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Literature summary for 2.5.1.61 extracted from

  • Bung, N.; Pradhan, M.; Srinivasan, H.; Bulusu, G.
    Structural insights into E. coli porphobilinogen deaminase during synthesis and exit of 1-hydroxymethylbilane (2014), PLoS Comput. Biol., 10, e1003484.
    View publication on PubMedView publication on EuropePMC

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
4 porphobilinogen + H2O Escherichia coli
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hydroxymethylbilane + 4 NH3
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?

Organism

Organism UniProt Comment Textmining
Escherichia coli P06983 gene hemC
-

Reaction

Reaction Comment Organism Reaction ID
4 porphobilinogen + H2O = hydroxymethylbilane + 4 NH3 reaction mechanism with active site residues R11, D84 and R176 that appear to be involved in controlling crucial steps during tetrapyrrole, detailed interaction analysis, overview. The compactness of the overall protein decreases progressively with addition of each pyrrole ring. domains move apart while the cofactor turn region moves towards the second domain, thus creating space for the pyrrole rings added at each stage. Residues of the flexible active site loop play a significant role in its modulation. During this movement, loop residue D50 interacts with R149 and K55 interacts with Q243, E305 and V306 with an occupancy of 41% along the trajectory. Upon removal of hydroxymethylbilane, the structure of the enzyme gradually relaxes to resemble its initial stage structure, indicating its readiness to resume a new catalytic cycle Escherichia coli

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4 porphobilinogen + H2O
-
Escherichia coli hydroxymethylbilane + 4 NH3
-
?

Synonyms

Synonyms Comment Organism
PBGD
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Escherichia coli
porphobilinogen deaminase
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Escherichia coli

Cofactor

Cofactor Comment Organism Structure
dipyrromethane
-
Escherichia coli

General Information

General Information Comment Organism
metabolism porphobilinogen deaminase, an enzyme in the heme biosynthetic pathway, catalyzes the formation of a linear tetrapyrrole product, 1-hydroxymethylbilane, from four units of porphobilinogen Escherichia coli
additional information molecular dynamics simulations for determmination of the exit mechanism of hydroxymethylbilane from the enzyme at the end of the catalytic cycle Escherichia coli
physiological function porphobilinogen deaminase catalyzes the formation of 1-hydroxymethylbilane, a crucial intermediate in tetrapyrrole biosynthesis, through a step-wise polymerization of four molecules of porphobilinogen, using a unique dipyrromethane cofactor Escherichia coli