You are using an unsupported browser. Please upgrade your browser to a newer version to get the best experience on Yeast Metabolome Database.

Xylulose 5-phosphate (YMDB00362)

Identification
YMDB IDYMDB00362
NameXylulose 5-phosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionXylulose 5-phosphate 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. Xylulose 5-phosphate exists in all living species, ranging from bacteria to plants to humans. In yeast, xylulose 5-phosphate is involved in the metabolic pathway called the xylitol degradation pathway. Based on a literature review a significant number of articles have been published on Xylulose 5-phosphate.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • D-xylulose 5-phosphate
  • D-xylulose 5-PO4
  • D-xylulose-5-P
  • D-xylulose-5-phosphate
  • Xu-5-P
  • Xylulose 5-phosphate
  • Xylulose 5-phosphic acid
  • xylulose-P
  • Xylulose-phosphate
  • 5-O-Phosphono-D-threo-pentos-2-ulose
  • 5-O-Phosphono-D-xylulose
  • D-Xylulose-5-phosphoric acid
  • Xylulose 5-phosphoric acid
  • Xylulose-5-phosphate
  • Xylulose-5-phosphate, (D)-isomer
  • keto-D-Xylulose 5-phosphate
CAS number4212-65-1
WeightAverage: 230.1098
Monoisotopic: 230.01915384
InChI KeyFNZLKVNUWIIPSJ-RFZPGFLSSA-N
InChIInChI=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
IUPAC Name{[(2R,3S)-2,3,5-trihydroxy-4-oxopentyl]oxy}phosphonic acid
Traditional IUPAC Nameribulose-5-phosphate
Chemical FormulaC5H11O8P
SMILES[H]OC([H])([H])C(=O)[C@@]([H])(O[H])[C@]([H])(O[H])C([H])([H])OP(=O)(O[H])O[H]
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
StateSolid
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
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
Organoleptic PropertiesNot Available
SMPDB Pathways
RiboneogenesisPW002511 ThumbThumb?image type=greyscaleThumb?image type=simple
xylitol degradationPW002433 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Methane metabolismec00680 Map00680
Pentose and glucuronate interconversionsec00040 Map00040
Pentose phosphate pathwayec00030 Map00030
SMPDB Reactions
D-Xylulose + Adenosine triphosphate → Xylulose 5-phosphate + ADP + hydron
Xylulose 5-phosphate → L-ribulose 5-phosphate
Xylulose 5-phosphate → D-ribulose 5-phosphate
Xylulose 5-phosphate ↔ D-ribulose 5-phosphate
Xylulose 5-phosphate + D-Ribose 5-phosphate → L-Glyceraldehyde 3-phosphate + D-Sedoheptulose 7-phosphate
KEGG Reactions
D-ribulose 5-phosphate ↔ Xylulose 5-phosphate
Glycine + hydron + L-Cysteine + Xylulose 5-phosphate + O-Acetyl-L-homoserine → Pyruvic acid + Acetic acid + Carbon dioxide + gamma-Aminobutyric acid + 4-Methyl-5-(2-phosphonooxyethyl)thiazole + Ammonium + water
alpha-D-ribose 5-phosphate + Xylulose 5-phosphate ↔ D-Glyceraldehyde 3-phosphate + D-Sedoheptulose 7-phosphate
D-Erythrose 4-phosphate + Xylulose 5-phosphate ↔ D-Glyceraldehyde 3-phosphate + Fructose 6-phosphate
Adenosine triphosphate + D-Xylulose → hydron + Xylulose 5-phosphate + ADP
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-0592-9800000000-d336b0e2eff1402939d8JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positivesplash10-0a4i-9023200000-1dd7d8e1f64921beb234JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_14) - 70eV, PositiveNot AvailableJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_2_15) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - QTOF 4V, negativesplash10-004j-9170000000-997b74cb48ace33cccd6JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 23V, negativesplash10-004j-9000000000-6bc02f4fe0074c9abd68JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 25V, negativesplash10-004j-9000000000-bdadc167eb24a88aac33JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 27V, negativesplash10-004j-9000000000-93d31d83892e88720b87JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 30V, negativesplash10-004i-9000000000-10cd88e85162e6269751JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 