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D-Xylulose (YMDB00161)

Identification
YMDB IDYMDB00161
NameD-Xylulose
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionD-Xylulose, also known as D-lyxulose or D-threo-pentulose, belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. D-Xylulose is an extremely weak basic (essentially neutral) compound (based on its pKa). Within yeast, D-xylulose participates in a number of enzymatic reactions. In particular, D-xylulose can be biosynthesized from D-xylitol through its interaction with the enzyme D-xylulose reductase. In addition, D-xylulose can be converted into xylulose 5-phosphate through the action of the enzyme xylulose kinase. In yeast, D-xylulose is involved in the metabolic pathway called the xylitol degradation pathway.
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms
  • D-threo-Pentulose
  • D-Xylulose
  • Xylulose
  • D-Lyxulose
  • D-Xul
  • Lyxulose
  • Xylulose, (D-threo)-isomer
  • Xylulose, (L-threo)-isomer
CAS number551-84-8
WeightAverage: 150.1299
Monoisotopic: 150.05282343
InChI KeyZAQJHHRNXZUBTE-WUJLRWPWSA-N
InChIInChI=1S/C5H10O5/c6-1-3(8)5(10)4(9)2-7/h3,5-8,10H,1-2H2/t3-,5+/m1/s1
IUPAC Name(3S,4R)-1,3,4,5-tetrahydroxypentan-2-one
Traditional IUPAC NameD-xylulose
Chemical FormulaC5H10O5
SMILES[H]OC([H])([H])C(=O)[C@@]([H])(O[H])[C@]([H])(O[H])C([H])([H])O[H]
Chemical Taxonomy
Description belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentoses
Alternative Parents
Substituents
  • Pentose monosaccharide
  • Beta-hydroxy ketone
  • Acyloin
  • Alpha-hydroxy ketone
  • Secondary alcohol
  • Ketone
  • Polyol
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Carbonyl group
  • Alcohol
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateLiquid
Charge0
Melting point15 °C
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility678 g/LALOGPS
logP-2.2ALOGPS
logP-2.6ChemAxon
logS0.65ALOGPS
pKa (Strongest Acidic)10.57ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area97.99 ŲChemAxon
Rotatable Bond Count4ChemAxon
Refractivity31.6 m³·mol⁻¹ChemAxon
Polarizability13.53 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
xylitol degradationPW002433 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Pentose and glucuronate interconversionsec00040 Map00040
SMPDB Reactions
D-Xylitol + NAD → NADH + hydron + D-Xylulose
D-Xylulose + Adenosine triphosphate → Xylulose 5-phosphate + ADP + hydron
KEGG Reactions
NAD + Xylitol → NADH + D-Xylulose + hydron
Adenosine triphosphate + D-Xylulose → hydron + Xylulose 5-phosphate + ADP
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (Non-derivatized)splash10-00kb-0930000000-c3a525ee2ad524114f0dJSpectraViewer | MoNA
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-03di-9100000000-1304cf35b8860cd7a456JSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS ( TMS) - 70eV, Positivesplash10-00g3-9127300000-b6aed5448276d0184bc2JSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-014r-4900000000-0a4d51584b79dc230edbJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-000i-9000000000-2131da3ca52caffed55fJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 40V, Positive (Annotated)splash10-014i-9000000000-305f431957b24a5b888aJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-2900000000-3e1ebc07944b3d190ec8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-03di-9300000000-9be7fcf2c9ec6f8829c7JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-08fv-9000000000-931753afec5aa068bca8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-000j-9400000000-1c39b6f316e1745d355cJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-06ri-9100000000-095c1d8c10895109ecb1JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-0a4l-9000000000-5ea417513158cb617f30JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,1H] 2D NMR SpectrumNot AvailableJSpectraViewer
2D NMR[1H,13C] 2D 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
  • Senac, T., Hahn-Hagerdal, B. (1990). "Intermediary Metabolite Concentrations in Xylulose- and Glucose-Fermenting Saccharomyces cerevisiae Cells." Appl Environ Microbiol 56:120-126.16348083
Synthesis Reference:Takeuchi, Sonoko; Tonouchi, Naoto; Yokozeki, Kenzo. Production of xylitol or D-xylulose by fermentation of glucose with Gluconobacter, Acetobacter, and Frateuria. Eur. Pat. Appl. (2000), 10 pp.
External Links:
ResourceLink
CHEBI ID17140
HMDB IDHMDB01644
Pubchem Compound ID619
Kegg IDC00310
ChemSpider IDNot Available
FOODB IDFDB022698
WikipediaXylulose
BioCyc IDD-XYLULOSE

Enzymes

Protein Details
1. 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
2. D-xylulose reductase
General function:
Involved in zinc ion binding
Specific function:
Xylitol + NAD(+) = D-xylulose + NADH
Gene Name:
XYL2
Uniprot ID:
Q07993
Molecular weight:
38600.10156
Reactions
Xylitol + NAD(+) → D-xylulose + NADH.