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discounted EARLY registration ends Dec 31, 2014
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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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Metabolic Modeling Tutorial
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BioCyc websites down
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MetaCyc Compound: D-ribulose 5-phosphate

Synonyms: ribulose-5P, D-ribulose-5-P, ribulose-5-P

Superclasses: all carbohydrates a carbohydrate a glycan a carbohydrate derivative a sugar phosphate a pentose phosphate a pentose 5-phosphate L(or D)-ribulose 5-phosphate
all carbohydrates a carbohydrate a glycan a carbohydrate derivative a sugar phosphate a sugar 5-phosphate a pentose 5-phosphate L(or D)-ribulose 5-phosphate

Chemical Formula: C5H9O8P

Molecular Weight: 228.1 Daltons

Monoisotopic Molecular Weight: 230.01915383989999 Daltons

SMILES: C(C(C(C(CO)=O)O)O)OP([O-])([O-])=O

InChI: InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/p-2/t4-,5+/m1/s1

InChIKey: InChIKey=FNZLKVNUWIIPSJ-UHNVWZDZSA-L

Unification Links: CAS:4151-19-3 , ChEBI:58121 , ChemSpider:20015724 , HMDB:HMDB00618 , IAF1260:34237 , KEGG:C00199 , MetaboLights:MTBLC58121 , PubChem:21144996

Standard Gibbs Free Energy of Change Formation (ΔfG in kcal/mol): -302.30817 Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

flavin biosynthesis I (bacteria and plants) , flavin biosynthesis II (archaea) , flavin biosynthesis III (fungi) :
D-ribulose 5-phosphate → formate + 1-deoxy-L-glycero-tetrulose 4-phosphate + H+

formaldehyde assimilation II (RuMP Cycle) , formaldehyde oxidation I :
hexulose 6-phosphate ← D-ribulose 5-phosphate + formaldehyde

Not in pathways:
a sugar phosphate + H2O → a sugar + phosphate

Reactions known to produce the compound:

formaldehyde oxidation I :
D-gluconate 6-phosphate + NAD+D-ribulose 5-phosphate + CO2 + NADH

heterolactic fermentation :
D-gluconate 6-phosphate + NAD(P)+D-ribulose 5-phosphate + CO2 + NAD(P)H

pentose phosphate pathway (oxidative branch) I :
D-gluconate 6-phosphate + NADP+D-ribulose 5-phosphate + CO2 + NADPH
D-gluconate 6-phosphate + NAD(P)+D-ribulose 5-phosphate + CO2 + NAD(P)H

pentose phosphate pathway (oxidative branch) II :
D-gluconate 6-phosphate + NADP+D-ribulose 5-phosphate + CO2 + NADPH

Not in pathways:
an N-acetyl-β-D-galactosalaminyl-[glycan] + H2O → a glycan + N-acetyl-β-D-galactosamine

Reactions known to both consume and produce the compound:

Bifidobacterium shunt :
D-ribose 5-phosphate ↔ D-ribulose 5-phosphate
D-ribulose 5-phosphate ↔ D-xylulose 5-phosphate

Calvin-Benson-Bassham cycle :
D-ribose 5-phosphate ↔ D-ribulose 5-phosphate
D-ribulose 5-phosphate + ATP ↔ D-ribulose-1,5-bisphosphate + ADP + H+
D-ribulose 5-phosphate ↔ D-xylulose 5-phosphate

CMP-KDO biosynthesis I :
D-arabinose 5-phosphate ↔ D-ribulose 5-phosphate

D-arabinose degradation II , ribitol degradation :
ATP + D-ribulose ↔ ADP + D-ribulose 5-phosphate + H+

formaldehyde assimilation II (RuMP Cycle) :
D-ribose 5-phosphate ↔ D-ribulose 5-phosphate
D-ribulose 5-phosphate ↔ D-xylulose 5-phosphate

formaldehyde assimilation III (dihydroxyacetone cycle) :
D-ribose 5-phosphate ↔ D-ribulose 5-phosphate
D-ribulose 5-phosphate ↔ D-xylulose 5-phosphate

heterolactic fermentation , pentose phosphate pathway (partial) :
D-ribulose 5-phosphate ↔ D-xylulose 5-phosphate

pentose phosphate pathway (non-oxidative branch) :
D-ribose 5-phosphate ↔ D-ribulose 5-phosphate
D-ribulose 5-phosphate ↔ D-xylulose 5-phosphate

Rubisco shunt :
D-ribose 5-phosphate ↔ D-ribulose 5-phosphate
D-ribulose 5-phosphate + ATP ↔ D-ribulose-1,5-bisphosphate + ADP + H+
D-ribulose 5-phosphate ↔ D-xylulose 5-phosphate

In Reactions of unknown directionality:

Not in pathways:
D-glyceraldehyde 3-phosphate = D-ribulose 5-phosphate
D-arabitol 5-phosphate + NAD+ = D-ribulose 5-phosphate + NADH + H+
D-ribitol 5-phosphate + NAD(P)+ = D-ribulose 5-phosphate + NAD(P)H + H+


ATP + ribulose = ADP + L(or D)-ribulose 5-phosphate + H+

In Transport reactions:
a [PTS enzyme I]-Nπ-phospho-L-histidine + a sugar[out] → a [PTS enzyme I]-L-histidine + a sugar phosphate[in]

Enzymes inhibited by D-ribulose 5-phosphate, sorted by the type of inhibition, are:

Inhibitor (Competitive) of: phosphohexose isomerase [Sangwan90]

Inhibitor (Mechanism unknown) of: 6-phosphogluconate dehydrogenase , glucose-6-phosphate dehydrogenase [Chistoserdova00]


References

Chistoserdova00: Chistoserdova L, Gomelsky L, Vorholt JA, Gomelsky M, Tsygankov YD, Lidstrom ME (2000). "Analysis of two formaldehyde oxidation pathways in Methylobacillus flagellatus KT, a ribulose monophosphate cycle methylotroph." Microbiology 146 ( Pt 1);233-8. PMID: 10658669

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

Sangwan90: Sangwan RS, Singh R (1990). "Characterization of amyloplastic phosphohexose isomerase from immature wheat (Triticum aestivum L.) endosperm." Indian J Biochem Biophys 27(1);23-7. PMID: 2341161


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 Sun Dec 21, 2014, biocyc14.