Xylulose 5-phosphate (PAMDB000653)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 11:54:54 AM
Metabolite IDPAMDB000653
Identification
Name: Xylulose 5-phosphate
Description:Xylulose 5-phosphate (Xu-5-P) is a metabolite of the hexose monophosphate pathway that activates protein phosphatase 2A to mediate the acute effects of carbohydrate feeding on the glycolytic pathway, as well as the coordinate long-term control of the enzymes required for fatty acid and triglyceride synthesis. Xu-5-P is the signal for the coordinated control of lipogenesis. Feeding carbohydrates to cells causes levels of glucose, Glucose-6-phosphate (Glc-6-P), and Fructose-6-phosphate (Fru-6-P) to rise. Elevation of Fru-6-P leads to elevation of Xu-5-P in reactions catalyzed by the near-equilibrium isomerases of the nonoxidative portion of the hexose monophosphate pathway (ribulose 5-phosphate (Ru5P) epimerase [EC 5.1.3.1], ribose 5-phosphate (Rib5P) isomerase [EC 5.3.1.6], transaldolase [EC 2.2.1.2], and transketolase [EC 2.2.1.1]). The elevation of Xu-5-P is the coordinating signal that both acutely activates phosphofructokinase [PFK; EC 2.7.1.11] in glycolysis and will increase transcription of the genes for the enzymes of lipogenesis, the hexose monophosphate shunt, and glycolysis, all of which are required for the de novo synthesis of fat. (PMID 12721358)
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • D-Xylulose 5-phosphate
  • D-Xylulose 5-phosphoric acid
  • D-Xylulose 5-PO4
  • D-Xylulose-5-P
  • D-Xylulose-5-phosphate
  • D-Xylulose-5-phosphoric acid
  • X5P
  • Xu-5-P
  • Xylulose 5-phosphate
  • Xylulose 5-phosphoric acid
  • Xylulose-P
  • Xylulose-phosphate
  • Xylulose-phosphoric acid
Chemical Formula: C5H11O8P
Average Molecular Weight: 230.1098
Monoisotopic Molecular Weight: 230.01915384
InChI Key: FNZLKVNUWIIPSJ-RFZPGFLSSA-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-/m1/s1
CAS number: 4212-65-1
IUPAC Name:{[(2R,3S)-2,3,5-trihydroxy-4-oxopentyl]oxy}phosphonic acid
Traditional IUPAC Name: ribulose-5-phosphate
SMILES:OCC(=O)[C@@H](O)[C@H](O)COP(O)(O)=O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.
Kingdom Organic compounds
Super ClassOrganooxygen compounds
Class Carbohydrates and carbohydrate conjugates
Sub ClassMonosaccharides
Direct Parent Monosaccharide phosphates
Alternative Parents
Substituents
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic phosphate
  • Beta-hydroxy ketone
  • Beta-ketoaldehyde
  • Acyloin
  • Alpha-hydroxy ketone
  • Secondary alcohol
  • Polyol
  • Ketone
  • 1,2-diol
  • Hydrocarbon derivative
  • Primary alcohol
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular Framework Aliphatic acyclic compounds
External Descriptors
Physical Properties
State: Solid
Charge:-2
Melting point: Not Available
Experimental Properties:
PropertyValueSource
LogP:-3.209PhysProp
Predicted Properties
PropertyValueSource
Water Solubility26.1 mg/mLALOGPS
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 Å2ChemAxon
Rotatable Bond Count6ChemAxon
Refractivity42.47 m3·mol-1ChemAxon
Polarizability18.05 Å3ChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Adenosine triphosphate + D-Xylulose <> ADP + Hydrogen ion + Xylulose 5-phosphate
D-Ribose-5-phosphate + Xylulose 5-phosphate <> D-Glyceraldehyde 3-phosphate + D-Sedoheptulose 7-phosphate
L-Ribulose 5-phosphate <> Xylulose 5-phosphate
D-Ribulose 5-phosphate <> Xylulose 5-phosphate
D-Ribulose 5-phosphate <> Xylulose 5-phosphate
Adenosine triphosphate + D-Xylulose <> ADP + Xylulose 5-phosphate
Sedoheptulose 7-phosphate + D-Glyceraldehyde 3-phosphate + D-Sedoheptulose 7-phosphate <> D-Ribose-5-phosphate + Xylulose 5-phosphate
beta-D-Fructose 6-phosphate + D-Glyceraldehyde 3-phosphate <> D-Erythrose 4-phosphate + Xylulose 5-phosphate
D-Erythrose 4-phosphate + Xylulose 5-phosphate <> Fructose 6-phosphate + D-Glyceraldehyde 3-phosphate
D-Ribulose 5-phosphate <> Xylulose 5-phosphate + Xylulose 5-phosphate
Xylulose 5-phosphate + D-Ribose-5-phosphate + Xylulose 5-phosphate <> D-Sedoheptulose 7-phosphate + D-Glyceraldehyde 3-phosphate + D-Sedoheptulose 7-phosphate + D-Glyceraldehyde 3-phosphate
L-Threo-2-pentulose + Adenosine triphosphate + L-Threo-2-pentulose > Xylulose 5-phosphate + Adenosine diphosphate + Xylulose 5-phosphate + ADP
3-keto-L-gulonate 6-phosphate + Hydrogen ion + 3-Keto-L-gulonate 6-phosphate > Xylulose 5-phosphate + Carbon dioxide + Xylulose 5-phosphate
2,3-Diketo-L-gulonate + Hydrogen ion + 2,3-Diketo-L-gulonate > Carbon dioxide + Xylulose 5-phosphate + Xylulose 5-phosphate
Xylulose 5-phosphate + Xylulose 5-phosphate > L-ribulose 5-phosphate + L-ribulose 5-phosphate
More...

Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-MSNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-01q9-3790000000-6f5913e9948fa7667e41View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0btd-9710000000-3724bb9f611bbdc1fe11View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9200000000-8bc9cecb2dddad8ca5e3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-002r-9520000000-c36fdbcc1d3b19b2fafdView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-b67b8ea484aa4ddb40e3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-82b17cf4f5a8c927fe64View in MoNA
References
References:
  • Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
  • Himmo SD, Thomson M, Gubler CJ: Isolation of transketolase from human erythrocytes. Prep Biochem. 1988;18(3):261-76. Pubmed: 3237644
  • 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
  • Nakayama Y, Kinoshita A, Tomita M: Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition. Theor Biol Med Model. 2005 May 9;2(1):18. Pubmed: 15882454
  • Sanchez B, Champomier-Verges MC, Anglade P, Baraige F, de Los Reyes-Gavilan CG, Margolles A, Zagorec M: Proteomic analysis of global changes in protein expression during bile salt exposure of Bifidobacterium longum NCIMB 8809. J Bacteriol. 2005 Aug;187(16):5799-808. Pubmed: 16077128
  • van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
  • Veech, R. L. (2003). "A humble hexose monophosphate pathway metabolite regulates short- and long-term control of lipogenesis." Proc Natl Acad Sci U S A 100:5578-5580. Pubmed: 12721358
  • Williams DG: Effect of added xylulose-5-phosphate on the assay of erythrocyte transketolase. Clin Chem. 1977 Jul;23(7):1368. Pubmed: 872397
  • Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064
Synthesis Reference: Shaeri, Jobin; Wohlgemuth, Roland; Woodley, John M. Semiquantitative Process Screening for the Biocatalytic Synthesis of D-Xylulose-5-phosphate. Organic Process Research & Development (2006), 10(3), 605-610.
Material Safety Data Sheet (MSDS) Not Available
External Links:
ResourceLink
CHEBI ID16332
HMDB IDHMDB00868
Pubchem Compound ID850
Kegg IDC00231
ChemSpider ID388330
WikipediaXylulose 5-phosphate
BioCyc IDXYLULOSE-5-PHOSPHATE
EcoCyc IDXYLULOSE-5-PHOSPHATE
Ligand Expo5SP

Enzymes

Protein Details
• Ribulose-phosphate 3-epimerase
General function:
Involved in catalytic activity
Specific function:
D-ribulose 5-phosphate = D-xylulose 5- phosphate
Gene Name:
rpe
Locus Tag:
PA0607
Molecular weight:
24.1 kDa
Reactions
D-ribulose 5-phosphate = D-xylulose 5-phosphate.
Protein Details
• Transketolase 1
General function:
Involved in catalytic activity
Specific function:
Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate
Gene Name:
tktA
Locus Tag:
PA0548
Molecular weight:
72.2 kDa
Reactions
Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate.