Browsing Pathways

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 process of oxidative phosphorylation involves multiple interactions of ubiquinone with succinic acid, resulting in a fumaric acid and ubiquinol. Ubiquinone interacts with succinic acid through a succinate:quinone oxidoreductase resulting in a fumaric acid an ubiquinol. This enzyme has various cofactors, ferroheme b, 2FE-2S, FAD, and 3Fe-4S iron-sulfur cluster. Then 2 ubiquinol interact with oxygen and 4 hydrogen ion through a cytochrome bd-I terminal oxidase resulting in a 4 hydrogen ion transferred into the periplasmic space, 2 water returned into the cytoplasm and 2 ubiquinone, which stay in the inner membrane. The ubiquinone interacts with succinic acid through a succinate:quinone oxidoreductase resulting in a fumaric acid an ubiquinol. Then 2 ubiquinol interacts with oxygen and 4 hydrogen ion through a cytochrome bd-II terminal oxidase resulting in a 4 hydrogen ion transferred into the periplasmic space, 2 water returned into the cytoplasm and 2 ubiquinone, which stay in the inner membrane. The ubiquinone interacts with succinic acid through a succinate:quinone oxidoreductase resulting in a fumaric acid an ubiquinol. The 2 ubiquinol interact with oxygen and 8 hydrogen ion through a cytochrome bo terminal oxidase resulting in a 8 hydrogen ion transferred into the periplasmic space, 2 water returned into the cytoplasm and 2 ubiquinone, which stays in the inner membrane. The ubiquinone then interacts with 5 hydrogen ion through a NADH dependent ubiquinone oxidoreductase I resulting in NAD, hydrogen ion released into the periplasmic space and an ubiquinol. The ubiquinol is then processed reacting with oxygen, and 4 hydrogen through a ion cytochrome bd-I terminal oxidase resulting in 4 hydrogen ions released into the periplasmic space, 2 water molecules into the cytoplasm and 2 ubiquinones. The ubiquinone then interacts with 5 hydrogen ion through a NADH dependent ubiquinone oxidoreductase I resulting in NAD, hydrogen ion released into the periplasmic space and an ubiquinol. The 2 ubiquinol interact with oxygen and 8 hydrogen ion through a cytochrome bo terminal oxidase resulting in a 8 hydrogen ion transferred into the periplasmic space, 2 water returned into the cytoplasm and 2 ubiquinone, which stays in the inner membrane.

S-adenosyl-L-methionine biosynthesis(SAM) is synthesized in the cytosol of the cell from L-methionine and ATP. This reaction is catalyzed by methionine adenosyltransferase. L methione is taken up from the environment through a complex reaction coupled transport and then proceeds too synthesize the s adenosylmethionine through a adenosylmethionine synthase. S-adenosylmethionine then interacts with a hydrogen ion through an adenosylmethionine decarboxylase resulting in a carbon dioxide and a S-adenosyl 3-methioninamine. This compound interacts with a putrescine through a spermidine synthase resulting in a spermidine, a hydrogen ion and a S-methyl-5'-thioadenosine. The latter compound is degraded by interacting with a water molecule through a 5' methylthioadenosine nucleosidase resulting in an adenine and a S-methylthioribose which is then release into the environment

