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Pathways

Showing 1 - 10 of 40471 pathways
SMPDB ID Pathway Chemical Compounds Proteins

SMP02079

Pw002067 View Pathway
metabolic

biotin-carboxyl carrier protein assembly

Escherichia coli
The assembly of a biotin-carboxyl carrier protein starts with a biotin carboxyl carrier protein monomer interacting with an ATP, and a biotin through a biotin -acetyl-coa-carboxylase ligase resulting in the release of a hydrogen ion, an AMP, a diphosphate and a biotynylated BCCP monomer. The latter compound reacts spontaneously to create a biotinylated BCCP dimer. This compound in turn reacts with a hydrogen carbonate and an ATP driven biotin carboxylase resulting in the release of ADP, a hydrogen Ion , a phosphate and a carboxylated biotinylated BCCP dimer. This complex can be degraded by reacting with water, an acetyl0CoA, and an ATP driven acetyl-CoA carboxyltransferase resulting in the release of a hydrogen ion, a phosphate, an ADP, a malonyl-CoA and a biotynylated BCCP dimer

SMP00967

Pw000951 View Pathway
metabolic

colanic acid building blocks biosynthesis

Escherichia coli
The colonic acid building blocks biosynthesis starts with a Beta-D-Glucose undergoing a transport reaction mediated by a glucose PTS permease. The permease phosphorylates the Beta-D-Glucose, producing a Beta-D-Glucose 6-phosphate. This compound can either change to an Alpha-D-Glucose 6-phosphate spontaneously or into a fructose 6-phosphate through a glucose-6-phosphate isomerase. The latter compound can also be present in E.coli through the interaction of D-fructose and a mannose PTS permease which phosphorylate the D-fructose. Fructose 6-phosphate interacts in a reversible reaction with mannose-6-phosphate isomerase in order to produce a Alpha-D-mannose 6-phosphate. This compound can also be present in E.coli through the interaction of Alpha-D-mannose and a mannose PTS permease which phosphorylates the alpha-D-mannose. Alpha-D-mannose 6-phosphate interacts in a reversible reaction with a phosphomannomutase to produce a alpha-D-mannose 1-phosphate. This compound in turn with a hydrogen ion and gtp undergoes a reaction with a mannose-1-phosphate guanylyltransferase, releasing a pyrophosphate and producing a guanosine diphosphate mannose. Guanosine diphosphate mannose interacts with gdp-mannose 4,6-dehydratase releasing a water, and gdp-4-dehydro-6-deoxy-D-mannose. This compound in turn with hydrogen ion and NADPH interact with GDP-L-fucose synthase releasing NADP and producing a GDP-L-fucose. The Alpha-D-Glucose 6-phosphate interacts in a reversible reaction with phosphoglucomutase-1 to produce a alpha-D-glucose 1-phosphate. This in turn with UTP and hydrogen ion interact with UTP--glucose-1-phosphate uridyleltransferase releasing a pyrophosphate and UDP-glucose. UDP-glucose can either interact with galactose-1-phosphate uridylyltransferase to produce a UDP-galactose or in turn with NAD and water interact with UDP-glucose 6-dehydrogenase releasing a NADH and a hydrogen ion and producing a UDP-glucuronate. GDP-L-fucose, UDP-glucose, UDP-galactose and UDP-glucuronate are sugars that need to be activated in the form of nucleotide sugar prior to their assembly into colanic acid, also known as M antigen. Colanic acid is an extracellular polysaccharide which has been linked to a cluster of 19 genes(wca).

