Pathway · 1 proteins
Ribose and PRPP supply
Activated ribose supports nucleotide synthesis and salvage.
How it works
- Nucleotide synthesis starts from ribose 5-phosphate, drawn from the pentose-phosphate pool. Ribulose-phosphate 3-epimerase and ribose 5-phosphate isomerase B interconvert the pentose phosphates so that ribose 5-phosphate can be supplied on demand.
- Ribose-phosphate diphosphokinase transfers pyrophosphate from ATP to the C1 hydroxyl, producing PRPP (5-phospho-alpha-D-ribose 1-diphosphate) and releasing AMP.
- PRPP is the shared activated sugar for the de novo purine and pyrimidine routes and for salvage, so this three-enzyme module feeds every nucleotide pathway that follows.
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 |
|---|---|---|---|---|---|
| Ribose 5-phosphate isomerase B | — | — | D-ribulose 5-phosphate | 154 | 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 |
|---|---|---|---|---|---|
| Ribulose-phosphate 3-epimeraseHome: Sugar-phosphate supply | 5.1.3.1 | D-ribulose 5-phosphate = D-xylulose 5-phosphate | — | 222 | Step named |
| Ribose-phosphate pyrophosphokinaseHome: Purine metabolism | 2.7.6.1 | D-ribose 5-phosphate + ATP = 5-phospho-alpha-D-ribose 1-diphosphate + AMP + H(+) | Mg(2+), D-ribose 5-phosphate | 311 | Step named |
Origins
Where would activated ribose (PRPP), the base on which nucleotides are built, have come from?
A ribozyme produced by laboratory selection (Unrau and Bartel, 1998) joins 4-thiouracil to PRPP, at least ten million times faster than the uncatalysed reaction. The PRPP was attached to the ribozyme by the researchers.
The books describe no prebiotic route to PRPP itself. In the cell one enzyme makes it from ribose 5-phosphate and ATP.
Cells do not build the purine first and then attach the sugar. They start from PRPP and build the ring on it, so the sugar has to be activated before any nucleotide can be made.
From the books: Atkins, Gesteland & Cech (eds.), RNA Worlds, p. 33; Zubay, Origins of Life on Earth and in the Cosmos, PDF p. 248.
The wider question for this part of the cell: origins for building carbon into molecules.
Sources
- Atlas pathway grouping from the VF5 reference-genome system map (Deckert et al. 1998; Braakman & Smith 2014)
Other pathways in this group: Reductive TCA machinery · Sugar-phosphate supply · Pyruvate and acetyl-CoA · Lipid A and outer envelope · Glycolysis / Gluconeogenesis · Amino sugar and nucleotide sugar metabolism · Pentose phosphate pathway · Not yet placed in a pathway