Pathway · 8 proteins
Terpenoid backbone biosynthesis
Proteins of this group that KEGG places on its “Terpenoid backbone biosynthesis” map for Aquifex aeolicus.
How it works
This map shows how isoprenoid units are made by the MEP route and joined into longer chains. The proteins here run the MEP route from deoxyxylulose phosphate to the two five-carbon building units, then link them into the farnesyl, octaprenyl and undecaprenyl chains used for quinones and for the carrier that builds the cell wall.
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 |
|---|---|---|---|---|---|
| Isoprenyl transferase | 2.5.1.- | — | Mg(2+) | 231 | Step named |
| 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase | 2.7.7.60 | 2-C-methyl-D-erythritol 4-phosphate + CTP + H(+) = 4-CDP-2-C-methyl-D-erythritol + diphosphate | — | 213 | Step named |
| 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin) | 1.17.7.3 | (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + oxidized [flavodoxin] + H2O + 2 H(+) = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + reduced [flavodoxin] | [4Fe-4S] cluster | 357 | Step named |
| 4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 1.17.7.4 | isopentenyl diphosphate + 2 oxidized [2Fe-2S]-[ferredoxin] + H2O = (2E)-4-hydroxy-3-methylbut-2-enyl diphosphate + 2 reduced [2Fe-2S]-[ferredoxin] + 2 H(+) | [4Fe-4S] cluster | 289 | Step named |
| 1-deoxy-D-xylulose 5-phosphate reductoisomerase | 1.1.1.267 | 2-C-methyl-D-erythritol 4-phosphate + NADP(+) = 1-deoxy-D-xylulose 5-phosphate + NADPH + H(+) | 1-deoxy-D-xylulose 5-phosphate, Mn(2+), Mg(2+) | 380 | Step named |
| Farnesyl diphosphate synthase | 2.5.1.10 | isopentenyl diphosphate + (2E)-geranyl diphosphate = (2E,6E)-farnesyl diphosphate + diphosphate | Mg(2+) | 262 | Step named |
| Octoprenyl-diphosphate synthase | — | — | Mg(2+) | 304 | Step named |
| 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 4.6.1.12 | 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP | — | 156 | 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 |
|---|---|---|---|---|---|
| 4-diphosphocytidyl-2-C-methyl-D-erythritol kinaseHome: Not yet placed in a pathway | 2.7.1.148 | 4-CDP-2-C-methyl-D-erythritol + ATP = 4-CDP-2-C-methyl-D-erythritol 2-phosphate + ADP + H(+) | — | 268 | Step named |
| Flavin prenyltransferase UbiXHome: Riboflavin metabolism | 2.5.1.129 | dimethylallyl phosphate + FMNH2 = prenylated FMNH2 + phosphate | FMN | 189 | Step named |
| 1-deoxy-D-xylulose-5-phosphate synthaseHome: Thiamine metabolism | 2.2.1.7 | D-glyceraldehyde 3-phosphate + pyruvate + H(+) = 1-deoxy-D-xylulose 5-phosphate + CO2 | Mg(2+) | 628 | Step named |
Origins
Could isoprenoids, the building blocks of quinones and membrane carriers, have formed before this pathway existed?
Polyprenyl chains have been proposed as possible parts of early membranes.
Terpenoid derivatives do not seem easy to produce without enzymes, and the review authors note that cells make them by complex pathways. More than 20,000 isoprenoids are known in nature, all built from the same five-carbon units.
Eight proteins of the minimal set serve this pathway.
From the books: Ruiz-Mirazo et al., Prebiotic Systems Chemistry, PDF p. 5; Nelson & Cox, Lehninger Principles of Biochemistry, p. 845.
The wider question for this part of the cell: origins for building and maintaining the membrane.
Sources
- KEGG map aae00900 (enzymes of this organism highlighted)
Other pathways in this group: Glycerolipid assembly · Lipid A and outer envelope · Fatty-acid elongation · Substrate recognition · Fatty acid biosynthesis · Lipopolysaccharide biosynthesis · Biosynthesis of various nucleotide sugars · Not yet placed in a pathway