Beta-D-glucuronosides, D-glucuronate and D-fructuronate can be used as a source of carbon for E.coli. They are imported into E.coli's periplasmic space by membrane-associated protein (UidC/gusC), and are further imported into cytoplasm by hydrogen symporter. Beta-glucuronides undergoes hydrolysis by beta-D-glucuronidase to form D-glucuronate. D-glucuronate is isomerized by D-glucuronate isomerase to form D-fructuronate. D-fructuronate is further reduced to D-mannonate by D-mannonate oxidoreductase. D-mannonate dehydratase dehydrated to yield 2-dehydro-3-deoxy-D-gluconate. At this point, a common enzyme, 2-keto-3-deoxygluconokinase, phosphorylates 2-dehydro-3-deoxy-D-gluconate to yield 2-dehydro-3-deoxy-D-gluconate-6-phosphate. This product is then process by KHG/KDPG aldolase which in turn produces D-Glyceraldehyde 3-phosphate and Pyruvic Acid which then go into their respective sub pathways: glycolysis and pyruvate dehydrogenase. The pathway can also start from 3 other points: a hydrogen ion symporter (gluconate/fructuronate transporter GntP) of D-fructuronate, a hydrogen ion symporter (Hexuronate transporter) of aldehydo-D-galacturonate that spontaneously turns into D-tagaturonate. This compound can also be obtained by the reaction of aldehydo-L-galactonate with a NAD dependent l-galactonate oxidoreductase resulting in the release of NADH, hydrogen ion. Tagaturonate then undergoes an NADH-dependent reduction to D-altronate through an altronate oxidoreductase. D-altronate undergoes dehydration to yield 2-dehydro-3-deoxy-D-gluconate, the third and last point where the reaction can start from a hydrogen symporter of a 2-dehydro-3-deoy-D-gluconate.

The biosynthesis of purine nucleotides is a complex process that begins with a phosphoribosyl pyrophosphate. This compound interacts with water and L-glutamine through a amidophosphoribosyl transferase resulting in a pyrophosphate, L-glutamic acid and a 5-phosphoribosylamine. The latter compound proceeds to interact with a glycine through an ATP driven phosphoribosylamine-glycine ligase resulting in the addition of glycine to the compound. This reaction releases an ADP, a phosphate, a hydrogen ion and a N1-(5-phospho-β-D-ribosyl)glycinamide. The latter compound interacts with formic acid, through an ATP driven phosphoribosylglycinamide formyltransferase 2 resulting in a phosphate, an ADP, a hydrogen ion and a 5-phosphoribosyl-N-formylglycinamide. The latter compound interacts with L-glutamine, and water through an ATP-driven phosphoribosylformylglycinamide synthetase resulting in a release of a phosphate, an ADP, a hydrogen ion, a L-glutamic acid and a 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine. The latter compound interacts with an ATP driven phosphoribosylformylglycinamide cyclo-ligase resulting in a release of ADP, a phosphate, a hydrogen ion and a 5-aminoimidazole ribonucleotide. The latter compound interacts with a hydrogen carbonate through an ATP driven N5-carboxyaminoimidazole ribonucleotide synthetase resulting in a release of a phosphate, an ADP, a hydrogen ion and a N5-carboxyaminoimidazole ribonucleotide.The latter compound then interacts with a N5-carboxyaminoimidazole ribonucleotide mutase resulting in a 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate. This compound interacts with an L-aspartic acid through an ATP driven phosphoribosylaminoimidazole-succinocarboxamide synthase resulting in a phosphate, an ADP, a hydrogen ion and a SAICAR. SAICAR interacts with an adenylosuccinate lyase resulting in a fumaric acid and an AICAR. AICAR interacts with a formyltetrahydrofolate through a AICAR transformylase / IMP cyclohydrolase resulting in a release of a tetrahydropterol mono-l-glutamate and a FAICAR. The latter compound, FAICAR, interacts in a reversible reaction through a AICAR transformylase / IMP cyclohydrolase resulting in a release of water and Inosinic acid. Inosinic acid can be metabolized to produce dGTP and dATP three different methods each. dGTP: Inosinic acid, water and NAD are processed by IMP dehydrogenase resulting in a release of NADH, a hydrogen ion and Xanthylic acid. Xanthylic acid interacts with L-glutamine, and water through an ATP driven GMP synthetase resulting in pyrophosphate, AMP, L-glutamic acid, a hydrogen ion and Guanosine monophosphate. The latter compound is the phosphorylated by reacting with an ATP driven guanylate kinase resulting in a release of ADP and a Gaunosine diphosphate. Guanosine diphosphate can be metabolized in three different ways: 1.-Guanosine diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and a Guanosine triphosphate. This compound interacts with a reduced flavodoxin protein through a ribonucleoside-triphosphate reductase resulting in a oxidized flavodoxin a water moleculer and a dGTP 2.-Guanosine diphosphate interacts with a reduced NrdH glutaredoxin-like proteins through a ribonucleoside-diphosphate reductase 2 resulting in the release of an oxidized NrdH glutaredoxin-like protein, a water molecule and a dGDP. The dGDP is then phosphorylated by interacting with an ATP-driven nucleoside diphosphate kinase resulting in an ADP and dGTP. 3.-Guanosine diphosphate interacts with a reduced thioredoxin ribonucleoside diphosphate reductase 1 resulting in a release of a water molecule, an oxidized thioredoxin and a dGDP. The dGDP is then phosphorylated by interacting with an ATP-driven nucleoside diphosphate kinase resulting in an ADP and dGTP. dATP: Inosinic acid interacts with L-aspartic acid through an GTP driven adenylosuccinate synthase results in the release of GDP, a hydrogen ion, a phosphate and N(6)-(1,2-dicarboxyethyl)AMP. The latter compound is then cleaved by a adenylosuccinate lyase resulting in a fumaric acid and an Adenosine monophosphate. This compound is then phosphorylated by an adenylate kinase resulting in the release of ATP and an adenosine diphosphate. Adenosine diphosphate can be metabolized in three different ways: 1.-Adenosine diphosphate is involved in a reversible reaction by interacting with a hydrogen ion and a phosphate through a ATP synthase / thiamin triphosphate synthase resulting in a hydrogen ion, a water molecule and an Adenosine triphosphate. The adenosine triphosphate interacts with a reduced flavodoxin through a ribonucleoside-triphosphate reductase resulting in an oxidized flavodoxin, a water molecule and a dATP 2.- Adenosine diphosphate interacts with an reduced thioredoxin through a ribonucleoside diphosphate reductase 1 resulting in a release of a water molecule, a oxidized thioredoxin and a dADP. The dADP is then phosphorylated by a nucleoside diphosphate kinase resulting in the release of ADP and a dATP 3.- Adenosine diphosphate interacts with an reduced NrdH glutaredoxin-like protein through a ribonucleoside diphosphate reductase 2 resulting in a release of a water molecule, a oxidized glutaredoxin-like protein and a dADP. The dADP is then phosphorylated by a nucleoside diphosphate kinase resulting in the release of ADP and a dATP

