D-ribulose 5-phosphate (YMDB00948)

Identification

YMDB ID

YMDB00948

Name

D-ribulose 5-phosphate

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

D-Ribulose 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. D-Ribulose 5-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI

Synonyms

alpha-D-Ribose 5-phosphate
D-Ribulose 5-phosphate
D-Ribulose 5-phosphic acid
erythro-Pentulose 5-phosphate
Ribulose 5-phosphate
Ribulose phosphate
D-Erythro-pent-2-ulose 5-(dihydrogen phosphate)
D-Erythro-pent-2-ulose 5-(dihydrogen phosphoric acid)
D-Ribulose 5-phosphoric acid
Ribulose 5-phosphate, (D)-isomer
Ribulose 5-phosphate, (L)-isomer

CAS number

4151-19-3

Weight

Average: 230.1098
Monoisotopic: 230.01915384

InChI Key

FNZLKVNUWIIPSJ-UHNVWZDZSA-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

IUPAC Name

{[(2R,3R)-2,3,5-trihydroxy-4-oxopentyl]oxy}phosphonic acid

Traditional IUPAC Name

Ara

Chemical Formula

C₅H₁₁O₈P

SMILES

OCC(=O)[C@H](O)[C@H](O)COP(O)(O)=O

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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose 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 Framework

Aliphatic acyclic compounds

External Descriptors

ribulose 5-phosphate (CHEBI:17363 )

Physical Properties

State

Solid

Charge

Melting point

Not Available

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	26.1 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-2.8	ChemAxon
logS	-0.95	ALOGPS
pKa (Strongest Acidic)	1.48	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	144.52 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	42.47 m³·mol⁻¹	ChemAxon
Polarizability	17.95 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

cytoplasm

Organoleptic Properties

Not Available

SMPDB Pathways

Riboflavin metabolism	PW002443
Riboneogenesis	PW002511
xylitol degradation	PW002433

KEGG Pathways

Methane metabolism	ec00680
Pentose and glucuronate interconversions	ec00040
Pentose phosphate pathway	ec00030
Riboflavin metabolism	ec00740
Vitamin B6 metabolism	ec00750

