Pathway · 4 proteins
Pyrimidine metabolism
Proteins of this group that KEGG places on its “Pyrimidine metabolism” map for Aquifex aeolicus.
How it works
This map covers the making and conversion of pyrimidine nucleotides (C, U and T). The proteins here add phosphates to the nucleotide building blocks (cytidylate, uridylate and thymidylate kinases) and convert dCTP to dUMP on the way to the thymine nucleotides of DNA.
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 |
|---|---|---|---|---|---|
| dCTP deaminase, dUMP-forming | 3.5.4.30 | dCTP + 2 H2O = dUMP + NH4(+) + diphosphate | — | 180 | Step named |
| Cytidylate kinase | 2.7.4.25 | CMP + ATP = CDP + ADP | — | 222 | Step named |
| Uridylate kinase | 2.7.4.22 | UMP + ATP = UDP + ADP | — | 240 | Step named |
| Thymidylate kinase | 2.7.4.9 | dTMP + ATP = dTDP + ADP | — | 195 | 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 |
|---|---|---|---|---|---|
| Putative dihydroorotate dehydrogenase A (fumarate)Home: Pyrimidine biosynthesis | 1.3.98.1 | (S)-dihydroorotate + fumarate = orotate + succinate | FMN | 306 | Step named |
| Ribonucleoside-diphosphate reductase subunit alphaHome: Deoxyribonucleotide supply | 1.17.4.1 | a 2'-deoxyribonucleoside 5'-diphosphate + [thioredoxin]-disulfide + H2O = a ribonucleoside 5'-diphosphate + [thioredoxin]-dithiol | — | 801 | 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 |
| Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homologHome: Pyrimidine biosynthesis | — | — | [2Fe-2S] cluster | 251 | Step named |
| CTP synthaseHome: Interconversion and salvage | 6.3.4.2 | UTP + L-glutamine + ATP + H2O = CTP + L-glutamate + ADP + phosphate + 2 H(+) | Mg(2+) | 531 | Step named |
| Ribonucleoside-diphosphate reductase subunit betaHome: Deoxyribonucleotide supply | 1.17.4.1 | a 2'-deoxyribonucleoside 5'-diphosphate + [thioredoxin]-disulfide + H2O = a ribonucleoside 5'-diphosphate + [thioredoxin]-dithiol | Fe cation | 696 | Step named |
| Orotidine 5'-phosphate decarboxylaseHome: Pyrimidine biosynthesis | 4.1.1.23 | orotidine 5'-phosphate + H(+) = UMP + CO2 | — | 231 | Step named |
| Nucleoside diphosphate kinaseHome: Interconversion and salvage | 2.7.4.6 | a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP | Mg(2+) | 142 | Step named |
| Orotate phosphoribosyltransferaseHome: Pyrimidine biosynthesis | 2.4.2.10 | orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate | 5-phospho-alpha-D-ribose 1-diphosphate, Mg(2+) | 183 | 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 |
| Uracil phosphoribosyltransferaseHome: Interconversion and salvage | 2.4.2.9 | UMP + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + uracil | 5-phospho-alpha-D-ribose 1-diphosphate, Mg(2+) | 208 | Step named |
| Deoxyuridine 5'-triphosphate nucleotidohydrolaseHome: Deoxyribonucleotide supply | 3.6.1.23 | dUTP + H2O = dUMP + diphosphate + H(+) | Mg(2+) | 150 | Step named |
| Aspartate carbamoyltransferase catalytic subunitHome: Pyrimidine biosynthesis | 2.1.3.2 | carbamoyl phosphate + L-aspartate = N-carbamoyl-L-aspartate + phosphate + H(+) | — | 291 | 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 |
| DihydroorotaseHome: Pyrimidine biosynthesis | 3.5.2.3 | (S)-dihydroorotate + H2O = N-carbamoyl-L-aspartate + H(+) | Zn(2+) | 422 | Step named |
| 5'-nucleotidase SurEHome: Purine metabolism | 3.1.3.5 | a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate | — | 251 | Step named |
| Flavin-dependent thymidylate synthaseHome: Not yet placed in a pathway | 2.1.1.148 | dUMP + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NADPH + H(+) = dTMP + (6S)-5,6,7,8-tetrahydrofolate + NADP(+) | — | 317 | Step named |
| dTTP/UTP pyrophosphataseHome: Not yet placed in a pathway | 3.6.1.9 | dTTP + H2O = dTMP + diphosphate + H(+) | — | 190 | Unspecified |
| TIGR00282 family metallophosphoesteraseHome: Purine metabolism | — | — | Fe cation | 260 | Unspecified |
| Nucleoside triphosphate pyrophosphohydrolaseHome: Purine metabolism | 3.6.1.8 | ATP + H2O = AMP + diphosphate + H(+) | — | 257 | Unspecified |
Origins
Could pyrimidine nucleotides have joined with purines into chains before cells?
In a chamber simulating the wetting and drying of hot-spring pools, Deamer's group mixed AMP with UMP, its pairing partner, and looked for polymers that could form paired regions (DeGuzman et al. 2014).
Pyrimidines decay too: cytosine deaminates to uracil. In these experiments the researchers choose and supply the nucleotides, while Deamer himself notes that a prebiotic setting would never have held a pure nucleotide.
From the books: Deamer, Assembling Life, pp. 86 and 119.
The wider question for this part of the cell: origins for making dna and rna letters.
Sources
- KEGG map aae00240 (enzymes of this organism highlighted)
Other pathways in this group: Purine biosynthesis · Pyrimidine biosynthesis · Interconversion and salvage · Deoxyribonucleotide supply · Aromatic amino acids · Purine metabolism · Histidine metabolism · Not yet placed in a pathway