Pathway · 2 proteins
Amino-acid connections
Carbon skeletons enter nitrogen-containing biomass.
How it works
- Glutamine synthetase GlnA and an NADPH-dependent glutamate synthase form the GS-GOGAT pair that assimilates ammonium into glutamate, using 2-oxoglutarate from the cycle as the acceptor.
- Aspartate aminotransferase family proteins and serine hydroxymethyltransferase move amino groups and one-carbon units between the carbon-skeleton pools and the amino-acid branches.
- Glutamate and glutamine are the nitrogen donors for most other transfers, so this short module is the junction between carbon and nitrogen metabolism rather than a pathway of its own.
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 |
|---|---|---|---|---|---|
| Acetylornithine aminotransferase | 2.6.1.11 | N(2)-acetyl-L-ornithine + 2-oxoglutarate = N-acetyl-L-glutamate 5-semialdehyde + L-glutamate | — | 376 | Step named |
| Serine hydroxymethyltransferase | 2.1.2.1 | (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine | — | 428 | 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 |
|---|---|---|---|---|---|
| Glutamine synthetaseHome: Nitrogen assimilation | 6.3.1.2 | L-glutamate + NH4(+) + ATP = L-glutamine + ADP + phosphate + H(+) | Mg(2+) | 469 | Step named |
| Glutamate synthase [NADPH] large chainHome: Nitrogen assimilation | 1.4.1.13 | 2 L-glutamate + NADP(+) = L-glutamine + 2-oxoglutarate + NADPH + H(+) | FMN, [3Fe-4S] cluster | 1493 | Step named |
| Glutamate synthase small subunit gltDHome: Nitrogen assimilation | — | — | — | 476 | Step named |
| tetrahydrofolate synthaseHome: Folate and pterin chemistry | 6.3.2.17 | (6S)-5,6,7,8-tetrahydrofolyl-(gamma-L-Glu)(n) + L-glutamate + ATP = (6S)-5,6,7,8-tetrahydrofolyl-(gamma-L-Glu)(n+1) + ADP + phosphate + H(+) | Mg(2+) | 410 | Step named |
Origins
How were amino groups moved between molecules before transaminases existed?
Glutamate, aspartate, valine, alanine and glycine are found in the Murchison meteorite and also form in early-Earth simulation experiments.
In the cell most amino acids receive their amino group by transamination from glutamate, and glutamate must then be regenerated from ammonia or glutamine. Each of these steps needs its own enzyme and the cofactor pyridoxal phosphate.
From the books: Slonczewski & Foster, Microbiology, p. 595; 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: 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 · 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