Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

MetaCyc Pathway: adenosine nucleotides degradation IV

Enzyme View:

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

Some taxa known to possess this pathway include ? : Archaeoglobus fulgidus , Methanocaldococcus jannaschii , Thermococcus kodakarensis

Expected Taxonomic Range: Archaea

Summary:
General Background

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].

Variants: adenosine nucleotides degradation I , adenosine nucleotides degradation II , adenosine nucleotides degradation III

Credits:
Created 20-Jul-2007 by Caspi R , SRI International


References

Finn04: Finn MW, Tabita FR (2004). "Modified pathway to synthesize ribulose 1,5-bisphosphate in methanogenic archaea." J Bacteriol 186(19);6360-6. PMID: 15375115

MuellerCajar07: Mueller-Cajar O, Badger MR (2007). "New roads lead to Rubisco in archaebacteria." Bioessays 29(8);722-4. PMID: 17621634

Sato07: Sato T, Atomi H, Imanaka T (2007). "Archaeal type III RuBisCOs function in a pathway for AMP metabolism." Science 315(5814);1003-6. PMID: 17303759

Other References Related to Enzymes, Genes, Subpathways, and Substrates of this Pathway

Bowien: Bowien B, editor, Schlegel HG, editor "Autotrophic Bacteria." Science Tech Publishers Madison, WI.

Ezaki99: 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

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."

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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Wed Nov 26, 2014, biocyc14.