Pathways

PathWhiz ID Pathway Meta Data

PW127284

Pw127284 View Pathway
disease

UMP Synthase Deficiency (Orotic Aciduria)

Homo sapiens
Orotic aciduria, also known as UMP synthase deficiency, is an autosomal recessive disorder of pyrimidine metabolism caused by a defective uridine monophosphate synthetase (UMPS). UMPS is a multifunctional protein which carries out the functions of both orotate phosphoribosyltransferase (OPRT) and orotidine 5'-phosphate decarboxylase (ODC). UMPS catalyzes the conversion of orotic acid into uridine monophosphate (UMP) which is a nucleotide incorporated into ribonucleic acid (RNA). This disease is characterized by a very large accumulation of orotic acid in the urine, occasionally causing urinary obstruction. Symptoms of the disease include megaloblastic anemia as well as retarded growth and development.

PW002026

Pw002026 View Pathway
metabolic

Uracil Degradation III

Escherichia coli
Uracil is a pyrimidine nucleobase found in RNA, and can be used as a source of nitrogen for E. coli. There are at least three pathways through which uracil is degraded. This one begins with uracil, which originates from purine degradation. The putative monooxygenase enzyme rutA catalyzes the breakdown of uracil into peroxyaminoacrylate, using FMNH2 as a cofactor. Peroxyaminoacrylate is then broken down into both carbamic acid and 3-aminoacrylate following the addition of a water molecule by the putative isochorismatase family protein rutB. Carbamic acid can then spontaneously, with the addition of a hydrogen ion, split into an ammonium ion and a molecule of carbon dioxide. 3-aminoacrylate, on the other hand, is catalyzed by the UPF0076 protein rutC to form 2-aminoacrylic acid. This compound enters into a reaction catalyzed by protein rutD, which adds a water molecule and hydrogen ion and forms malonic semialdehyde with ammonium being a byproduct. Finally, the putative NADH dehydrogenase/NAD(P)H nitroreductase rutE complex converts malonic semialdehyde into hydroxypropionic acid, which is then used to form other necessary chemicals. The ammonium ions produced will be the important source of nitrogen for the bacteria.

PW123529

Pw123529 View Pathway
metabolic

Uracil Degradation III

Pseudomonas aeruginosa
Uracil is a pyrimidine nucleobase found in RNA, and can be used as a source of nitrogen for E. coli. There are at least three pathways through which uracil is degraded. This one begins with uracil, which originates from purine degradation. The putative monooxygenase enzyme rutA catalyzes the breakdown of uracil into peroxyaminoacrylate, using FMNH2 as a cofactor. Peroxyaminoacrylate is then broken down into both carbamic acid and 3-aminoacrylate following the addition of a water molecule by the putative isochorismatase family protein rutB. Carbamic acid can then spontaneously, with the addition of a hydrogen ion, split into an ammonium ion and a molecule of carbon dioxide. 3-aminoacrylate, on the other hand, is catalyzed by the UPF0076 protein rutC to form 2-aminoacrylic acid. This compound enters into a reaction catalyzed by protein rutD, which adds a water molecule and hydrogen ion and forms malonic semialdehyde with ammonium being a byproduct. Finally, the putative NADH dehydrogenase/NAD(P)H nitroreductase rutE complex converts malonic semialdehyde into hydroxypropionic acid, which is then used to form other necessary chemicals. The ammonium ions produced will be the important source of nitrogen for the bacteria.

PW012928

Pw012928 View Pathway
metabolic

Urate Degradation to Glyoxylate

Arabidopsis thaliana
Purine nucleotides are eventually degraded to ammonia and carbon dioxide. This pathway begins in the peroxisome and follows the degradation a urate intermediate to glyoxylate. The last three steps take place in the endoplasmic reticulum. First, uricase converts urate into 5-hydroxyisourate. Steps two and three are catalyzed by the bifunctional enzyme S-allantoin synthase: the conversion of 5-hydroxyisourate into 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate (OHCU) and the conversion of OHCU into S-allantoin. Fourth, allantoinase requires zinc ion as a cofactor to catalyze the conversion of S-allantoin into allantoate. Next allantoate must be transported out of the peroxisome and into the endoplasmic reticulum. Fifth, allantoate amidohydrolase catalyzes the conversion of allantoate into S-ureidoglycine. This enzyme is a homodimer and requires manganese ion as a cofactor. Sixth, ureidoglycine aminohydrolase requires a manganese ion as a cofactor to catalyze the conversion of S-ureidoglycine into S-ureidoglycolate. Seventh, ureidoglycolate amidohydrolase catalyzes the conversion of S-ureidoglycolate into glyoxylate.

