate is then degraded. The first step involves phenylacetate interacting with an coenzyme A and an ATP driven phenylacetate-CoA ligase resulting in the release of a AMP, a diphosphate and a phenylacetyl-CoA. This resulting compound the interacts with a hydrogen ion, NADPH, and oxygen molecule through a ring 1,2-phenylacetyl-CoA epoxidase protein complex resulting in the release of a water molecule, an NADP and a 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA. This compound is then metabolized by a ring 1,2 epoxyphenylacetyl-CoA isomerase resulting in a 2-oxepin-2(3H)-ylideneacetyl-CoA. This compound is then hydrolated through a oxepin-CoA hydrolase resulting in a 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde. This commpound then interacts with a water molecule and NADP driven 3-oxo-5,6-dehydrosuberyl-CoA semialadehyde dehydrogenase resulting in 2 hydrogen ions, a NADPH and a 3-oxo-5,6-didehydrosuberyl-CoA. The resulting compound interacts with a coenzyme A and a 3-oxo-5,6 dehydrosuberyl-CoA thiolase resulting in an acetyl-CoA and a 2,3-didehydroadipyl-CoA. This resulting compound is the hydrated by a 2,3-dehydroadipyl-CoA hydratas resulting in a 3-hydroxyadipyl-CoA whuch is dehydrogenated through an NAD driven 3-hydroxyadipyl-CoA dehydrogenase resulting in a NADH, a hydrogen ion and a 3-oxoadipyl-CoA. The latter compound then interacts with conezyme A through a beta-ketoadipyl-CoA thiolase resulting in an acetyl-CoA and a succinyl-CoA. The succinyl-CoA is then integrated into the TCA cycle.

The process of phenylethylamine metabolism starts with 2-phenylethylamine interacting with an oxygen molecule and a water molecule in the periplasmic space through a phenylethylamine oxidase. This reaction results in the release of a hydrogen peroxide, ammonium and phenylacetaldehyde. Phenylacetaldehyde is introduced into the cytosol and degraded into phenylacetate by reaction with a phenylacetaldehyde dehydrogenase. This reaction involves phenylacetaldehyde interacting with NAD, and a water molecule and then resulting in the release of NADH, and 2 hydrogen ion. Phenylacetate is then degraded. The first step involves phenylacetate interacting with an coenzyme A and an ATP driven phenylacetate-CoA ligase resulting in the release of a AMP, a diphosphate and a phenylacetyl-CoA. This resulting compound the interacts with a hydrogen ion, NADPH, and oxygen molecule through a ring 1,2-phenylacetyl-CoA epoxidase protein complex resulting in the release of a water molecule, an NADP and a 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA. This compound is then metabolized by a ring 1,2 epoxyphenylacetyl-CoA isomerase resulting in a 2-oxepin-2(3H)-ylideneacetyl-CoA. This compound is then hydrolated through a oxepin-CoA hydrolase resulting in a 3-oxo-5,6-didehydrosuberyl-CoA semialdehyde. This commpound then interacts with a water molecule and NADP driven 3-oxo-5,6-dehydrosuberyl-CoA semialadehyde dehydrogenase resulting in 2 hydrogen ions, a NADPH and a 3-oxo-5,6-didehydrosuberyl-CoA. The resulting compound interacts with a coenzyme A and a 3-oxo-5,6 dehydrosuberyl-CoA thiolase resulting in an acetyl-CoA and a 2,3-didehydroadipyl-CoA. This resulting compound is the hydrated by a 2,3-dehydroadipyl-CoA hydratas resulting in a 3-hydroxyadipyl-CoA whuch is dehydrogenated through an NAD driven 3-hydroxyadipyl-CoA dehydrogenase resulting in a NADH, a hydrogen ion and a 3-oxoadipyl-CoA. The latter compound then interacts with conezyme A through a beta-ketoadipyl-CoA thiolase resulting in an acetyl-CoA and a succinyl-CoA. The succinyl-CoA is then integrated into the TCA cycle.