SMP00816

Pw000795 View Pathway
metabolic

D-glucarate and D-galactarate degradation

Escherichia coli
Galactarate is a naturally occurring dicarboxylic acid analog of D-galactose. E. coli can use both diacid sugars galactarate and D-glucarate as the sole source of carbon for growth. The initial step in the degradation of galactarate is its dehydration to 5-dehydro-4-deoxy-D-glucarate(2--) by galactarate dehydratase. Glucaric acid can also be dehydrated by a glucarate dehydratase resulting in water and 5-dehydro-4-deoxy-D-glucarate(2--). The 5-dehydro-4-deoxy-D-glucarate(2--) is then metabolized by a alpha-dehydro-beta-deoxy-D-glucarate aldolase resulting in pyruvic acid and a tartonate semialdehyde. Pyruvic acid interacts with coenzyme A through a NAD driven Pyruvate dehydrogenase complex resulting in a carbon dioxide, an NADH and an acetyl-CoA. The tartronate semialdehyde interacts with a hydrogen ion through a NADPH driven tartronate semialdehyde reductase resulting in a NADP and a glyceric acid. The glyceric acid is phosphorylated by an ATP-driven glycerate kinase 2 resulting in an ADP, a hydrogen ion and a 2-phosphoglyceric acid. The latter compound is dehydrated by an enolase resulting in the release of water and a phosphoenolpyruvic acid. The phosphoenolpyruvic acid interacts with a hydrogen ion through an ADP driven pyruvate kinase resulting in an ATP and a pyruvic acid. The pyruvic acid then interacts with water and an ATP through a phosphoenolpyruvate synthetase resulting in the release of a hydrogen ion, a phosphate, an AMP and a Phosphoenolpyruvic acid.

SMP00854

Pw000834 View Pathway
metabolic

hexuronide and hexuronate degradation

Escherichia coli
E. coli can use β-D-glucuronosides, D-glucuronate and D-fructuronate as an only sources of carbon for growth. β-D-glucuronosides are detoxification products that are excreted into the mammalian gut in the bile. They enter E.coli through an outer membrane protein called gusC. Once in the periplasmic space it is transported through a hydrogen symporter into the cytoplasm. Once inside the cytoplasm, the initial step in the degradation of β-glucuronides is hydrolysis by β-D-glucuronidase to yield D-glucuronate. This is then isomerized to D-fructuronate by D-glucuronate isomerase. D-fructuronate then undergoes an NADH-dependent reduction to D-mannonate by D-mannonate oxidoreductase. D-mannonate dehydratase subsequently catalyzes dehydration 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.