The synthesis of amino sugars and nucleotide sugars starts with the phosphorylation of N-Acetylmuramic acid (MurNac) through its transport from the periplasmic space to the cytoplasm. Once in the cytoplasm, MurNac and water undergo a reversible reaction catalyzed by N-acetylmuramic acid 6-phosphate etherase, producing a D-lactic acid and N-Acetyl-D-Glucosamine 6-phosphate. This latter compound can also be introduced into the cytoplasm through a phosphorylating PTS permase in the inner membrane that allows for the transport of N-Acetyl-D-glucosamine from the periplasmic space. N-Acetyl-D-Glucosamine 6-phosphate can also be obtained from chitin dependent reactions. Chitin is hydrated through a bifunctional chitinase to produce chitobiose. This in turn gets hydrated by a beta-hexosaminidase to produce N-acetyl-D-glucosamine. The latter undergoes an atp dependent phosphorylation leading to the production of N-Acetyl-D-Glucosamine 6-phosphate. N-Acetyl-D-Glucosamine 6-phosphate is then be deacetylated in order to produce Glucosamine 6-phosphate through a N-acetylglucosamine-6-phosphate deacetylase. This compound can either be isomerized or deaminated into Beta-D-fructofuranose 6-phosphate through a glucosamine-fructose-6-phosphate aminotransferase and a glucosamine-6-phosphate deaminase respectively. Glucosamine 6-phosphate undergoes a reversible reaction to glucosamine 1 phosphate through a phosphoglucosamine mutase. This compound is then acetylated through a bifunctional protein glmU to produce a N-Acetyl glucosamine 1-phosphate. N-Acetyl glucosamine 1-phosphate enters the nucleotide sugar synthesis by reacting with UTP and hydrogen ion through a bifunctional protein glmU releasing pyrophosphate and a Uridine diphosphate-N-acetylglucosamine.This compound can either be isomerized into a UDP-N-acetyl-D-mannosamine or undergo a reaction with phosphoenolpyruvic acid through UDP-N-acetylglucosamine 1-carboxyvinyltransferase releasing a phosphate and a UDP-N-Acetyl-alpha-D-glucosamine-enolpyruvate. UDP-N-acetyl-D-mannosamine undergoes a NAD dependent dehydrogenation through a UDP-N-acetyl-D-mannosamine dehydrogenase, releasing NADH, a hydrogen ion and a UDP-N-Acetyl-alpha-D-mannosaminuronate, This compound is then used in the production of enterobacterial common antigens. UDP-N-Acetyl-alpha-D-glucosamine-enolpyruvate is reduced through a NADPH dependent UDP-N-acetylenolpyruvoylglucosamine reductase, releasing a NADP and a UDP-N-acetyl-alpha-D-muramate. This compound is involved in the D-glutamine and D-glutamate metabolism.