The citric acid cycle (also named tricarboxylic acid (TCA) cycle or the Krebs cycle), is a collection of 9 enzyme-catalyzed chemical reactions that occur in all living cells undergoing aerobic respiration. The citric acid cycle itself was officially identified in 1937 by Hans Adolf Krebs, who received the Nobel Prize for this discovery in 1953. In eukaryotes, the citric acid cycle occurs in the mitochondria. In prokaryotes, the TCA cycle occurs in the cytoplasm. The TCA cycle starts with acetyl-CoA, which is the “fuel” for the entire cycle. This important molecule comes from the breakdown of glycogen (a stored form of glucose), fats, and many amino acids. At beginning, acetyl-CoA first transfers its 2-carbon acetyl group to the 4-carbon acceptor compound called oxaloacetate to form the 6-carbon compound (citrate) for which the cycle is named. The resulting citrate will have numbers of chemical transformations, whereby it loses one carboxyl group (leading to the 5-carbon compound called alpha-ketoglutarate) and then a second carboxyl group (leading to the 4-carbon compound called succinate). Succinate molecule is further oxidized to fumarate, then malate and finally oxaloacetate. The regeneration of the 4-carbon oxaloacetate, allows the TCA cycle to continue. Oxidation step generates energy that is transferring energy-rich electrons for NAD+ to form NADH in TCA cycle. Each acetyl group will generate 3 NADH in TCA cycle.

Cardiolipin (CL) is an important component of the inner mitochondrial membrane where it constitutes about 20% of the total lipid composition. It is essential for the optimal function of numerous enzymes that are involved in mitochondrial energy metabolism (Wikipedia). Cardiolipin biosynthesis occurs mainly in the mitochondria, but there also exists an alternative synthesis route for CDP-diacylglycerol that takes place in the endoplasmic reticulum. This second route may supplement this pathway. All membrane-localized enzymes are coloured dark green in the image. First, dihydroxyacetone phosphate (or glycerone phosphate) from glycolysis is used by the cytosolic enzyme glycerol-3-phosphate dehydrogenase [NAD(+)] to synthesize sn-glycerol 3-phosphate. Second, the mitochondrial outer membrane enzyme glycerol-3-phosphate acyltransferase esterifies an acyl-group to the sn-1 position of sn-glycerol 3-phosphate to form 1-acyl-sn-glycerol 3-phosphate (lysophosphatidic acid or LPA). Third, the enzyme 1-acyl-sn-glycerol-3-phosphate acyltransferase converts LPA into phosphatidic acid (PA or 1,2-diacyl-sn-glycerol 3-phosphate) by esterifying an acyl-group to the sn-2 position of the glycerol backbone. PA is then transferred to the inner mitochondrial membrane to continue cardiolipin synthesis. Fourth, magnesium-dependent phosphatidate cytidylyltransferase catalyzes the conversion of PA into CDP-diacylglycerol. Fifth, CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase synthesizes phosphatidylglycerophosphate (PGP). Sixth, phosphatidylglycerophosphatase and protein-tyrosine phosphatase dephosphorylates PGP to form phosphatidylglycerol (PG). Last, cardiolipin synthase catalyzes the synthesis of cardiolipin by transferring a phosphatidyl group from a second CDP-diacylglycerol to PG. It requires a divalent metal cation cofactor.

Cardiolipin (CL) is an important component of the inner mitochondrial membrane where it constitutes about 20% of the total lipid composition. It is essential for the optimal function of numerous enzymes that are involved in mitochondrial energy metabolism (Wikipedia). Cardiolipin biosynthesis occurs mainly in the mitochondria, but there also exists an alternative synthesis route for CDP-diacylglycerol that takes place in the endoplasmic reticulum. This second route may supplement this pathway. All membrane-localized enzymes are coloured dark green in the image. First, dihydroxyacetone phosphate (or glycerone phosphate) from glycolysis is used by the cytosolic enzyme glycerol-3-phosphate dehydrogenase [NAD(+)] to synthesize sn-glycerol 3-phosphate. Second, the mitochondrial outer membrane enzyme glycerol-3-phosphate acyltransferase esterifies an acyl-group to the sn-1 position of sn-glycerol 3-phosphate to form 1-acyl-sn-glycerol 3-phosphate (lysophosphatidic acid or LPA). Third, the enzyme 1-acyl-sn-glycerol-3-phosphate acyltransferase converts LPA into phosphatidic acid (PA or 1,2-diacyl-sn-glycerol 3-phosphate) by esterifying an acyl-group to the sn-2 position of the glycerol backbone. PA is then transferred to the inner mitochondrial membrane to continue cardiolipin synthesis. Fourth, magnesium-dependent phosphatidate cytidylyltransferase catalyzes the conversion of PA into CDP-diacylglycerol. Fifth, CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase synthesizes phosphatidylglycerophosphate (PGP). Sixth, phosphatidylglycerophosphatase and protein-tyrosine phosphatase dephosphorylates PGP to form phosphatidylglycerol (PG). Last, cardiolipin synthase catalyzes the synthesis of cardiolipin by transferring a phosphatidyl group from a second CDP-diacylglycerol to PG. It requires a divalent metal cation cofactor.

