Browsing Pathways

The process of oleic acid B-oxidation starts with a 2-trans,5-cis-tetradecadienoyl-CoA that can be either be processed by an enoyl-CoA hydratase by interacting with a water molecules resulting in a 3-hydroxy-5-cis-tetradecenoyl-CoA, which can be oxidized in the fatty acid beta-oxidation. On the other hand 2-trans,5-cis-tetradecadienoyl-CoA can become a 3-trans,5-cis-tetradecadienoyl-CoA through a isomerase. This results interact with a water molecule through a acyl-CoA thioesterase resulting in a hydrogen ion, a coenzyme A and a 3,5-tetradecadienoate

Curcumin is metabolized by being reduced through a NADPH dependent curcumin reductase resulting in a dihydrocurcumin. This compound is then reduced again through a NADPH-dependent dihydrocurcumin reductase resulting in a tetrahydrocurcumin. It is not know yet how this compound enters E.coli

The biosynthesis of Valine and L-leucine from pyruvic acid starts with pyruvic acid interacting with a hydrogen ion through a acetolactate synthase / acetohydroxybutanoate synthase resulting in a release of a carbon dioxide, a (S)-2-acetolactate. The latter compound then interacts with a hydrogen ion through a NADPH-driven acetohydroxy acid isomeroreductase resulting in the release of a NADP, a (R) 2,3-dihydroxy-3-methylvalerate. The latter compound is then dehydrated by a dihydroxy acid dehydratase resulting in the release of a water molecule an 3-methyl-2-oxovaleric acid. The 3-methyl-2-oxovaleric acid can produce an L-valine by interacting with a L-glutamic acid through a Valine Transaminase resulting in the release of a Oxoglutaric acid and a L-valine. The 3-methyl-2-oxovaleric acid then interacts with an acetyl-CoA and a water molecule through a 2-isopropylmalate synthase resulting in the release of a hydrogen ion, a Coenzyme A and a 2-Isopropylmalic acid. The isopropylimalic acid is then hydrated by interacting with a isopropylmalate isomerase resulting in a 3-isopropylmalate. This compound then interacts with an NAD driven 3-isopropylmalate dehydrogenase resulting in a NADH, a hydrogen ion and a 2-isopropyl-3-oxosuccinate. The latter compound then interacts with hydrogen ion spontaneously resulting in a carbon dioxide and a ketoleucine. The ketoleucine then interacts with a L-glutamic acid through a branched-chain amino-acid aminotransferase resulting in the oxoglutaric acid and L-leucine.

The pathway starts with trans-cinnamate interacting with a hydrogen ion, an oxygen molecule, and a NADH through a cinnamate dioxygenase resulting in a NAD and a cis-3-(3-Carboxyethenyl)-3,5-cyclohexadiene-1,2-diol which then interact together through a 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase resulting in the release of a hydrogen ion, an NADH molecule and a 2,3 dihydroxy-trans-cinnamate. The second way by which the 2,3 dihydroxy-trans-cinnamate is acquired is through a 3-hydroxy-trans-cinnamate interacting with a hydrogen ion, a NADH and an oxygen molecule through a 3-(3-hydroxyphenyl)propionate 2-hydroxylase resulting in the release of a NAD molecule, a water molecule and a 2,3-dihydroxy-trans-cinnamate. The compound 2,3 dihydroxy-trans-cinnamate then interacts with an oxygen molecule through a 2,3-dihydroxyphenylpropionate 1,2-dioxygenase resulting in a hydrogen ion and a 2-hydroxy-6-oxonona-2,4,7-triene-1,9-dioate. The latter compound then interacts with a water molecule through a 2-hydroxy-6-oxononatrienedioate hydrolase resulting in a release of a hydrogen ion, a fumarate molecule and (2Z)-2-hydroxypenta-2,4-dienoate. The latter compound reacts spontaneously to isomerize into a 2-oxopent-4-enoate. This compound is then hydrated through a 2-oxopent-4-enoate hydratase resulting in a 4-hydroxy-2-oxopentanoate. This compound then interacts with a 4-hydroxy-2-ketovalerate aldolase resulting in the release of a pyruvate, and an acetaldehyde. The acetaldehyde then interacts with a coenzyme A and a NAD molecule through a acetaldehyde dehydrogenase resulting in a hydrogen ion, a NADH and an acetyl-coa which can be incorporated into the TCA cycle

