Pathway · 12 proteins
Heme and quinones
Supply redox-active components to respiratory enzymes.
How it works
- Haem branches from uroporphyrinogen III. Uroporphyrinogen-III synthase and a C-methyltransferase build the intermediates, uroporphyrinogen decarboxylase removes four carboxylates, and ferrochelatase inserts iron to give haem.
- VF5 also carries a precorrin-2 dehydrogenase/sirohydrochlorin ferrochelatase family protein, which routes the same branch toward sirohaem rather than haem, so the two products compete for shared intermediates.
- Menaquinone is built through the futalosine route, marked here by aminofutalosine synthase MqnE and cyclic dehypoxanthinyl futalosine synthase, a bacterial variant that does not start from chorismate. Haem and quinones are the redox cofactors of the respiratory chains in system 3.
Grouped by the atlas’s curated pathway map. The table order is not a proven reaction order.
Its proteins
| Protein | EC | Reaction (UniProt) | Metal or cluster | Amino acids | Certainty |
|---|---|---|---|---|---|
| Chorismate dehydratase | 4.2.1.151 | chorismate = 3-[(1-carboxyvinyl)-oxy]benzoate + H2O | — | 236 | Step named |
| precorrin-2 dehydrogenase | 1.3.1.76 | precorrin-2 + NAD(+) = sirohydrochlorin + NADH + 2 H(+) | — | 187 | Step named |
| Uncharacterized protein aq_1612 | — | — | — | 486 | Step named |
| Uroporphyrinogen-III synthase | 4.2.1.75 | hydroxymethylbilane = uroporphyrinogen III + H2O | — | 250 | Step named |
| Coproporphyrinogen III oxidase | 1.3.3.15 | coproporphyrinogen III + 3 O2 = coproporphyrin III + 3 H2O2 | — | 436 | Step named |
| uroporphyrinogen-III C-methyltransferase | 2.1.1.107 | — | — | 244 | Step named |
| Delta-aminolevulinic acid dehydratase | 4.2.1.24 | 2 5-aminolevulinate = porphobilinogen + 2 H2O + H(+) | Zn(2+), Mg(2+) | 330 | Step named |
| Oxygen-independent coproporphyrinogen III oxidase | 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 decarboxylase | 4.1.1.37 | uroporphyrinogen III + 4 H(+) = coproporphyrinogen III + 4 CO2 | — | 338 | Step named |
| Aminodeoxyfutalosine synthase | 2.5.1.120 | 3-[(1-carboxyvinyl)-oxy]benzoate + S-adenosyl-L-methionine + H2O = 6-amino-6-deoxyfutalosine + hydrogencarbonate + L-methionine + H(+) | [4Fe-4S] cluster | 371 | Step named |
| Cyclic dehypoxanthine futalosine synthase | 1.21.98.1 | dehypoxanthine futalosine + S-adenosyl-L-methionine = cyclic dehypoxanthinylfutalosinate + 5'-deoxyadenosine + L-methionine + H(+) | [4Fe-4S] cluster | 361 | Step named |
| Ferrochelatase | 4.98.1.1 | heme b + 2 H(+) = protoporphyrin IX + Fe(2+) | Fe cation | 309 | Step named |
Origins
Could heme and the quinones that carry electrons have been available before these pathways existed?
Porphyrins, the ring systems of heme, have not been convincingly made under simulated prebiotic conditions. A major review of prebiotic chemistry leaves porphyrins, flavins and quinones aside for lack of detailed results.
In bacteria the heme pathway starts from glutamate attached to a transfer RNA, the same activated form used to make proteins. Heme production thus draws on the translation machinery, while translation and energy production in turn need heme-containing proteins.
Twelve proteins of the minimal set serve this pathway.
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
- Atlas pathway grouping from the VF5 reference-genome system map (Deckert et al. 1998; Braakman & Smith 2014)
Other pathways in this group: 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 · Porphyrin metabolism · Pyruvate metabolism · Not yet placed in a pathway