SMP00924

Pw000906 View Pathway
metabolic

peptidoglycan biosynthesis I

Escherichia coli
Peptidoglycan is a net-like polymer which surrounds the cytoplasmic membrane of most bacteria and functions to maintain cell shape and prevent rupture due to the internal turgor.In E. coli K-12, the peptidoglycan consists of glycan strands of alternating subunits of N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) which are cross-linked by short peptides. The pathway for constructing this net involves two cell compartments: cytoplasm and periplasmic space. The pathway starts with a beta-D-fructofuranose going through a mannose PTS permease, phosphorylating the compund and producing a beta-D-fructofuranose 6 phosphate. This compound can be obtained from the glycolysis and pyruvate dehydrogenase or from an isomerization reaction of Beta-D-glucose 6-phosphate through a glucose-6-phosphate isomerase.The compound Beta-D-fructofuranose 6 phosphate and L-Glutamine react with a glucosamine fructose-6-phosphate aminotransferase, thus producing a glucosamine 6-phosphate and a l-glutamic acid. The glucosamine 6-phosphate interacts with phosphoglucosamine mutase in a reversible reaction producing glucosamine-1P. Glucosamine-1p and acetyl coa undergo acetylation throuhg a bifunctional protein glmU releasing Coa and a hydrogen ion and producing a N-acetyl-glucosamine 1-phosphate. Glmu, being a bifunctional protein, follows catalyze the interaction of N-acetyl-glucosamine 1-phosphate, hydrogen ion and UTP into UDP-N-acetylglucosamine and pyrophosphate. UDP-N-acetylglucosamine then interacts with phosphoenolpyruvic acid and a UDP-N acetylglucosamine 1- carboxyvinyltransferase realeasing a phosphate and the compound UDP-N-acetyl-alpha-D-glucosamine-enolpyruvate. This compound undergoes a NADPH dependent reduction producing a UDP-N-acetyl-alpha-D-muramate through a UDP-N-acetylenolpyruvoylglucosamine reductase. UDP-N-acetyl-alpha-D-muramate and L-alanine react in an ATP-mediated ligation through a UDP-N-acetylmuramate-alanine ligase releasing an ADP, hydrogen ion, a phosphate and a UDP-N-acetylmuramoyl-L-alanine. This compound interacts with D-glutamic acid and ATP through UDP-N-acetylmuramoylalanine-D-glutamate ligase releasing ADP, A phosphate and UDP-N-acetylmuramoyl-L-alanyl-D-glutamate. The latter compound then interacts with meso-diaminopimelate in an ATP mediated ligation through a UDP-N-acetylmuramoylalanine-D-glutamate-2,6-diaminopimelate ligase resulting in ADP, phosphate, hydrogen ion and UDP-N-Acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate. This compound in turn with D-alanyl-D-alanine react in an ATP-mediated ligation through UDP-N-Acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase to produce UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gama-D-glutamyl-meso-2,6-diaminopimeloyl-Dalanyl-D-alanine and hydrogen ion, ADP, phosphate. UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gama-D-glutamyl-meso-2,6-diaminopimeloyl-Dalanyl-D-alanine interacts with di-trans,octa-cis-undecaprenyl phosphate through a phospho-N-acetylmuramoyl-pentapeptide-transferase, resulting in UMP and Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine which in turn reacts with a UDP-N-acetylglucosamine through a N-acetylglucosaminyl transferase to produce a hydrogen, UDP and ditrans,octacis-undecaprenyldiphospho-N-acetyl-(N-acetylglucosaminyl)muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine. This compound ends the cytoplasmic part of the pathway. ditrans,octacis-undecaprenyldiphospho-N-acetyl-(N-acetylglucosaminyl)muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine is transported through a lipi II flippase. Once in the periplasmic space, the compound reacts with a penicillin binding protein 1A prodducing a peptidoglycan dimer, a hydrogen ion, and UDP. The peptidoglycan dimer then reacts with a penicillin binding protein 1B producing a peptidoglycan with D,D, cross-links and a D-alanine.