PreQ0 or 7-cyano-7-carbaguanine is biosynthesized by degrading GTP. GTP first interacts with water through a GTP cyclohydrolase resulting in the release of a formate, a hydrogen ion and a 7,8-dihydroneopterin 3'-triphosphate. The latter compound then interacts with water through a 6-carboxy-5,6,7,8-tetrahydropterin synthase resulting in a acetaldehyde, triphosphate, 2 hydrogen ion and 6-carboxy-5,6,7,8-tetrahydropterin. The latter compound then reacts spontaneously with a hydrogen ion resulting in the release of a ammonium molecule and a 7-carboxy-7-deazaguanine. This compound then interacts with ATP and ammonium through 7-cyano-7-deazaguanine synthase resulting in the release of water, phosphate, ADP, hydrogen ion and a 7-cyano-7-carbaguanine. The degradation of 7-cyano-7-deazaguanine can lead to produce a preQ1 or a queuine by reacting with 3 hydrogen ions and 2 NADPH through a 7-cyano-7-deazaguanine reductase. PreQ1 then interacts with a guanine 34 in tRNA through a tRNA-guanine transglycosylase resulting in a release of a guanine and a 7-aminomethyl-7-deazaguanosine 34 in tRNA. This nucleic acid then interacts with SAM through a S-adenosylmethionine tRNA ribosyltransferase-isomerase resulting in a release of a hydrogen ion, L-methionine, adenine and an epoxyqueuosine

The pathway can start in various spots. First step in this case starts with NADH interacting with a menaquinone oxidoreductase resulting in the release of a NADH and a hydrogen Ion, at the same time in the inner membrane a menaquinone interacts with 2 electrons and 2 hydrogen ions thus releasing a menaquinol. This allows for 4 hydrogen ions to be transferred from the cytosol to the periplasmic space. The menaquinol then interacts with a trimethylamine N-oxide reductase resulting in the release of 2 hydrogen ion and 2 electrons. At the same time trimethylamine N-oxide and 3 hydrogen ions interact with the enzyme trimethylamine N-oxide reductase resulting in the release of a trimethylamine and a water molecule, this reaction happening in the periplasmic space. The second set of reactions starts with a hydrogen interacting with a menaquinone oxidoreductase resulting in the release of two electrons being released into the inner membrane which then react with with 2 hydrogen ion and a menaquinone to produce a menaquinol. This menaquinol then reacts with a trimethylamine N-oxide reductase following the same steps as mentioned before. The third set of reactions starts with with formate interacting with a formate dehydrogenase-O resulting in a release of carbon dioxide and a hydrogen ion, this releases 2 electrons that interact with a menaquinone and two hydrogen ions. This releases a menaquinol which then reacts with a trimethylamine N-oxide reductase following the same steps as mentioned before

The biosynthesis of shikimate starts with D-Erythrose-4-phosphate getting transformed into 3-deoxy-D-arabino-heptulosonate-7-phosphate through a phospho-2-dehydro-3-deoxyheptonate aldolase. This is followed by a 3-dehydroquinate synthase converting the 3-deoxy-D-arabino-heptulosonate-7-phosphate into a 3-dehydroquinate which in turn is conveted to 3-dehydroshikimate through a 3-dehydroquinate dehydratase. A this point 3-dehydroshikimate can be turned into Shikimic acid through 2 different reactions involving an NADPH driven Quinate/shikimate dehydrogenase or a NADPH driven shikimate dehydrogenase 2. Shikimate can also be transported through a shikimate:H+ symporter.

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.

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.