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L-Ribulose 5-phosphate (M2MDB001014)

Record Information
Version2.0
Creation Date2012-05-31 14:31:03 -0600
Update Date2015-06-03 17:19:26 -0600
Secondary Accession Numbers
  • ECMDB20167
Identification
Name:L-Ribulose 5-phosphate
DescriptionL-ribulose 5-phosphate is a member of the chemical class known as Pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. In Escherichia coli, RpiA catalyzes the interconversion of ribose-5-phosphate and ribulose-5-phosphate and is a key enzyme in the pentose phosphate pathway. (PMID 12182339) Interconversion of D-ribose-5-phosphate (R5P) and D-ribulose-5-phosphate is an important step in the pentose phosphate pathway. (PMID 18640127) A key player in LPS synthesis is the enzyme D-arabinose-5-phosphate isomerase (API), which catalyzes the reversible isomerization of D-ribulose-5-phosphate to D-arabinose-5-phosphate, a precursor of 3-deoxy-D-manno-octulosonate that is an essential residue of the LPS inner core. (PMID 20954237) Dihydroxybutanone phosphate synthase (DS) catalyzes a commitment step in riboflavin biosynthesis where ribulose 5-phosphate is converted to dihydroxybutanone phosphate and formate. (PMID 11053863) Ribose-5-phosphate isomerase A (RpiA) plays an important role in interconverting between ribose-5-phosphate (R5P) and ribulose-5-phosphate in the pentose phosphate pathway and the Calvin cycle. (PMID 19214439)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 5-O-Phosphono-L-erythro-pent-2-ulose
  • 5-O-Phosphono-L-ribulose
  • L-Erythro-pent-2-ulose 5-(dihydrogen phosphate)
  • L-erythro-Pent-2-ulose 5-(dihydrogen phosphoric acid)
  • L-Ribulose 5-(dihydrogen phosphate)
  • L-Ribulose 5-(dihydrogen phosphoric acid)
  • L-Ribulose 5-phosphoric acid
  • L-Ribulose-5-P
  • Ribulose 5-phosphate
  • Ribulose 5-phosphoric acid
  • Ribulose-5-P
  • Ribulose-5-phosphate
  • Ribulose-5-phosphoric acid
Chemical Formula:C5H11O8P
Weight:Average: 230.1098
Monoisotopic: 230.01915384
InChI Key:FNZLKVNUWIIPSJ-CRCLSJGQSA-N
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)/t4-,5+/m0/s1
CAS number:2922-69-2
IUPAC Name:{[(2S,3S)-2,3,5-trihydroxy-4-oxopentyl]oxy}phosphonic acid
Traditional IUPAC Name:L-ribulose 5-phosphate
SMILES:[H][C@](O)(COP(O)(O)=O)[C@]([H])(O)C(=O)CO
Chemical Taxonomy
Description belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentose phosphates
Alternative Parents
Substituents
  • Pentose phosphate
  • Pentose-5-phosphate
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Acyloin
  • Beta-hydroxy ketone
  • Organic phosphoric acid derivative
  • Alkyl phosphate
  • Phosphoric acid ester
  • Alpha-hydroxy ketone
  • Ketone
  • Secondary alcohol
  • Polyol
  • Hydrocarbon derivative
  • Organic oxide
  • Carbonyl group
  • Alcohol
  • Primary alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:-2
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility26.1 g/LALOGPS
logP-1.8ALOGPS
logP-2.8ChemAxon
logS-0.95ALOGPS
pKa (Strongest Acidic)1.48ChemAxon
pKa (Strongest Basic)-3.3ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count7ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area144.52 ŲChemAxon
Rotatable Bond Count6ChemAxon
Refractivity42.47 m³·mol⁻¹ChemAxon
Polarizability18.05 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
L-Ribulose 5-phosphate <> Xylulose 5-phosphate
Adenosine triphosphate + L-Ribulose > ADP + Hydrogen ion + L-Ribulose 5-phosphate
L-Xylulose 5-phosphate <> L-Ribulose 5-phosphate
Adenosine triphosphate + L-Ribulose <> ADP + L-Ribulose 5-phosphate
L-Ribulose 5-phosphate <> L-Xylulose 5-phosphate
L-Ribulose 5-phosphate < L-Xylulose 5-phosphate
L-Ribulose 5-phosphate > Xylulose 5-phosphate
L-Ribulose 5-phosphate > L-Xylulose 5-phosphate
