This view shows enzymes only for those organisms listed below, in the list of taxa known to possess the pathway. If an enzyme name is shown in bold, there is experimental evidence for this enzymatic activity.
Synonyms: AMP recycling, adenosine 5'-monophosphate degradation
|Superclasses:||Degradation/Utilization/Assimilation → Nucleosides and Nucleotides Degradation → Purine Nucleotides Degradation → Adenosine Nucleotides Degradation|
Expected Taxonomic Range: Archaea
The distinction between nucleoside degradation and salvage is not always straight forward. A general rule is that degradation pathways start with the nucleotide forms and convert them to simpler forms, eventually leading to complete mineralization, while salvage pathways start with either the nucleoside or the free base form, and convert those to the nucleotide forms.
Nucleotide recycling is achieved by a combination of both types - a nucleotide is partially degraded via a degradation pathway, but the products are shuttled into a salvage pathway rather then towrds complete mineralization.
About This Pathway
Type III RubisCO enzymes, capable of fixing CO2 into D-ribulose-1,5-bisphosphate, are commonly found in archaebacteria. The importance of carbon fixation in these organisms has been unclear, though, since there seemed to be no obvious way for the organisms to replenish the substrate for these enzymes. The enzyme that generates D-ribulose-1,5-bisphosphate in organisms that contain the Calvin-Benson-Bassham cycle, phosphoribulokinase, is missing from almost all archaebacteria.
A new route for the synthesis of D-ribulose-1,5-bisphosphate has been discovered in some archaebacteria, which involves an isomerization reaction from α-D-ribose 1,5-bisphosphate, catalyzed by ribulose 1,5-bisphosphate isomerase.
In the hyper thermophile Thermococcus kodakarensis it was shown that α-D-ribose 1,5-bisphosphate is produced from AMP by the enzyme AMP phosphorylase [Sato07]. In the methanogen Methanocaldococcus jannaschii, on the other hand, it has been shawn that α-D-ribose 1,5-bisphosphate is produced from 5-phospho-α-D-ribose 1-diphosphate [Finn04].
Thus it seems that archaebacteria possess different pathways for RubisCO-mediated carbon fixation, in which the enzyme's substrate is generated by either salvage of AMP, or by production from 5-phospho-α-D-ribose 1-diphosphate, which can be produced from D-ribose 5-phosphate, an intermediate of the pentose phosphate pathway [MuellerCajar07].
Ezaki99a: Ezaki S, Maeda N, Kishimoto T, Atomi H, Imanaka T (1999). "Presence of a structurally novel type ribulose-bisphosphate carboxylase/oxygenase in the hyperthermophilic archaeon, Pyrococcus kodakaraensis KOD1." J Biol Chem 274(8);5078-82. PMID: 9988755
Fukui05: Fukui T, Atomi H, Kanai T, Matsumi R, Fujiwara S, Imanaka T (2005). "Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes." Genome Res 15(3);352-63. PMID: 15710748
HoveJensen03: Hove-Jensen B, Rosenkrantz TJ, Haldimann A, Wanner BL (2003). "Escherichia coli phnN, encoding ribose 1,5-bisphosphokinase activity (phosphoribosyl diphosphate forming): dual role in phosphonate degradation and NAD biosynthesis pathways." J Bacteriol 185(9);2793-801. PMID: 12700258
Maeda99: Maeda N, Kitano K, Fukui T, Ezaki S, Atomi H, Miki K, Imanaka T (1999). "Ribulose bisphosphate carboxylase/oxygenase from the hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1 is composed solely of large subunits and forms a pentagonal structure." J Mol Biol 293(1);57-66. PMID: 10512715
Tabita74: Tabita FR, McFadden BA (1974). "D-ribulose 1,5-diphosphate carboxylase from Rhodospirillum rubrum. II. Quaternary structure, composition, catalytic, and immunological properties." J Biol Chem 249(11);3459-64. PMID: 4208662
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