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Identification
YMDB IDYMDB00362
NameXylulose 5-phosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionXylulose 5-phosphate, also known as xylulose-p or xu-5-p, 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 is an extremely weak basic (essentially neutral) compound (based on its pKa). Xylulose 5-phosphate exists in all living species, ranging from bacteria to humans. Within yeast, xylulose 5-phosphate participates in a number of enzymatic reactions. In particular, xylulose 5-phosphate can be biosynthesized from D-xylulose; which is catalyzed by the enzyme xylulose kinase. In addition, xylulose 5-phosphate can be converted into D-ribulose 5-phosphate; which is catalyzed by the enzyme ribulose-phosphate 3-epimerase. In yeast, xylulose 5-phosphate is involved in the metabolic pathway called the xylitol degradation pathway.
Structure
Thumb
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
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 triphosphateXylulose 5-phosphate + ADP + hydron
Xylulose 5-phosphate → L-ribulose 5-phosphate
Xylulose 5-phosphateD-ribulose 5-phosphate
Xylulose 5-phosphateD-ribulose 5-phosphate
Xylulose 5-phosphate + D-Ribose 5-phosphate → L-Glyceraldehyde 3-phosphate + D-Sedoheptulose 7-phosphate
KEGG Reactions
D-ribulose 5-phosphateXylulose 5-phosphate
Glycine + hydron + L-Cysteine + Xylulose 5-phosphate + O-Acetyl-L-homoserinePyruvic acid + Acetic acid + Carbon dioxide + gamma-Aminobutyric acid + 4-Methyl-5-(2-phosphonooxyethyl)thiazole + Ammonium + water
alpha-D-ribose 5-phosphate + Xylulose 5-phosphateD-Glyceraldehyde 3-phosphate + D-Sedoheptulose 7-phosphate
D-Erythrose 4-phosphate + Xylulose 5-phosphateD-Glyceraldehyde 3-phosphate + Fructose 6-phosphate
Adenosine triphosphate + D-Xylulosehydron + Xylulose 5-phosphate + ADP
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
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

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.
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.
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.
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.