Adenosine triphosphate + L-Ribulose + D-Ribulose <> ADP + L-Ribulose 5-phosphate + D-Ribulose 5-phosphate
SMPDB Pathways:Not Available
KEGG Pathways:
  • Ascorbate and aldarate metabolism ec00053
  • Metabolic pathways eco01100
  • Microbial metabolism in diverse environments ec01120
  • Pentose and glucuronate interconversions ec00040
EcoCyc Pathways:
Concentrations
ConcentrationStrainMediaGrowth StatusGrowth SystemTemperatureDetails
2± 0 uMW31104.0 g/L Na2SO4; 5.36 g/L (NH4)2SO4; 1.0 g/L NH4Cl; 7.3 g/L K2HPO4; 1.8 g/L NaH2PO4 H2O; 12.0 g/L (NH4)2-H-citrate; 4.0 mL/L MgSO4 (1 M); 6.0 mL/L trace element solution; 0.02 g/L thiamine, 20 g/L glucoseMid Log PhaseBioreactor, pH controlled, aerated, dilution rate=0.125 L/h37 oCPark, C., Park, C., Lee, Y., Lee, S.Y., Oh, H.B., Lee, J. (2011) Determination of the Intracellular Concentration of Metabolites in Escherichia coli Collected during the Exponential and Stationary Growth Phases using Liquid Chromatography-Mass Spectrometry. Bull Korean Chem. Soc. 32: 524-530.
2± 0 uMW31104.0 g/L Na2SO4; 5.36 g/L (NH4)2SO4; 1.0 g/L NH4Cl; 7.3 g/L K2HPO4; 1.8 g/L NaH2PO4 H2O; 12.0 g/L (NH4)2-H-citrate; 4.0 mL/L MgSO4 (1 M); 6.0 mL/L trace element solution; 0.02 g/L thiamine, 20 g/L glucoseStationary PhaseBioreactor, pH controlled, aerated37 oCPark, C., Park, C., Lee, Y., Lee, S.Y., Oh, H.B., Lee, J. (2011) Determination of the Intracellular Concentration of Metabolites in Escherichia coli Collected during the Exponential and Stationary Growth Phases using Liquid Chromatography-Mass Spectrometry. Bull Korean Chem. Soc. 32: 524-530.
Find out more about how we convert literature concentrations.
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-01q9-3790000000-2c11b3331f617fcac827View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0btd-9710000000-28813a9eaf50967c87e7View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9200000000-5ba5e3b7a9495a17a555View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-002r-9520000000-88185c13004c51d8fbb9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-4b58e89007a1a7f893ddView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-8cddc9cbb874799a0cedView in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • Gourlay, L. J., Sommaruga, S., Nardini, M., Sperandeo, P., Deho, G., Polissi, A., Bolognesi, M. (2010). "Probing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate isomerase via X-ray crystallography." Protein Sci 19:2430-2439. Pubmed: 20954237
  • Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114. Pubmed: 22080510
  • Keseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590. Pubmed: 21097882
  • Kim, T. G., Kwon, T. H., Min, K., Dong, M. S., Park, Y. I., Ban, C. (2009). "Crystal structures of substrate and inhibitor complexes of ribose 5-phosphate isomerase A from Vibrio vulnificus YJ016." Mol Cells 27:99-103. Pubmed: 19214439
  • Liao, D. I., Viitanen, P. V., Jordan, D. B. (2000). "Cloning, expression, purification and crystallization of dihydroxybutanone phosphate synthase from Magnaporthe grisea." Acta Crystallogr D Biol Crystallogr 56:1495-1497. Pubmed: 11053863
  • Lohrke, S. M., Dery, P. D., Li, W., Reedy, R., Kobayashi, D. Y., Roberts, D. R. (2002). "Mutation of rpiA in Enterobacter cloacae decreases seed and root colonization and biocontrol of damping-off caused by Pythium ultimum on cucumber." Mol Plant Microbe Interact 15:817-825. Pubmed: 12182339
  • Park, C., Park, C., Lee, Y., Lee, S.Y., Oh, H.B., Lee, J. (2011) Determination of the Intracellular Concentration of Metabolites in Escherichia coli Collected during the Exponential and Stationary Growth Phases using Liquid Chromatography-Mass Spectrometry. Bull Korean Chem. Soc. 32: 524-530.