SMP02074

Pw002062 View Pathway
metabolic

peptidoglycan biosynthesis I 2

Escherichia coli
Peptidoglycan is a net-like polymer which surrounds the cytoplasmic membrane of most bacteria and functions to maintain cell shape and prevent rupture due to the internal turgor.In E. coli K-12, the peptidoglycan consists of glycan strands of alternating subunits of N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) which are cross-linked by short peptides. The pathway for constructing this net involves two cell compartments: cytoplasm and periplasmic space. The pathway starts with a beta-D-fructofuranose going through a mannose PTS permease, phosphorylating the compund and producing a beta-D-fructofuranose 6 phosphate. This compound can be obtained from the glycolysis and pyruvate dehydrogenase or from an isomerization reaction of Beta-D-glucose 6-phosphate through a glucose-6-phosphate isomerase.The compound Beta-D-fructofuranose 6 phosphate and L-Glutamine react with a glucosamine fructose-6-phosphate aminotransferase, thus producing a glucosamine 6-phosphate and a l-glutamic acid. The glucosamine 6-phosphate interacts with phosphoglucosamine mutase in a reversible reaction producing glucosamine-1P. Glucosamine-1p and acetyl coa undergo acetylation throuhg a bifunctional protein glmU releasing Coa and a hydrogen ion and producing a N-acetyl-glucosamine 1-phosphate. Glmu, being a bifunctional protein, follows catalyze the interaction of N-acetyl-glucosamine 1-phosphate, hydrogen ion and UTP into UDP-N-acetylglucosamine and pyrophosphate. UDP-N-acetylglucosamine then interacts with phosphoenolpyruvic acid and a UDP-N acetylglucosamine 1- carboxyvinyltransferase realeasing a phosphate and the compound UDP-N-acetyl-alpha-D-glucosamine-enolpyruvate. This compound undergoes a NADPH dependent reduction producing a UDP-N-acetyl-alpha-D-muramate through a UDP-N-acetylenolpyruvoylglucosamine reductase. UDP-N-acetyl-alpha-D-muramate and L-alanine react in an ATP-mediated ligation through a UDP-N-acetylmuramate-alanine ligase releasing an ADP, hydrogen ion, a phosphate and a UDP-N-acetylmuramoyl-L-alanine. This compound interacts with D-glutamic acid and ATP through UDP-N-acetylmuramoylalanine-D-glutamate ligase releasing ADP, A phosphate and UDP-N-acetylmuramoyl-L-alanyl-D-glutamate. The latter compound then interacts with meso-diaminopimelate in an ATP mediated ligation through a UDP-N-acetylmuramoylalanine-D-glutamate-2,6-diaminopimelate ligase resulting in ADP, phosphate, hydrogen ion and UDP-N-Acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate. This compound in turn with D-alanyl-D-alanine react in an ATP-mediated ligation through UDP-N-Acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase to produce UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gama-D-glutamyl-meso-2,6-diaminopimeloyl-Dalanyl-D-alanine and hydrogen ion, ADP, phosphate. UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gama-D-glutamyl-meso-2,6-diaminopimeloyl-Dalanyl-D-alanine interacts with di-trans,octa-cis-undecaprenyl phosphate through a phospho-N-acetylmuramoyl-pentapeptide-transferase, resulting in UMP and N-Acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine-diphosphoundecaprenol which in turn reacts with a UDP-N-acetylglucosamine through a N-acetylglucosaminyl transferase to produce a hydrogen, UDP and Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine. This compound ends the cytoplasmic part of the pathway. Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-alanyl-D-glutaminyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine is transported through a lipi II flippase. Once in the periplasmic space, the compound reacts with a penicillin binding protein 1A prodducing a peptidoglycan dimer, a hydrogen ion, and UDP. The peptidoglycan dimer then reacts with a penicillin binding protein 1B producing a peptidoglycan with D,D, cross-links and a D-alanine.

SMP02076

Pw002064 View Pathway
metabolic

1,6-anhydro-<i>N</i>-acetylmuramic acid recycling

Escherichia coli
Anhydromuropeptides (mainly GlcNAc-1,6-anhMurNAc-L-Ala-γ-D-Glu-DAP-D-Ala) are steadily released during growth by lytic transglycosylases and endopeptidases and imported back into the cytoplasm for recycling. During bacterial growth, a very large proportion of the peptidoglycan polymer is degraded and reused in a process termed cell wall recycling. For example, the Gram-negative bacterium Escherichia coli recovers about half of its cell wall within one generation. The anhydromuropeptides are imported by the ampG-encoded muropeptide:H+ symporter. Once inside the cytoplasm, the anhydromuropeptides are hydrolyzed by N-acetylmuramoyl-L-alanine amidase (ampD), β-N-acetylhexosaminidase (nagZ) and L,D-carboxypeptidase A (ldcA), yielding N-acetyl-β-D-glucosamine, 1,6-anhydro-N-acetyl-β-muramate, L-alanyl-γ-D-glutamyl-meso-diaminopimelate and D-alanine. 1,6-anhydro-N-acetyl-β-muramate is phosphorylated by anhydro-N-acetylmuramic acid kinase (anmK) and then converted into N-acetyl-D-glucosamine 6-phosphate by N-acetylmuramic acid 6-phosphate etherase (murQ). This is a branch point, as this compound could be directed either for further degradation or for recycling into new peptidoglycan monomers, as described in this pathway. The final product of this pathway, UDP-N-acetyl-α-D-muramate, is one of the precursors for peptidoglycan biosynthesis. The tripeptide L-alanyl-γ-D-glutamyl-meso-diaminopimelate, which is generated by muramoyltetrapeptide carboxypeptidase, can be degraded further, as described in muropeptide degradation. However, the vast majority is recycled by muropeptide ligase (mpl). This enzyme is a dedicated recycling enzyme that attaches the recovered Ala-Glu-DAP tripeptide to UDP-N-acetyl-α-D-muramate, thereby substituting three amino acid ligases of the peptidoglycan de novobiosynthetic pathway. Although exogenously provided 1,6-anhydro-N-acetyl-β-muramate can be taken up by Escherichia coli, it can not serve as the sole source of carbon for growth, suggesting that it may be toxic to the cell. (EcoCyc)

