Pathway · 3 proteins
Lysine biosynthesis
Proteins of this group that KEGG places on its “Lysine biosynthesis” map for Aquifex aeolicus.
How it works
This map shows how lysine is made from aspartate through diaminopimelate. The proteins here condense aspartate semialdehyde with pyruvate, reduce the ring that forms, and later remove a protecting succinyl group on the way to diaminopimelate and lysine.
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 |
|---|---|---|---|---|---|
| 4-hydroxy-tetrahydrodipicolinate synthase | 4.3.3.7 | L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O + H(+) | — | 294 | Step named |
| Succinyl-diaminopimelate desuccinylase | — | — | Zn(2+) | 299 | Step named |
| 4-hydroxy-tetrahydrodipicolinate reductase | 1.17.1.8 | (S)-2,3,4,5-tetrahydrodipicolinate + NAD(+) + H2O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NADH + H(+) | — | 265 | 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 |
|---|---|---|---|---|---|
| AspartokinaseHome: Aspartate-family branches | 2.7.2.4 | L-aspartate + ATP = 4-phospho-L-aspartate + ADP | — | 415 | Step named |
| Homoserine dehydrogenaseHome: Aspartate-family branches | 1.1.1.3 | L-homoserine + NADP(+) = L-aspartate 4-semialdehyde + NADPH + H(+) | — | 435 | Step named |
| Diaminopimelate epimeraseHome: Aspartate-family branches | 5.1.1.7 | (2S,6S)-2,6-diaminopimelate = meso-2,6-diaminopimelate | — | 279 | 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 |
| Acetylornithine aminotransferaseHome: Amino-acid connections | 2.6.1.11 | N(2)-acetyl-L-ornithine + 2-oxoglutarate = N-acetyl-L-glutamate 5-semialdehyde + L-glutamate | — | 376 | Step named |
| Diaminopimelate decarboxylaseHome: Aspartate-family branches | 4.1.1.20 | meso-2,6-diaminopimelate + H(+) = L-lysine + CO2 | — | 420 | Step named |
| LL-diaminopimelate aminotransferaseHome: Aspartate-family branches | 2.6.1.83 | (2S,6S)-2,6-diaminopimelate + 2-oxoglutarate = (S)-2,3,4,5-tetrahydrodipicolinate + L-glutamate + H2O + H(+) | — | 387 | Step named |
| UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligaseHome: Peptidoglycan precursors | 6.3.2.13 | UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-D-glutamate + meso-2,6-diaminopimelate + ATP = UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimelate + ADP + phosphate + H(+) | Mg(2+) | 482 | Step named |
| UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligaseHome: Peptidoglycan precursors | 6.3.2.10 | D-alanyl-D-alanine + UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimelate + ATP = UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-gamma-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine + ADP + phosphate + H(+) | — | 445 | Step named |
Origins
Could lysine have been available before this pathway existed?
Lysine has not been convincingly made under simulated prebiotic conditions, and Cairns-Smith lists it with arginine and histidine as lacking any plausible prebiotic route.
In bacteria lysine is made from aspartate through diaminopimelate. It shares its first steps with methionine, threonine and isoleucine, so its supply has to be coordinated with theirs.
From the books: Garrett & Grisham, Biochemistry, p. 665; Cairns-Smith, Genetic Takeover and the Mineral Origins of Life, p. 22; Zubay, Origins of Life on Earth and in the Cosmos, PDF p. 306.
The wider question for this part of the cell: origins for making the twenty amino acids.
Sources
- KEGG map aae00300 (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 · Arginine and proline metabolism · Phenylalanine, tyrosine and tryptophan biosynthesis · Not yet placed in a pathway