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protoporphyrinogen IX biosynthetic process

Definition

Target type: biologicalprocess

The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX. [GOC:go_curators]

Protoporphyrinogen IX biosynthesis is a crucial metabolic pathway responsible for the synthesis of heme, a vital prosthetic group found in hemoglobin, myoglobin, cytochromes, and other heme proteins. Heme plays a critical role in oxygen transport, electron transport, and cellular respiration. The biosynthesis of protoporphyrinogen IX involves a series of enzymatic reactions that convert the amino acid glycine and succinyl CoA to protoporphyrinogen IX.

The pathway begins with the condensation of glycine and succinyl CoA to form α-amino-β-ketoadipate. This reaction is catalyzed by the enzyme δ-aminolevulinate synthase (ALAS). α-amino-β-ketoadipate is then decarboxylated to δ-aminolevulinate (ALA) by the enzyme α-amino-β-ketoadipate decarboxylase. Two molecules of ALA condense to form porphobilinogen (PBG) in a reaction catalyzed by the enzyme porphobilinogen synthase (hydroxymethylbilane synthase). Four molecules of PBG then assemble into a linear tetrapyrrole known as protoporphyrinogen IX through a series of enzymatic steps.

The biosynthesis of protoporphyrinogen IX is tightly regulated to ensure adequate heme production while preventing the accumulation of toxic intermediates. The first committed step in the pathway, catalyzed by ALAS, is subject to feedback inhibition by heme. This regulation ensures that heme synthesis is only initiated when necessary. In addition, the enzyme ferrochelatase, which catalyzes the final step in heme synthesis, is also regulated by heme levels.

Defects in protoporphyrinogen IX biosynthesis can lead to a variety of human diseases known as porphyrias. These disorders result from the accumulation of porphyrin precursors in erythrocytes, body fluids, and tissues. Symptoms of porphyrias can vary depending on the specific enzyme deficiency and the amount of porphyrin precursors accumulated. Some common symptoms include photosensitivity, abdominal pain, neurological disorders, and skin lesions.

The protoporphyrinogen IX biosynthetic pathway is a complex and tightly regulated process that is essential for life. It is a fascinating example of how metabolic pathways are integrated into cellular function and how defects in these pathways can lead to human disease. '
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Proteins (5)

ProteinDefinitionTaxonomy
Delta-aminolevulinic acid dehydrataseA delta-aminolevulinic acid dehydratase that is encoded in the genome of Escherichia coli K-12. [OMA:P0ACB2, PRO:DNx]Escherichia coli K-12
Protoporphyrinogen oxidaseA protoporphyrinogen oxidase that is encoded in the genome of human. [PRO:DNx, UniProtKB:P50336]Homo sapiens (human)
Oxygen-dependent coproporphyrinogen-III oxidase, mitochondrialAn oxygen-dependent coproporphyrinogen-III oxidase, mitochondrial that is encoded in the genome of human. [PRO:DNx, UniProtKB:P36551]Homo sapiens (human)
Delta-aminolevulinic acid dehydrataseA delta-aminolevulinic acid dehydratase that is encoded in the genome of human. [PRO:DNx, UniProtKB:P13716]Homo sapiens (human)
Porphobilinogen deaminaseA porphobilinogen deaminase that is encoded in the genome of human. [PRO:DNx, UniProtKB:P08397]Homo sapiens (human)

Compounds (11)

CompoundDefinitionClassesRoles
coproporphyrinogen iiicoproporphyrinogenEscherichia coli metabolite;
mouse metabolite
succinic acidsuccinic acid : An alpha,omega-dicarboxylic acid resulting from the formal oxidation of each of the terminal methyl groups of butane to the corresponding carboxy group. It is an intermediate metabolite in the citric acid cycle.

Succinic Acid: A water-soluble, colorless crystal with an acid taste that is used as a chemical intermediate, in medicine, the manufacture of lacquers, and to make perfume esters. It is also used in foods as a sequestrant, buffer, and a neutralizing agent. (Hawley's Condensed Chemical Dictionary, 12th ed, p1099; McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1851)
alpha,omega-dicarboxylic acid;
C4-dicarboxylic acid
anti-ulcer drug;
fundamental metabolite;
micronutrient;
nutraceutical;
radiation protective agent
3-nitropropionic acid3-nitropropanoic acid : A C-nitro compound that is propanoic acid in which one of the methyl hydrogens has been replaced by a nitro group.

3-nitropropionic acid: succinate dehydrogenase inactivator; biosynthesized by FABACEAE plants from ASPARAGINE
C-nitro compoundantimycobacterial drug;
EC 1.3.5.1 [succinate dehydrogenase (quinone)] inhibitor;
mycotoxin;
neurotoxin
aceturic acidaceturic acid: structure

N-acetylglycine : An N-acylglycine where the acyl group is specified as acetyl.
N-acetyl-amino acid;
N-acylglycine
human metabolite
levulinic acid4-oxopentanoic acid : An oxopentanoic acid with the oxo group in the 4-position.

levulinic acid: inhibits 5-aminolevulinic acid dehydratase; RN given refers to parent cpd; structure in Merck Index, 9th ed, #5316
oxopentanoic acid;
straight-chain saturated fatty acid
plant metabolite
2,5-dimethylpyrrole2,5-dimethylpyrrole: structure given in first sourcepyrroles
oxadiazonoxadiazon: manufactured by the Societe Rhone-poulenc, France; structurearomatic ether
acifluorfenaromatic ether;
benzoic acids;
C-nitro compound;
monocarboxylic acid;
organochlorine compound;
organofluorine compound
agrochemical;
EC 1.3.3.4 (protoporphyrinogen oxidase) inhibitor;
herbicide
monomethyl succinatemonomethyl succinate : A dicarboxylic acid monoester that is succinic acid in which one of the carboxy groups has been converted to its methyl ester.

monomethyl succinate: RN given refers to parent cpd
dicarboxylic acid monoester;
hemisuccinate
n-(2,4-dichloro-5-(4-(difluoromethyl)-4,5-dihydro-3-methyl-5-oxo-1h-1,2,4-triazol-1-yl)phenyl)methanesulfonamideN-(2,4-dichloro-5-(4-(difluoromethyl)-4,5-dihydro-3-methyl-5-oxo-1H-1,2,4-triazol-1-yl)phenyl)methanesulfonamide: FP 846 is purified form of sulfentrazone; protoporphyrinogen oxidase inhibitor

sulfentrazone : A member of the class of triazoles that is 5-oxo-1,2,4-triazole which is substituted at positions 1, 3, and 4 by 2,4-dichloro-5-[(methylsulfonyl)amino]phenyl, methyl, and difluoromethyl groups, respectively. A protoporphyrinogen oxidase inhibitor, it is used as a herbicide to control broad-leaved weeds in soya and tobacco crops. Not approved for use within the European Union.
dichlorobenzene;
organofluorine compound;
sulfonamide;
triazoles
agrochemical;
EC 1.3.3.4 (protoporphyrinogen oxidase) inhibitor;
herbicide
5-benzimidazolecarboxylic acid5-benzimidazolecarboxylic acid: structure in first source