Pathway · 6 proteins
Purine metabolism
Proteins of this group that KEGG places on its “Purine metabolism” map for Aquifex aeolicus.
How it works
This map covers the making, conversion and breakdown of purine nucleotides (A and G). The proteins on these pages include steps of purine ring building and PRPP synthesis, enzymes that remove damaged or unusual nucleotides such as dITP and XTP so they are not built into DNA or RNA, and enzymes that handle sulfate activation and polyphosphate.
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 |
|---|---|---|---|---|---|
| Probable bifunctional SAT/APS kinase | 2.7.1.25; 2.7.7.4 | sulfate + ATP + H(+) = adenosine 5'-phosphosulfate + diphosphate | — | 546 | Unspecified |
| Nucleoside-triphosphatase THEP1 | 3.6.1.15 | a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'-diphosphate + phosphate + H(+) | — | 178 | Unspecified |
| TIGR00282 family metallophosphoesterase | — | — | Fe cation | 260 | Unspecified |
| HIT domain-containing protein | — | — | — | 191 | Unspecified |
| Nucleoside triphosphate pyrophosphohydrolase | 3.6.1.8 | ATP + H2O = AMP + diphosphate + H(+) | — | 257 | Unspecified |
| Exopolyphosphatase | — | — | Ca(2+) | 312 | Unspecified |
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 |
|---|---|---|---|---|---|
| Adenylate kinaseHome: Interconversion and salvage | 2.7.4.3 | AMP + ATP = 2 ADP | — | 206 | 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 |
| 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 |
| AmidophosphoribosyltransferaseHome: Purine biosynthesis | 2.4.2.14 | 5-phospho-beta-D-ribosylamine + L-glutamate + diphosphate = 5-phospho-alpha-D-ribose 1-diphosphate + L-glutamine + H2O | [4Fe-4S] cluster, Mg(2+) | 465 | Step named |
| N5-carboxyaminoimidazole ribonucleotide mutaseHome: Purine metabolism | 5.4.99.18 | 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole + H(+) = 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate | — | 167 | Step named |
| Adenylosuccinate synthetaseHome: Purine biosynthesis | 6.3.4.4 | IMP + L-aspartate + GTP = N(6)-(1,2-dicarboxyethyl)-AMP + GDP + phosphate + 2 H(+) | Mg(2+) | 432 | 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 |
| 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 |
| 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 |
| Phosphoribosylformylglycinamidine synthase subunit PurLHome: Purine biosynthesis | 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(+) | Mg(2+) | 745 | Step named |
| Bifunctional purine biosynthesis protein PurHHome: Purine biosynthesis | 2.1.2.3; 3.5.4.10 | (6R)-10-formyltetrahydrofolate + 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide = 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide + (6S)-5,6,7,8-tetrahydrofolate | — | 506 | Step named |
| dITP/XTP pyrophosphataseHome: Purine metabolism | 3.6.1.66 | XTP + H2O = XMP + diphosphate + H(+) | Mg(2+) | 202 | Step named |
| Inosine-5'-monophosphate dehydrogenaseHome: Interconversion and salvage | 1.1.1.205 | IMP + NAD(+) + H2O = XMP + NADH + H(+) | K(+) | 490 | Step named |
| Phosphoribosylaminoimidazole-succinocarboxamide synthaseHome: Purine biosynthesis | 6.3.2.6 | 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate + L-aspartate + ATP = (2S)-2-[5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamido]succinate + ADP + phosphate + 2 H(+) | — | 216 | Step named |
| GMP synthase [glutamine-hydrolyzing]Home: Interconversion and salvage | 6.3.5.2 | XMP + L-glutamine + ATP + H2O = GMP + L-glutamate + AMP + diphosphate + 2 H(+) | — | 510 | Step named |
| N5-carboxyaminoimidazole ribonucleotide synthaseHome: Purine metabolism | 6.3.4.18 | 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + hydrogencarbonate + ATP = 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole + ADP + phosphate + 2 H(+) | — | 365 | Step named |
| Hypoxanthine-guanine phosphoribosyltransferaseHome: Interconversion and salvage | 2.4.2.8 | IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate | Mg(2+) | 178 | Step named |
| Adenylosuccinate lyaseHome: Purine biosynthesis | 4.3.2.2 | N(6)-(1,2-dicarboxyethyl)-AMP = fumarate + AMP | — | 437 | Step named |
| Phosphoribosylamine--glycine ligaseHome: Purine biosynthesis | 6.3.4.13 | 5-phospho-beta-D-ribosylamine + glycine + ATP = N(1)-(5-phospho-beta-D-ribosyl)glycinamide + ADP + phosphate + H(+) | Mg(2+), Mn(2+) | 424 | Step named |
| Phosphoribosylformylglycinamidine cyclo-ligaseHome: Purine biosynthesis | 6.3.3.1 | 2-formamido-N(1)-(5-O-phospho-beta-D-ribosyl)acetamidine + ATP = 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + ADP + phosphate + H(+) | — | 331 | Step named |
| 5'-nucleotidase SurEHome: Purine metabolism | 3.1.3.5 | a ribonucleoside 5'-phosphate + H2O = a ribonucleoside + phosphate | — | 251 | Step named |
| Phosphoribosylglycinamide formyltransferaseHome: Purine biosynthesis | 2.1.2.2 | N(1)-(5-phospho-beta-D-ribosyl)glycinamide + (6R)-10-formyltetrahydrofolate = N(2)-formyl-N(1)-(5-phospho-beta-D-ribosyl)glycinamide + (6S)-5,6,7,8-tetrahydrofolate + H(+) | — | 216 | Step named |
| Peptidoglycan editing factor PgeFHome: Cysteine and methionine metabolism | 3.5.-.- | — | Zn(2+), Cu(2+) | 206 | Step named |
| Guanosine-3',5'-bis(diphosphate) 3'-pyrophosphohydrolaseHome: Nutrient and metabolic state | 3.1.7.2 | guanosine 3',5'-bis(diphosphate) + H2O = GDP + diphosphate + H(+) | Mn(2+) | 696 | Unspecified |
Origins
Could purine nucleotides have lasted long enough before cells to be useful?
Joining nucleotides into chains has been demonstrated experimentally. Deamer argues that decomposition could be balanced by repeated cycles of synthesis, but agrees that further research is needed.
Purine nucleotides decompose: ester bonds hydrolyse and purines fall off the sugar, and in hydrothermal simulations below pH 3 the loss is significant (Mungi and Rajamani 2015). In the cell, five proteins in this group keep purine nucleotides supplied and converted as they are used and lost.
From the books: Deamer, Assembling Life, p. 86.
The wider question for this part of the cell: origins for conserved, but we cannot say what they do.
Sources
- KEGG map aae00230 (enzymes of this organism highlighted)
Other pathways in this group: tRNA charging · Nutrient and metabolic state · Biosynthesis of various nucleotide sugars · Bacterial secretion system · Glyoxylate and dicarboxylate metabolism · Starch and sucrose metabolism · Homologous recombination · Fructose and mannose metabolism · Streptomycin biosynthesis · Other carbon fixation pathways · Nicotinate and nicotinamide metabolism · Not yet placed in a pathway