PW012915

Pw012915 View Pathway
metabolic

Urate Degradation to Ureidoglycolate

Arabidopsis thaliana
Purine nucleotides are eventually degraded to ammonia and carbon dioxide. This pathway begins in the peroxisome and follows the degradation a urate intermediate to S-ureidoglycolate. The last two steps take place in the endoplasmic reticulum. First, uricase converts urate into 5-hydroxyisourate. Steps two and three are catalyzed by the bifunctional enzyme S-allantoin synthase: the conversion of 5-hydroxyisourate into 5-hydroxy-2-oxo-4-ureido-2,5-dihydro-1H-imidazole-5-carboxylate (OHCU) and the conversion of OHCU into S-allantoin. Fourth, allantoinase requires zinc ion as a cofactor to catalyze the conversion of S-allantoin into allantoate. Next allantoate must be transported out of the peroxisome and into the endoplasmic reticulum. Fifth, allantoate amidohydrolase catalyzes the conversion of allantoate into S-ureidoglycine. This enzyme is a homodimer and requires manganese ion as a cofactor. Sixth, ureidoglycine aminohydrolase requires a manganese ion as a cofactor to catalyze the conversion of S-ureidoglycine into S-ureidoglycolate.

PW088338

Pw088338 View Pathway
metabolic

Urea Cycle

Rattus norvegicus
Urea, also known as carbamide, is a waste product made by a large variety of living organisms and is the main component of urine. Urea is created in the liver, through a string of reactions that are called the Urea Cycle. This cycle is also called the Ornithine Cycle, as well as the Krebs-Henseleit Cycle. There are some essential compounds required for the completion of this cycle, such as arginine, citrulline and ornithine. Arginine cleaves and creates urea and ornithine, and the reactions that follow see urea residue build up on ornithine, which recreates arginine and keeps the cycle going. Ornithine is transported to the mitochondrial matrix, and once there, ornithine carbamoyltransferase uses carbamoyl phosphate to create citrulline. After this, citrulline is transported to the cytosol. Once here, citrulline and aspartate team up to create argininosuccinic acid. After this, argininosuccinate lyase creates l-arginine. L-arginine finally uses arginase-1 to create ornithine again, which will be transported to the mitochondrial matrix and restart the urea cycle once more.

PW000162

Pw000162 View Pathway
metabolic

Urea Cycle

Homo sapiens
Urea, also known as carbamide, is a waste product made by a large variety of living organisms and is the main component of urine. Urea is created in the liver, through a string of reactions that are called the Urea Cycle. This cycle is also called the Ornithine Cycle, as well as the Krebs-Henseleit Cycle. There are some essential compounds required for the completion of this cycle, such as arginine, citrulline and ornithine. Arginine cleaves and creates urea and ornithine, and the reactions that follow see urea residue build up on ornithine, which recreates arginine and keeps the cycle going. Ornithine is transported to the mitochondrial matrix, and once there, ornithine carbamoyltransferase uses carbamoyl phosphate to create citrulline. After this, citrulline is transported to the cytosol. Once here, citrulline and aspartate team up to create argininosuccinic acid. After this, argininosuccinate lyase creates l-arginine. L-arginine finally uses arginase-1 to create ornithine again, which will be transported to the mitochondrial matrix and restart the urea cycle once more.

PW064668

Pw064668 View Pathway
metabolic

Urea Cycle

Mus musculus
Urea, also known as carbamide, is a waste product made by a large variety of living organisms and is the main component of urine. Urea is created in the liver, through a string of reactions that are called the Urea Cycle. This cycle is also called the Ornithine Cycle, as well as the Krebs-Henseleit Cycle. There are some essential compounds required for the completion of this cycle, such as arginine, citrulline and ornithine. Arginine cleaves and creates urea and ornithine, and the reactions that follow see urea residue build up on ornithine, which recreates arginine and keeps the cycle going. Ornithine is transported to the mitochondrial matrix, and once there, ornithine carbamoyltransferase uses carbamoyl phosphate to create citrulline. After this, citrulline is transported to the cytosol. Once here, citrulline and aspartate team up to create argininosuccinic acid. After this, argininosuccinate lyase creates l-arginine. L-arginine finally uses arginase-1 to create ornithine again, which will be transported to the mitochondrial matrix and restart the urea cycle once more.

PW088243

Pw088243 View Pathway
metabolic

Urea Cycle

Bos taurus
Urea, also known as carbamide, is a waste product made by a large variety of living organisms and is the main component of urine. Urea is created in the liver, through a string of reactions that are called the Urea Cycle. This cycle is also called the Ornithine Cycle, as well as the Krebs-Henseleit Cycle. There are some essential compounds required for the completion of this cycle, such as arginine, citrulline and ornithine. Arginine cleaves and creates urea and ornithine, and the reactions that follow see urea residue build up on ornithine, which recreates arginine and keeps the cycle going. Ornithine is transported to the mitochondrial matrix, and once there, ornithine carbamoyltransferase uses carbamoyl phosphate to create citrulline. After this, citrulline is transported to the cytosol. Once here, citrulline and aspartate team up to create argininosuccinic acid. After this, argininosuccinate lyase creates l-arginine. L-arginine finally uses arginase-1 to create ornithine again, which will be transported to the mitochondrial matrix and restart the urea cycle once more.

PW122235

Pw122235 View Pathway
metabolic

Urea Cycle 55555

Candida albicans