The biosynthesis of folic acid begins as a product of purine nucleotides de novo biosynthesis pathway. Purine nucleotides are involved in a reaction with water through a GTP cyclohydrolase 1 protein complex, resulting in a hydrogen ion, formic acid and 7,8-dihydroneopterin 3-triphosphate. The latter compound is dephosphorylated through a dihydroneopterin triphosphate pyrophosphohydrolase resulting in the release of a pyrophosphate, hydrogen ion and 7,8-dihydroneopterin 3-phosphate. The latter product reacts with water spontaneously resulting in the release of a phosphate and a 7,8 -dihydroneopterin. 7,8 -dihydroneopterin reacts with a dihydroneopterin aldolase, releasing a glycoaldehyde and 6-hydroxymethyl-7,9-dihydropterin. Continuing, 6-hydroxymethyl-7,9-dihydropterin is phosphorylated with a ATP-driven 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase resulting in a (2-amino-4-hydroxy-7,8-dihydropteridin-6-yl)methyl diphosphate. Chorismate is metabolized by reacting with L-glutamine through a 4-amino-4-deoxychorismate synthase resulting in L-glutamic acid and 4-amino-4-deoxychorismate. The latter product is then catalyzed via an aminodeoxychorismate lyase resulting in pyruvic acid, hydrogen ion and p-aminobenzoic acid. (2-amino-4-hydroxy-7,8-dihydropteridin-6-yl)methyl diphosphate and p-aminobenzoic acid react with the help of a dihydropteroate synthase resulting in pyrophosphate and 7,8-dihydropteroic acid. This compound then reacts with L-glutamic acid through an ATP driven bifunctional folylpolyglutamate synthease / dihydrofolate synthease resulting in a 7,8-dihydrofolate monoglutamate. 7,8-dihydrofolate monoglutamate is then reduced via a NADPH mediated dihydrofolate reductase resulting in a tetrahydrofate which will continue and become a metabolite of the folate pathway

S-adenosyl-L-methionine biosynthesis(SAM) is synthesized in the cytosol of the cell from L-methionine and ATP. This reaction is catalyzed by methionine adenosyltransferase. L methione is taken up from the environment through a complex reaction coupled transport and then proceeds too synthesize the s adenosylmethionine through a adenosylmethionine synthase. S-adenosylmethionine then interacts with a hydrogen ion through an adenosylmethionine decarboxylase resulting in a carbon dioxide and a S-adenosyl 3-methioninamine. This compound interacts with a putrescine through a spermidine synthase resulting in a spermidine, a hydrogen ion and a S-methyl-5'-thioadenosine. The latter compound is degraded by interacting with a water molecule through a 5' methylthioadenosine nucleosidase resulting in an adenine and a S-methylthioribose which is then release into the environment

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.