Pathway · 3 proteins
Phenylalanine, tyrosine and tryptophan biosynthesis
Proteins of this group that KEGG places on its “Phenylalanine, tyrosine and tryptophan biosynthesis” map for Aquifex aeolicus.
How it works
This map shows the shikimate route that builds the aromatic ring shared by phenylalanine, tyrosine and tryptophan. The proteins on this page make the early ring compounds, including 3-dehydroquinate. The later steps are described on the aromatic amino acids pathway page.
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 |
|---|---|---|---|---|---|
| 3-dehydroquinate dehydratase | 4.2.1.10 | 3-dehydroquinate = 3-dehydroshikimate + H2O | — | 219 | Step named |
| 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase | 2.2.1.10 | 1-deoxy-D-threo-hexo-2,5-diulose 6-phosphate + L-aspartate 4-semialdehyde = 2,3-dioxopropyl phosphate + 2-amino-2,3,7-trideoxy-D-lyxo-hept-6-ulosonate | 1-deoxy-D-threo-hexo-2,5-diulose 6-phosphate | 264 | Step named |
| 3-dehydroquinate synthase homolog | 1.4.1.- | — | — | 331 | 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 |
|---|---|---|---|---|---|
| Chorismate synthaseHome: Aromatic amino acids | 4.2.3.5 | 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate | FMN | 398 | Step named |
| 3-phosphoshikimate 1-carboxyvinyltransferaseHome: Aromatic amino acids | 2.5.1.19 | 3-phosphoshikimate + phosphoenolpyruvate = 5-O-(1-carboxyvinyl)-3-phosphoshikimate + phosphate | — | 431 | Step named |
| Tryptophan synthase alpha chainHome: Aromatic amino acids | 4.2.1.20 | (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + L-tryptophan + H2O | — | 262 | Step named |
| prephenate dehydrogenaseHome: Aromatic amino acids | 1.3.1.12 | prephenate + NAD(+) = 3-(4-hydroxyphenyl)pyruvate + CO2 + NADH | — | 311 | Step named |
| Indole-3-glycerol phosphate synthaseHome: Aromatic amino acids | 4.1.1.48 | 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate + H(+) = (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + CO2 + H2O | — | 257 | Step named |
| Shikimate kinaseHome: Aromatic amino acids | 2.7.1.71 | shikimate + ATP = 3-phosphoshikimate + ADP + H(+) | Mg(2+) | 168 | Step named |
| Anthranilate synthase component IIHome: Aromatic amino acids | — | — | — | 197 | Step named |
| Anthranilate synthase component 1Home: Aromatic amino acids | 4.1.3.27 | chorismate + L-glutamine = anthranilate + pyruvate + L-glutamate + H(+) | Mg(2+) | 494 | Step named |
| Shikimate dehydrogenase (NADP(+))Home: Aromatic amino acids | 1.1.1.25 | shikimate + NADP(+) = 3-dehydroshikimate + NADPH + H(+) | — | 269 | Step named |
| Bifunctional chorismate mutase/prephenate dehydrataseHome: Aromatic amino acids | 4.2.1.51; 5.4.99.5 | chorismate = prephenate | — | 362 | Step named |
| Anthranilate phosphoribosyltransferaseHome: Aromatic amino acids | 2.4.2.18 | N-(5-phospho-beta-D-ribosyl)anthranilate + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + anthranilate | 5-phospho-alpha-D-ribose 1-diphosphate, Mg(2+) | 340 | Step named |
| N-(5'-phosphoribosyl)anthranilate isomeraseHome: Aromatic amino acids | 5.3.1.24 | N-(5-phospho-beta-D-ribosyl)anthranilate = 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate | — | 204 | Step named |
| Tryptophan synthase beta chain 2Home: Glycine, serine and threonine metabolism | 4.2.1.20 | (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + L-tryptophan + H2O | — | 434 | Step named |
| Probable aspartate/prephenate aminotransferaseHome: Cysteine and methionine metabolism | 2.6.1.1; 2.6.1.78 | L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate | — | 394 | Step named |
| Histidinol-phosphate aminotransferaseHome: Not yet placed in a pathway | 2.6.1.9 | L-histidinol phosphate + 2-oxoglutarate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + L-glutamate | — | 354 | Step named |
| Tryptophan synthase beta chain 1Home: Glycine, serine and threonine metabolism | 4.2.1.20 | (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate + L-serine = D-glyceraldehyde 3-phosphate + L-tryptophan + H2O | — | 397 | Step named |
Origins
Could the aromatic amino acids, and tryptophan above all, have been supplied before this pathway existed?
Proposed prebiotic routes to the aromatic amino acids are long, and Cairns-Smith doubts that more than traces have ever been formed from simple starting conditions.
Tryptophan synthase passes indole from one active site to the other through a tunnel whose width matches the indole molecule. It was the first enzyme found with such a tunnel.
Tan and Stadler use tryptophan as an example of coordination: a repressor protein senses free tryptophan and switches off the genes for tryptophan synthase. They argue that separate parts working together toward a shared purpose is a challenge for explanations without a designer.
From the books: Cairns-Smith, Genetic Takeover and the Mineral Origins of Life, p. 22; Horton et al., Principles of Biochemistry, p. 599; Garrett & Grisham, Biochemistry, p. 912; Tan & Stadler, The Stairway to Life, PDF p. 106.
The wider question for this part of the cell: origins for making the twenty amino acids.
Sources
- KEGG map aae00400 (enzymes of this organism highlighted)
Other pathways in this group: Aromatic amino acids · Branched-chain amino acids · Aspartate-family branches · Nitrogen assimilation · RNA maturation · Folate-linked carbon transfer · Arginine biosynthesis · Cysteine and methionine metabolism · Histidine metabolism · Lysine biosynthesis · Arginine and proline metabolism · Not yet placed in a pathway