Browsing Pathways

Most bacteria, including Escherichia coli, are composed of murein which protects and stabilizes the cell wall. Over half of the murein is broken down by Escherichia coli and recycled for the next generation. The main muropeptide is GlcNAc-anhydro-N-acetylmuramic acid (anhMurNAc)-l-Ala-γ-d-Glu-meso-Dap-d-Ala which enters the cytoplasm by AmpG protein. The peptide is then released from the muropeptide. 1,6-Anhydro-N-acetylmuramic acid (anhMurNAc) is recycled by its conversion to N-acetylglucosamine-phosphate (GlcNAc-P). The sugar is phosphorylated by anhydro-N-acetylmuramic acid kinase (AnmK) to produce MurNAc-P. Etherase cleaves MurNAc-P to produce N-acetyl-D-glucosamine 6-phosphate. The product can undergo further degradation or be recycled into peptidoglycan monomers. The pathway's final product is a peptidoglycan biosynthesis precursor, UDP-N-acetyl-α-D-muramate. The enzyme muropeptide ligase (mpl), attaches the recovered Ala-Glu-DAP tripeptide to the precursor UDP-N-acetyl-α-D-muramate to return to the peptide to the peptidoglycan biosynthetic pathway to synthesize the cell wall.

Most bacteria, including Escherichia coli, are composed of murein which protects and stabilizes the cell wall. Over half of the murein is broken down by Escherichia coli and recycled for the next generation. The main muropeptide is GlcNAc-anhydro-N-acetylmuramic acid (anhMurNAc)-l-Ala-γ-d-Glu-meso-Dap-d-Ala which enters the cytoplasm by AmpG protein. The peptide is then released from the muropeptide. 1,6-Anhydro-N-acetylmuramic acid (anhMurNAc) is recycled by its conversion to N-acetylglucosamine-phosphate (GlcNAc-P). The sugar is phosphorylated by anhydro-N-acetylmuramic acid kinase (AnmK) to produce MurNAc-P. Etherase cleaves MurNAc-P to produce N-acetyl-D-glucosamine 6-phosphate. The product can undergo further degradation or be recycled into peptidoglycan monomers. The pathway's final product is a peptidoglycan biosynthesis precursor, UDP-N-acetyl-α-D-muramate. The enzyme muropeptide ligase (mpl), attaches the recovered Ala-Glu-DAP tripeptide to the precursor UDP-N-acetyl-α-D-muramate to return to the peptide to the peptidoglycan biosynthetic pathway to synthesize the cell wall.

Allantoin can be degraded in anaerobic conditions. The first step involves allantoin being degraded by an allantoinase resulting in an allantoate. This compound in turn is metabolized by reacting with water and 2 hydrogen ions through an allantoate amidohydrolase resulting in the release of a carbon dioxide, ammonium and an S-ureidoglycine. The latter compund is further degrades through a S-ureidoglycine aminohydrolase resulting in the release of an ammonium and an S-ureidoglycolate. S-ureidoglycolate can be metabolized into oxalurate by two different reactions. The first reactions involves a NAD driven ureidoglycolate dehydrogenase resulting in the release of a hydrogen ion , an NADH and a oxalurate. On the other hand S-ureidoglycolate can react with NADP resulting in the release of an NADPH, a hydroge ion and an oxalurate. It is hypothesized that oxalurate can interact with a phosphate and release a a carbamoyl phosphate and an oxamate. The carbamoyl phosphate can be further degraded by reacting with an ADP, and a hydrogen ion through a carbamate kinase resulting in the release of an ammonium , ATP and carbon dioxide

The degradation of propanoyl-CoA starts with propanoyl-CoA undergoing a decarboxylase reaction by reacting with hydrogen carbonate and ATP resulting in the release of a phosphate, an ADP, a hydrogen ion and an S-methylmalonyl-CoA. This compound in turn reacts through an epimerase reaction resulting in the release of a R-methylmalonyl-CoA. This compound in turn can undergo a reversible reaction through a methylmalonyl-CoA mutase resulting in the release of a succinyl-CoA. This compound can be converted back to R-methylmalonyl-CoA through a methylmalonyl-CoA mutase. Methylmalonyl-CoA can then be converted into propanoyl-CoA through a methylmalonyl CoA decarboxylase . This compound in turn reacts with a succinate through a propionyl-CoA succinate CoA transferase resulting in the release of a propanoate and a succinyl-CoA.