L-alanine is an essential component of proteins and peptidoglycan. The latter also contains about three molecules of D-alanine for every L-alanine. Only about 10 percent of the total alanine synthesized flows into peptidoglycan.There are at least 3 ways to begin the biosynthesis of alanine. The first method for alanine biosynthesis begins with L-cysteine produced from L-cysteine biosynthesis pathway. L-cysteine reacts with an [L-cysteine desulfurase] L-cysteine persulfide through a cysteine desulfurase resulting in a release of [L-cysteine desulfurase] l-cysteine persulfide and L-alanine. The second method starts with pyruvic acid reacting with L-glutamic acid through a glutamate-pyruvate aminotransferase resulting in a oxoglutaric acid and L-alanine. The third method starts with L-glutamic acid interacting with Alpha-ketoisovaleric acid through a valine transaminase resulting in an oxoglutaric acid and L-valine. L-valine reacts with pyruvic acid through a valine-pyruvate aminotransferase resulting Alpha-ketoisovaleric acid and L-alanine. This first step of the pathway, which can be catalyzed by either of two racemases (biosynthetic or catabolic), also serves an essential role in biosynthesis because its product, D-alanine, is an essential component of cell wall peptidoglycan (murein). D-alanine is metabolized by an ATP driven D-alanine ligase A and B resulting in D-alanyl-D-alanine. This product is incorporated into the peptidoglycan biosynthesis. L-alanine is metabolized with alanine racemase, either catabolic or metabolic resulting in a D-alanine. This compound reacts with water and a quinone through a D-amino acid dehydrogenase resulting in Pyruvic acid, hydroquinone and ammonium, thus entering the central metabolism and thereby can serve as a total source of carbon and energy. The role of the dadX racemase is degradative and dadX racemase can be induced by alanine and is subject to catabolite repression.

L-alanine is an essential component of proteins and peptidoglycan. The latter also contains about three molecules of D-alanine for every L-alanine. Only about 10 percent of the total alanine synthesized flows into peptidoglycan.There are at least 3 ways to begin the biosynthesis of alanine. The first method for alanine biosynthesis begins with L-cysteine produced from L-cysteine biosynthesis pathway. L-cysteine reacts with an [L-cysteine desulfurase] L-cysteine persulfide through a cysteine desulfurase resulting in a release of [L-cysteine desulfurase] l-cysteine persulfide and L-alanine. The second method starts with pyruvic acid reacting with L-glutamic acid through a glutamate-pyruvate aminotransferase resulting in a oxoglutaric acid and L-alanine. The third method starts with L-glutamic acid interacting with Alpha-ketoisovaleric acid through a valine transaminase resulting in an oxoglutaric acid and L-valine. L-valine reacts with pyruvic acid through a valine-pyruvate aminotransferase resulting Alpha-ketoisovaleric acid and L-alanine. This first step of the pathway, which can be catalyzed by either of two racemases (biosynthetic or catabolic), also serves an essential role in biosynthesis because its product, D-alanine, is an essential component of cell wall peptidoglycan (murein). D-alanine is metabolized by an ATP driven D-alanine ligase A and B resulting in D-alanyl-D-alanine. This product is incorporated into the peptidoglycan biosynthesis. L-alanine is metabolized with alanine racemase, either catabolic or metabolic resulting in a D-alanine. This compound reacts with water and a quinone through a D-amino acid dehydrogenase resulting in Pyruvic acid, hydroquinone and ammonium, thus entering the central metabolism and thereby can serve as a total source of carbon and energy. The role of the dadX racemase is degradative and dadX racemase can be induced by alanine and is subject to catabolite repression.

Fatty acid oxidation is also known as beta-oxidation. Fatty acids are an important energy source because they are anhydrous and can be reduced. Fatty acids are good sources of energy as they yield more energy than carbohydrates. The fatty acid oxidation pathway degrades fatty acids into acetyl-CoA under anaerobic and aerobic conditions. Enzymes of this pathway can process short and long chain fatty acids. The first step in the pathway is the conversion of acyl-CoA to enoyl-CoA. The pathway continues in a cycle, each turn removing two carbon atoms from the input acyl-CoA to produce acetyl-CoA. Each turn also produces NADH.