33V, negativesplash10-004i-9000000000-e9f2bf02f0d01a879d20JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 35V, negativesplash10-004i-9000000000-732cd41f406b617c64a0JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 40V, negativesplash10-004i-9000000000-25a5607c50f3e9bb5a14JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 45V, negativesplash10-004i-9000000000-ea506b9429ed926c5f93JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 23V, negativesplash10-0002-9120000000-1172898b831a36b0afcbJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 25V, negativesplash10-0002-9110000000-132340cd62e8e4a0ccd2JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 27V, negativesplash10-0002-9110000000-297d4c6907686258e552JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 30V, negativesplash10-0002-9100000000-1cce49f995c912b1cc94JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 33V, negativesplash10-0002-9100000000-8bba2d7511cc9829eb36JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 35V, negativesplash10-0002-9100000000-89b3b4fdcb0326bfa0e0JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 40V, negativesplash10-0002-9100000000-91e850ff1cd255a2f7fdJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - QTOF 45V, negativesplash10-002b-9100000000-9c43f84a30add3ebce50JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 16V, negativesplash10-0002-9000000000-75847d481a06c31fa479JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 16V, negativesplash10-004i-0091000000-0af17cfb2eb7eab94967JSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-01q9-3790000000-6f5913e9948fa7667e41JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0btd-9710000000-3724bb9f611bbdc1fe11JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0a4i-9200000000-8bc9cecb2dddad8ca5e3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-002r-9520000000-c36fdbcc1d3b19b2fafdJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9100000000-b67b8ea484aa4ddb40e3JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-82b17cf4f5a8c927fe64JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Vaseghi, S., Baumeister, A., Rizzi, M., Reuss, M. (1999). "In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae." Metab Eng 1:128-140.10935926
  • Senac, T., Hahn-Hagerdal, B. (1990). "Intermediary Metabolite Concentrations in Xylulose- and Glucose-Fermenting Saccharomyces cerevisiae Cells." Appl Environ Microbiol 56:120-126.16348083
  • Bar, J., Naumann, M., Reuter, R., Kopperschlager, G. (1996). "Improved purification of ribulose 5-phosphate 3-epimerase from Saccharomyces cerevisiae and characterization of the enzyme." Bioseparation 6:233-241.9032985
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.
External Links:
ResourceLink
CHEBI ID16332
HMDB IDHMDB00868
Pubchem Compound ID850
Kegg IDC00231
ChemSpider ID388330
FOODB IDFDB022290
WikipediaXylulose_5-phosphate
BioCyc IDXYLULOSE-5-PHOSPHATE

Enzymes

Protein Details
1. Transketolase 2
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:
TKL2
Uniprot ID:
P33315
Molecular weight:
75028.79688
Reactions
Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate → D-ribose 5-phosphate + D-xylulose 5-phosphate.
Protein Details
2. 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:
TKL1
Uniprot ID:
P23254
Molecular weight:
73805.0
Reactions
Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate → D-ribose 5-phosphate + D-xylulose 5-phosphate.
Protein Details
3. Xylulose kinase
General function:
Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:
ATP + D-xylulose = ADP + D-xylulose 5- phosphate
Gene Name:
XKS1
Uniprot ID:
P42826
Molecular weight:
68320.29688
Reactions
ATP + D-xylulose → ADP + D-xylulose 5-phosphate.
Protein Details
4. Ribulose-phosphate 3-epimerase
General function:
Involved in catalytic activity
Specific function:
Involved in the protective response to oxidative stress
Gene Name:
RPE1
Uniprot ID:
P46969
Molecular weight:
25966.90039
Reactions
D-ribulose 5-phosphate → D-xylulose 5-phosphate.