Pathway · 4 proteins
Glycine, serine and threonine metabolism
Proteins of this group that KEGG places on its “Glycine, serine and threonine metabolism” map for Aquifex aeolicus.
How it works
This map links glycine, serine and threonine and the glycine cleavage system. The proteins here include parts of the glycine cleavage system, which uses lipoate and NAD to split glycine and pass a carbon to folate, and the two tryptophan synthase beta chains, which join serine to indole.
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 |
|---|---|---|---|---|---|
| Glycine cleavage system H protein 1 | — | — | — | 143 | Step named |
| Tryptophan synthase beta chain 2 | 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 |
| Tryptophan synthase beta chain 1 | 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 |
| Dihydrolipoyl dehydrogenase | 1.8.1.4 | N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + NAD(+) = N(6)-[(R)-lipoyl]-L-lysyl-[protein] + NADH + H(+) | — | 465 | 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 |
|---|---|---|---|---|---|
| Probable 2,3-bisphosphoglycerate-independent phosphoglycerate mutaseHome: Glycolysis / Gluconeogenesis | 5.4.2.12 | (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate | — | 407 | Step named |
| Probable glycine dehydrogenase (decarboxylating) subunit 1Home: Folate-linked carbon transfer | 1.4.4.2 | N(6)-[(R)-lipoyl]-L-lysyl-[glycine-cleavage complex H protein] + glycine + H(+) = N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[glycine-cleavage complex H protein] + CO2 | — | 439 | Step named |
| AspartokinaseHome: Aspartate-family branches | 2.7.2.4 | L-aspartate + ATP = 4-phospho-L-aspartate + ADP | — | 415 | Step named |
| Homoserine kinaseHome: Aspartate-family branches | 2.7.1.39 | L-homoserine + ATP = O-phospho-L-homoserine + ADP + H(+) | — | 297 | Step named |
| AminomethyltransferaseHome: Folate-linked carbon transfer | 2.1.2.10 | N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[protein] + (6S)-5,6,7,8-tetrahydrofolate = N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NH4(+) | — | 350 | 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 |
| Phosphoglycerate mutaseHome: Not yet placed in a pathway | — | — | — | 220 | Step named |
| Homoserine dehydrogenaseHome: Aspartate-family branches | 1.1.1.3 | L-homoserine + NADP(+) = L-aspartate 4-semialdehyde + NADPH + H(+) | — | 435 | Step named |
| Aspartate-semialdehyde dehydrogenaseHome: Aspartate-family branches | 1.2.1.11 | L-aspartate 4-semialdehyde + phosphate + NADP(+) = 4-phospho-L-aspartate + NADPH + H(+) | — | 340 | Step named |
| Probable glycine dehydrogenase (decarboxylating) subunit 2Home: Folate-linked carbon transfer | 1.4.4.2 | N(6)-[(R)-lipoyl]-L-lysyl-[glycine-cleavage complex H protein] + glycine + H(+) = N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[glycine-cleavage complex H protein] + CO2 | — | 482 | Step named |
| Serine hydroxymethyltransferaseHome: Amino-acid connections | 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 |
| Threonine synthaseHome: Aspartate-family branches | 4.2.3.1 | O-phospho-L-homoserine + H2O = L-threonine + phosphate | — | 409 | Step named |
| D-3-phosphoglycerate dehydrogenaseHome: Not yet placed in a pathway | 1.1.1.95 | (2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + NADH + H(+) | — | 533 | Step named |
Origins
Could glycine, serine and threonine have been available before cells made them?
How it was discovered
- 1953Stanley Miller's spark experiment produces glycine and alanine among its products.Cairns-Smith, Genetic Takeover and the Mineral Origins of Life, PDF p. 21
- 2011Samples Miller had kept from a 1958 run with hydrogen sulfide are analysed and found to contain 23 amino acids.Brooker, Biology, p. 71
Glycine is the most abundant amino acid in spark experiments and in the Murchison meteorite, where about 70 amino acids are dominated by glycine and alanine.
Only about 15 per cent of the carbon in Miller's experiment went into identifiable small molecules; the rest became an unanalysed tar.
Serine and threonine are among the amino acids the cell must make for itself, through four proteins in this group.
From the books: Cairns-Smith, Genetic Takeover and the Mineral Origins of Life, PDF p. 21; Brooker, Biology, p. 71; Deamer, Assembling Life, p. 35.
The wider question for this part of the cell: origins for manufacturing cofactors and vitamins.
Sources
- KEGG map aae00260 (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 · Riboflavin metabolism · Nicotinate and nicotinamide metabolism · Biotin metabolism · Cysteine and methionine metabolism · Porphyrin metabolism · Pyruvate metabolism · Not yet placed in a pathway