Pathway · 6 proteins
Arginine biosynthesis
Proteins of this group that KEGG places on its “Arginine biosynthesis” map for Aquifex aeolicus.
How it works
This map shows how arginine is built from glutamate. The amino group is first protected with an acetyl group so the chain cannot close into a ring. A carbamoyl group is then added to make citrulline, and aspartate supplies the last nitrogen. The proteins here carry out these steps, from acetylating glutamate to splitting argininosuccinate into arginine.
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 |
|---|---|---|---|---|---|
| Argininosuccinate synthase | 6.3.4.5 | L-citrulline + L-aspartate + ATP = 2-(N(omega)-L-arginino)succinate + AMP + diphosphate + H(+) | — | 401 | Step named |
| Argininosuccinate lyase | 4.3.2.1 | 2-(N(omega)-L-arginino)succinate = fumarate + L-arginine | — | 457 | Step named |
| Ornithine carbamoyltransferase | 2.1.3.3 | carbamoyl phosphate + L-ornithine = L-citrulline + phosphate + H(+) | — | 306 | Step named |
| N-acetyl-gamma-glutamyl-phosphate reductase | 1.2.1.38 | N-acetyl-L-glutamate 5-semialdehyde + phosphate + NADP(+) = N-acetyl-L-glutamyl 5-phosphate + NADPH + H(+) | — | 340 | Step named |
| Acetylglutamate kinase | 2.7.2.8 | N-acetyl-L-glutamate + ATP = N-acetyl-L-glutamyl 5-phosphate + ADP | — | 298 | Step named |
| Arginine biosynthesis bifunctional protein ArgJ | 2.3.1.1; 2.3.1.35 | N(2)-acetyl-L-ornithine + L-glutamate = N-acetyl-L-glutamate + L-ornithine | — | 379 | 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 |
| Phosphoribosylformylglycinamidine synthase subunit PurQHome: Purine biosynthesis | 3.5.1.2; 6.3.5.3 | N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide + L-glutamine + ATP + H2O = 2-formamido-N(1)-(5-O-phospho-beta-D-ribosyl)acetamidine + L-glutamate + ADP + phosphate + H(+) | — | 227 | Step named |
| Carbamoyl phosphate synthase large chain, C-terminal sectionHome: Pyrimidine biosynthesis | 6.3.4.16; 6.3.5.5 | hydrogencarbonate + L-glutamine + 2 ATP + H2O = carbamoyl phosphate + L-glutamate + 2 ADP + phosphate + 2 H(+) | Mg(2+), Mn(2+) | 537 | Step named |
| Carbamoyl phosphate synthase large chain, N-terminal sectionHome: Pyrimidine biosynthesis | 6.3.4.16; 6.3.5.5 | hydrogencarbonate + L-glutamine + 2 ATP + H2O = carbamoyl phosphate + L-glutamate + 2 ADP + phosphate + 2 H(+) | Mg(2+), Mn(2+) | 557 | Step named |
| Carbamoyl phosphate synthase small chainHome: Pyrimidine biosynthesis | 6.3.5.5 | hydrogencarbonate + L-glutamine + 2 ATP + H2O = carbamoyl phosphate + L-glutamate + 2 ADP + phosphate + 2 H(+) | — | 371 | 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 |
| 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 |
| N-acetyltransferase domain-containing proteinHome: Not yet placed in a pathway | — | — | — | 181 | Unspecified |
Origins
Could arginine have been available before this six-step pathway existed?
Arginine has not been convincingly made under simulated prebiotic conditions. Cairns-Smith writes that lysine, arginine and histidine lack any plausible prebiotic synthetic pathway.
Weber and Miller exclude ornithine, the step before arginine, as a prebiotic amino acid because it is unstable: it closes into a ring.
The cell avoids that ring closure by putting an acetyl group on the amino group in the first step and removing it later. Without that protecting step the pathway would lose its intermediate to the same reaction that makes proline.
From the books: Garrett & Grisham, Biochemistry, p. 665; Cairns-Smith, Genetic Takeover and the Mineral Origins of Life, p. 22; Ribas de Pouplana (ed.), The Genetic Code and the Origin of Life, p. 202; Nelson & Cox, Lehninger Principles of Biochemistry, p. 861.
The wider question for this part of the cell: origins for making the twenty amino acids.
Sources
- KEGG map aae00220 (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 · Cysteine and methionine metabolism · Histidine metabolism · Lysine biosynthesis · Arginine and proline metabolism · Phenylalanine, tyrosine and tryptophan biosynthesis · Not yet placed in a pathway