SMP00774

Pw000751 View Pathway
metabolic

2,3-dihydroxybenzoate biosynthesis

Escherichia coli
2,3-dihydroxybenzoate is synthesized from chorismate via isochorismate and 2,3-dihydroxy-2,3-dihydrobenzoate. Chorismate is a key intermediate and branch point in the biosynthesis of many aromatic compounds. The biosynthesis of 2,3-dihydroxybenzoate from chorismate is catalyzed by three enzymes EntC, EntB, and EntA. EntC catalyzes the conversion of chorismate to isochorismate. The N-terminal isochorismate lyase domain of EntB hydrolyzes the pyruvate group of isochorismate to produce 2,3-dihydro-2,3-dihydroxybenzoate. The conversion of this latter compound to 2,3-dihydroxybenzoate is catalyzed by the EntA dehydrogenase.

SMP02108

Pw002096 View Pathway
metabolic

2-O-alpha-mannosyl-D-glycerate degradation

Escherichia coli
2-O-α-Mannosyl-D-glycerate (MG) is an osmolyte utilized by hyperthermophilic archaea and bacteria. E. coli is able to utilize MG as a carbon source but not as protection against osmotic stress. MG utilization is controlled by the divergently transcribed mngR gene and mngAB operon. MngR acts as a repressor of the expression both mngR and mngAB. MngA is the EII of a PEP-dependent sugar phosphotransferase system responsible for the uptake and phosphorylation of MG to 2-O-(6-phospho-α-mannosyl)-D-glycerate, which is subsequently converted to mannose-6-phosphate and glycerate by the α-mannosidase MngB. Glycerate can be converted to 2-phosphoglycerate by glycerate kinase I encoded by the garK gene which is also induced when cells are grown in MG. (EcoCyc)

SMP02120

Pw002108 View Pathway
metabolic

2-oxoglutarate decarboxylation to succinyl-CoA

Escherichia coli
The pathway illustrated here shows the reactions catalyzed by the 2-oxoglutarate dehydrogenase complex, a key, rate-limiting enzyme of the TCA cycle I (prokaryotic). These reactions can be summarized by the general reaction 2-oxoglutarate + coenzyme A + NAD+ → succinyl-CoA + CO2 + NADH which is the form commonly found in the TCA cycle. During the OGDHC reaction cycle, 2-oxoglutarate is bound and decarboxylated by E1(o), a thiamin-diphosphate cofactor containing enzyme. The succinyl group is transferred to the lipoyl domain of E2(o) where it is carried to the active site and transferred to coenzyme A, forming succinyl-CoA. During this transfer the lipoyl group is reduced to dihydrolipoyl. The succinyl-CoA is released and the lipoyl domain of E2(o) is oxidized by E3 via transfer of protons to NAD, forming NADH and regenerating the lipoyl group back to lipoyllysine for another cycle. Under aerobic growth conditions the OGDHC not only catalyzes a key reaction in the TCA cycle, it also provides succinyl-CoA for methionine and lysine biosynthesis, the latter pathway also leading to peptidoglycan biosynthesis. The synthesis of the OGDHC is repressed by anaerobiosis and is also subject to glucose repression. It is induced by aerobic growth on acetate. (EcoCyc)
Showing 1 - 10 of 40471 pathways