Pathway · 4 proteins
Glyoxylate and dicarboxylate metabolism
Proteins of this group that KEGG places on its “Glyoxylate and dicarboxylate metabolism” map for Aquifex aeolicus.
How it works
This map covers two-carbon compounds such as glycolate and glyoxylate. The proteins here remove phosphoglycolate, a by-product of damaged sugar metabolism, oxidise glycolate and lactate, and activate acetate or propionate with coenzyme A.
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 |
|---|---|---|---|---|---|
| Phosphoglycolate phosphatase | 3.1.3.18 | 2-phosphoglycolate + H2O = glycolate + phosphate | Mg(2+) | 213 | Unspecified |
| Glycolate oxidase iron-sulfur subunit | 1.1.99.14 | (R)-lactate + A = pyruvate + AH2 | [4Fe-4S] cluster | 395 | Unspecified |
| D-lactate dehydrogenase | — | — | — | 482 | Unspecified |
| Propionate--CoA ligase | — | acetate + ATP + CoA = acetyl-CoA + AMP + diphosphate | — | 510 | 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 |
|---|---|---|---|---|---|
| Malate dehydrogenase 1Home: Reductive TCA machinery | 1.1.1.37 | (S)-malate + NAD(+) = oxaloacetate + NADH + H(+) | — | 335 | Step named |
| Aconitate hydratase AHome: Reductive TCA machinery | 4.2.1.3 | citrate = D-threo-isocitrate | [4Fe-4S] cluster | 659 | Step named |
| Probable glycine dehydrogenase (decarboxylating) subunit 1Home: Folate-linked carbon transfer | 1.4.4.2 | N(6)-[(R)-lipoyl]-L-lysyl-[glycine-cleavage complex H protein] + glycine + H(+) = N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[glycine-cleavage complex H protein] + CO2 | — | 439 | Step named |
| Glutamine synthetaseHome: Nitrogen assimilation | 6.3.1.2 | L-glutamate + NH4(+) + ATP = L-glutamine + ADP + phosphate + H(+) | Mg(2+) | 469 | Step named |
| AminomethyltransferaseHome: Folate-linked carbon transfer | 2.1.2.10 | N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[protein] + (6S)-5,6,7,8-tetrahydrofolate = N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NH4(+) | — | 350 | Step named |
| Glycine cleavage system H protein 1Home: Glycine, serine and threonine metabolism | — | — | — | 143 | Step named |
| Formyltetrahydrofolate deformylaseHome: Folate and pterin chemistry | 3.5.1.10 | (6R)-10-formyltetrahydrofolate + H2O = (6S)-5,6,7,8-tetrahydrofolate + formate + H(+) | — | 283 | Step named |
| Probable glycine dehydrogenase (decarboxylating) subunit 2Home: Folate-linked carbon transfer | 1.4.4.2 | N(6)-[(R)-lipoyl]-L-lysyl-[glycine-cleavage complex H protein] + glycine + H(+) = N(6)-[(R)-S(8)-aminomethyldihydrolipoyl]-L-lysyl-[glycine-cleavage complex H protein] + CO2 | — | 482 | Step named |
| Serine hydroxymethyltransferaseHome: Amino-acid connections | 2.1.2.1 | (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine | — | 428 | Step named |
| Dihydrolipoyl dehydrogenaseHome: Glycine, serine and threonine metabolism | 1.8.1.4 | N(6)-[(R)-dihydrolipoyl]-L-lysyl-[protein] + NAD(+) = N(6)-[(R)-lipoyl]-L-lysyl-[protein] + NADH + H(+) | — | 465 | Step named |
Origins
Why would the first cell need enzymes that clear by-products?
None of the books searched discusses these reactions in an origins context.
Some reactions make unwanted side products. When rubisco adds oxygen instead of carbon dioxide, it produces phosphoglycolate, which cells must remove. Clearing such by-products is part of making chemistry work in a cell, and four proteins in this pathway do it.
From the books: Brooker, Biology, p. 178.
The wider question for this part of the cell: origins for conserved, but we cannot say what they do.
Sources
- KEGG map aae00630 (enzymes of this organism highlighted)
Other pathways in this group: tRNA charging · Nutrient and metabolic state · Biosynthesis of various nucleotide sugars · Purine metabolism · Bacterial secretion system · 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