Fructosamines are compounds that result from glycation reactions between a sugar and a primary amine, followed by isomerization via the Amadori rearrangement. In fructoselysine degradation, fructoselysine firstly converts to 1-[(5-Amino-5-carboxypentyl)amino]-1-deoxyfructose by protein frlC, and then 1-[(5-Amino-5-carboxypentyl)amino]-1-deoxyfructose is transformed to fructoselysine-6-phosphate by fructoselysine kinase which is powered by ATP. Fructoselysine-6-phosphate finally degrades to β-D-Glucose 6-phosphate and L-lysine by fructoselysine 6-phosphate deglycase.

Fructosamines are compounds that result from glycation reactions between a sugar and a primary amine, followed by isomerization via the Amadori rearrangement. In fructoselysine degradation, fructoselysine firstly converts to 1-[(5-Amino-5-carboxypentyl)amino]-1-deoxyfructose by protein frlC, and then 1-[(5-Amino-5-carboxypentyl)amino]-1-deoxyfructose is transformed to fructoselysine-6-phosphate by fructoselysine kinase which is powered by ATP. Fructoselysine-6-phosphate finally degrades to β-D-Glucose 6-phosphate and L-lysine by fructoselysine 6-phosphate deglycase.

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 begins with the introduction of deoxycytidine into the cytosol, either through a nupG symporter or a nupC symporter. Once inside it is deaminated when reacting with a water molecule, a hydrogen ion and a deoxycytidine deaminase resulting in the release of an ammonium and a deoxyuridine. Deoxyuridine can also be imported through a nupG symporter or a nupC symporter. Deoxyuridine can react with an ATP through a deoxyuridine kinase resulting in the release of a ADP , a hydrogen ion and a dUMP. Deoxyuridine can also react with a phosphate through a uracil phosphorylase resulting in the release of a uracil and a deoxy-alpha-D-ribose 1-phosphate. This compound in turn reacts with a thymine through a thymidine phosphorylase resulting in the release of a phosphate and a thymidine. Thymidine in turn reacts with an ATP through a thymidine kinase resulting in a release of an ADP, a hydrogen ion and a dTMP

The pathway begins with the introduction of deoxycytidine into the cytosol, either through a nupG symporter or a nupC symporter. Once inside it is deaminated when reacting with a water molecule, a hydrogen ion and a deoxycytidine deaminase resulting in the release of an ammonium and a deoxyuridine. Deoxyuridine can also be imported through a nupG symporter or a nupC symporter. Deoxyuridine can react with an ATP through a deoxyuridine kinase resulting in the release of a ADP , a hydrogen ion and a dUMP. Deoxyuridine can also react with a phosphate through a uracil phosphorylase resulting in the release of a uracil and a deoxy-alpha-D-ribose 1-phosphate. This compound in turn reacts with a thymine through a thymidine phosphorylase resulting in the release of a phosphate and a thymidine. Thymidine in turn reacts with an ATP through a thymidine kinase resulting in a release of an ADP, a hydrogen ion and a dTMP

This pathway demonstrates the degradation of extracellular putrescine in E.coli. Putrescine is imported by putrescine transporter (encoded by puuP gene). Putrescine is γ-glutamylated by activation of ATP which generates γ-glutamyl-putrescine, phosphate, and ADP. γ-glutamyl-putrescine is oxidized by gamma-glutamylputrescine oxidoreductase to form γ-glutamyl-γ-butyraldehyde, also produce ammonium and water. Gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase dehydrogenates γ-glutamyl-γ-butyraldehyde to γ-glutamyl-γ-aminobutyrate, which is then dehydrogenated into γ-Aminobutyric acid and L-Glutamic acid by γ-glutamyl-γ-aminobutyrate hydrolase.