Pathway · 3 proteins
Porphyrin metabolism
Proteins of this group that KEGG places on its “Porphyrin metabolism” map for Aquifex aeolicus.
How it works
This map shows how the porphyrin rings of heme, siroheme and similar cofactors are made. The proteins here make 5-aminolevulinate from glutamate carried on a transfer RNA, and join four building units into a linear chain that the next enzyme closes into the first ring.
Grouped by KEGG pathway map. The explanation above is the atlas’s own; the map itself covers more organisms than Aquifex.
Its proteins
| Protein | EC | Reaction (UniProt) | Metal or cluster | Amino acids | Certainty |
|---|---|---|---|---|---|
| Glutamyl-tRNA reductase | 1.2.1.70 | (S)-4-amino-5-oxopentanoate + tRNA(Glu) + NADP(+) = L-glutamyl-tRNA(Glu) + NADPH + H(+) | — | 406 | Step named |
| Porphobilinogen deaminase | 2.5.1.61 | 4 porphobilinogen + H2O = hydroxymethylbilane + 4 NH4(+) | — | 304 | Step named |
| Glutamate-1-semialdehyde 2,1-aminomutase | 5.4.3.8 | (S)-4-amino-5-oxopentanoate = 5-aminolevulinate | — | 424 | Step named |
Also part of this pathway
These proteins are described under another pathway, but also take part here.
| Protein | EC | Reaction (UniProt) | Metal or cluster | Amino acids | Certainty |
|---|---|---|---|---|---|
| precorrin-2 dehydrogenaseHome: Heme and quinones | 1.3.1.76 | precorrin-2 + NAD(+) = sirohydrochlorin + NADH + 2 H(+) | — | 187 | Step named |
| Heme O oxygenaseHome: Oxidative phosphorylation | — | — | heme b | 296 | Step named |
| Protoheme IX farnesyltransferaseHome: Oxidative phosphorylation | 2.5.1.141 | heme b + (2E,6E)-farnesyl diphosphate + H2O = Fe(II)-heme o + diphosphate | — | 292 | Step named |
| Uroporphyrinogen-III synthaseHome: Heme and quinones | 4.2.1.75 | hydroxymethylbilane = uroporphyrinogen III + H2O | — | 250 | Step named |
| Coproporphyrinogen III oxidaseHome: Heme and quinones | 1.3.3.15 | coproporphyrinogen III + 3 O2 = coproporphyrin III + 3 H2O2 | — | 436 | Step named |
| uroporphyrinogen-III C-methyltransferaseHome: Heme and quinones | 2.1.1.107 | — | — | 244 | Step named |
| Delta-aminolevulinic acid dehydrataseHome: Heme and quinones | 4.2.1.24 | 2 5-aminolevulinate = porphobilinogen + 2 H2O + H(+) | Zn(2+), Mg(2+) | 330 | Step named |
| Oxygen-independent coproporphyrinogen III oxidaseHome: Heme and quinones | 1.3.98.3 | coproporphyrinogen III + 2 S-adenosyl-L-methionine = protoporphyrinogen IX + 2 5'-deoxyadenosine + 2 L-methionine + 2 CO2 | [4Fe-4S] cluster | 456 | Step named |
| Uroporphyrinogen decarboxylaseHome: Heme and quinones | 4.1.1.37 | uroporphyrinogen III + 4 H(+) = coproporphyrinogen III + 4 CO2 | — | 338 | Step named |
| FerrochelataseHome: Heme and quinones | 4.98.1.1 | heme b + 2 H(+) = protoporphyrin IX + Fe(2+) | Fe cation | 309 | Step named |
| Ferritin/DPS domain-containing proteinHome: Not yet placed in a pathway | — | — | — | 293 | Step named |
| Glutamate--tRNA ligaseHome: Translation interface | 6.1.1.17 | tRNA(Glu) + L-glutamate + ATP = L-glutamyl-tRNA(Glu) + AMP + diphosphate | Zn(2+) | 473 | Step named |
Origins
Could the porphyrin rings of heme and related cofactors have formed before cells?
Porphyrins have not been convincingly made under simulated prebiotic conditions. The common starting materials of prebiotic chemistry are one- to three-carbon molecules such as hydrogen cyanide and formaldehyde, far from a porphyrin ring.
In bacteria the porphyrin pathway begins with glutamate carried on a transfer RNA, so it depends on the same activated amino acids that translation uses.
From the books: Garrett & Grisham, Biochemistry, p. 665; Ruiz-Mirazo et al., Prebiotic Systems Chemistry, PDF p. 5; Zubay, Origins of Life on Earth and in the Cosmos, p. 542.
The wider question for this part of the cell: origins for manufacturing cofactors and vitamins.
Sources
- KEGG map aae00860 (enzymes of this organism highlighted)
Other pathways in this group: Heme and quinones · Biotin and lipoate · NAD and flavins · Thiamine and pyridoxal · Folate and pterin chemistry · Lipid and cofactor connections · Coenzyme A · Aspartate-family branches · Amino-acid connections · Folate-linked carbon transfer · Serine, glycine and sulfur · Folate biosynthesis · Oxidative phosphorylation · Thiamine metabolism · Pantothenate and CoA biosynthesis · Glycine, serine and threonine metabolism · Riboflavin metabolism · Nicotinate and nicotinamide metabolism · Biotin metabolism · Cysteine and methionine metabolism · Pyruvate metabolism · Not yet placed in a pathway