  • Roos, A. K., Mariano, S., Kowalinski, E., Salmon, L., Mowbray, S. L. (2008). "D-ribose-5-phosphate isomerase B from Escherichia coli is also a functional D-allose-6-phosphate isomerase, while the Mycobacterium tuberculosis enzyme is not." J Mol Biol 382:667-679. Pubmed: 18640127
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID17666
HMDB IDNot Available
Pubchem Compound ID439399
Kegg IDC01101
ChemSpider ID388516
Wikipedia IDNot Available
BioCyc IDL-RIBULOSE-5-P
EcoCyc IDL-RIBULOSE-5-P
Ligand ExpoHMS

Enzymes

Protein Details
1. L-ribulose-5-phosphate 4-epimerase
General function:
Involved in metal ion binding
Specific function:
L-ribulose 5-phosphate = D-xylulose 5- phosphate
Gene Name:
araD
Uniprot ID:
P08203
Molecular weight:
25519
Reactions
L-ribulose 5-phosphate = D-xylulose 5-phosphate.
Protein Details
2. Ribulokinase
General function:
Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:
ATP + L(or D)-ribulose = ADP + L(or D)- ribulose 5-phosphate
Gene Name:
araB
Uniprot ID:
P08204
Molecular weight:
61089
Reactions
ATP + L(or D)-ribulose = ADP + L(or D)-ribulose 5-phosphate.
Protein Details
3. L-ribulose-5-phosphate 4-epimerase sgbE
General function:
Involved in metal ion binding
Specific function:
Catalyzes the isomerization of L-ribulose 5-phosphate to D-xylulose 5-phosphate. May be involved in the utilization of 2,3- diketo-L-gulonate
Gene Name:
sgbE
Uniprot ID:
P37680
Molecular weight:
25561
Reactions
L-ribulose 5-phosphate = D-xylulose 5-phosphate.
Protein Details
4. L-ribulose-5-phosphate 3-epimerase ulaE
General function:
Involved in intramolecular oxidoreductase activity, interconverting aldoses and ketoses
Specific function:
Catalyzes the isomerization of L-xylulose-5-phosphate to L-ribulose-5-phosphate. Is involved in the anaerobic L-ascorbate utilization
Gene Name:
ulaE
Uniprot ID:
P39305
Molecular weight:
32006
Reactions
L-ribulose 5-phosphate = L-xylulose 5-phosphate.
Protein Details
5. L-ribulose-5-phosphate 4-epimerase ulaF
General function:
Involved in metal ion binding
Specific function:
Catalyzes the isomerization of L-ribulose 5-phosphate to D-xylulose 5-phosphate. Is involved in the anaerobic L-ascorbate utilization
Gene Name:
ulaF
Uniprot ID:
P39306
Molecular weight:
25278
Reactions
L-ribulose 5-phosphate = D-xylulose 5-phosphate.
Protein Details
6. predicted L-xylulose 5-phosphate 3-epimerase
General function:
Not Available
Specific function:
Not Available
Gene Name:
yiaR
Uniprot ID:
P37679
Molecular weight:
Not Available