SMPDB Reactions

Xylulose 5-phosphate → D-ribulose 5-phosphate

Xylulose 5-phosphate ↔ D-ribulose 5-phosphate

D-ribulose 5-phosphate → D-Ribose 5-phosphate

D-Ribose 5-phosphate ↔ D-ribulose 5-phosphate

D-ribulose 5-phosphate → Formic acid + 2-Hydroxy-3-oxobutyl phosphate

KEGG Reactions

D-ribulose 5-phosphate → Formic acid + 2-Hydroxy-3-oxobutyl phosphate + hydron

6-Phosphogluconic acid + NADP → Carbon dioxide + NADPH + D-ribulose 5-phosphate

alpha-D-ribose 5-phosphate ↔ D-ribulose 5-phosphate

D-ribulose 5-phosphate ↔ Xylulose 5-phosphate

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 5 TMS)	splash10-0a4i-2936000000-adde71232cd79c7c92aa	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-MS (1 MEOX; 5 TMS)	splash10-0a4i-2947000000-ae4da5853e1b24392d1d	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0a4j-1935000000-dfb75754c9a7045f108f	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0a4j-1935000000-31be2cabeeebc480c1b8	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0pba-1924000000-11aca642135096a8e378	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-014j-1943000000-34588179b9bd7796e907	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0pbj-2914000000-d91b422c677fd9231297	JSpectraViewer \| MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0592-9800000000-d336b0e2eff1402939d8	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-029t-9327100000-10a5d90f15e25f16925c	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF , negative	splash10-004j-9010000000-49c14e85e3a3dee61721	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 10V, positive	splash10-00ec-0970000000-6e833fd34cda3327e6ae	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 15V, positive	splash10-007o-0930000000-72bf0b63618d4b200421	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 17V, positive	splash10-007o-0920000000-fe7037f21876801587ec	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 20V, positive	splash10-007o-0910000000-5dacb5e16b8a32f079c0	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 23V, positive	splash10-007o-0900000000-1d35981b82e13d258d9d	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 25V, positive	splash10-00ec-0900000000-23938808d1a77a77203d	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - QTOF 27V, positive	splash10-00dl-0900000000-abc2b8be05c39eef69e6	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 3V, positive	splash10-00di-0190000000-f09b49c51cfa01814ef3	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 4V, positive	splash10-00di-0490000000-acd1f6a33bd147e29ac3	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 5V, positive	splash10-00ec-0980000000-e8070ccdca137f841520	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 7V, positive	splash10-007o-0940000000-0e8aaff469756dafc2ee	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 8V, positive	splash10-000x-0920000000-bef5b5a1a6528a057748	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 9V, positive	splash10-000x-0910000000-7a57ccc066185b618224	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 11V, positive	splash10-007o-0900000000-0412a8fa5b22fb04ec87	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 12V, positive	splash10-007o-0900000000-e655723668ec0397d76e	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 14V, positive	splash10-00dl-0900000000-4d7aa68ec0ea7a05fe8b	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 18V, positive	splash10-00di-1900000000-ef58c4a909999b72f8fa	JSpectraViewer \| MoNA
LC-MS/MS	LC-MS/MS Spectrum - Orbitrap 22V, positive	splash10-0229-4900000000-6c4c40d2771cf3aec25f	JSpectraViewer \| MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01q9-3790000000-6f5913e9948fa7667e41	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0btd-9710000000-3724bb9f611bbdc1fe11	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9200000000-8bc9cecb2dddad8ca5e3	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002r-9520000000-c36fdbcc1d3b19b2fafd	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-b67b8ea484aa4ddb40e3	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-82b17cf4f5a8c927fe64	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer

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
Kondo, H., Nakamura, Y., Dong, Y. X., Nikawa, J., Sueda, S. (2004). "Pyridoxine biosynthesis in yeast: participation of ribose 5-phosphate ketol-isomerase." Biochem J 379:65-70.14690456
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
Jin, C., Barrientos, A., Tzagoloff, A. (2003). "Yeast dihydroxybutanone phosphate synthase, an enzyme of the riboflavin biosynthetic pathway, has a second unrelated function in expression of mitochondrial respiration." J Biol Chem 278:14698-14703.12595523
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
Reuter, R., Naumann, M., Bar, J., Miosga, T., Kopperschlager, G. (1998). "Ribose-5-phosphate isomerase from Saccharomyces cerevisiae: purification and molecular analysis of the enzyme." Bioseparation 7:107-115.9763699

Synthesis Reference:

Wong, Chi-Huey; McCurry, Stephen D.; Whitesides, George M. Practical enzymic syntheses of ribulose 1,5 bisphosphate and ribose 5-phosphate. Journal of the American Chemical Society (1980), 102(27), 7938-9.

External Links:

Resource	Link
CHEBI ID	17363
HMDB ID	HMDB00618
Pubchem Compound ID	439167
Kegg ID	C00199
ChemSpider ID	23106877
FOODB ID	FDB022145
Wikipedia	Ribulose 5-phosphate
BioCyc ID	RIBULOSE-5P

Enzymes

Protein Details

1. Ribose-5-phosphate isomerase

General function:: Involved in ribose-5-phosphate isomerase activity
Specific function:: D-ribose 5-phosphate = D-ribulose 5-phosphate
Gene Name:: RKI1
Uniprot ID:: Q12189
Molecular weight:: 28257.80078

Reactions

D-ribose 5-phosphate → D-ribulose 5-phosphate.

Protein Details

2. 3,4-dihydroxy-2-butanone 4-phosphate synthase

General function:: Involved in 3,4-dihydroxy-2-butanone-4-phosphate synthase activity
Specific function:: Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate
Gene Name:: RIB3
Uniprot ID:: Q99258
Molecular weight:: 22567.40039

Reactions

D-ribulose 5-phosphate → formate + L-3,4-dihydroxybutan-2-one 4-phosphate.

Protein Details

3. 6-phosphogluconate dehydrogenase, decarboxylating 1

General function:: Involved in oxidoreductase activity
Specific function:: Catalyzes the oxidative decarboxylation of 6- phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH
Gene Name:: GND1
Uniprot ID:: P38720
Molecular weight:: 53542.69922

Reactions

6-phospho-D-gluconate + NADP(+) → D-ribulose 5-phosphate + CO(2) + NADPH.

Protein Details

4. 6-phosphogluconate dehydrogenase, decarboxylating 2

General function:: Involved in oxidoreductase activity
Specific function:: Catalyzes the oxidative decarboxylation of 6- phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH
Gene Name:: GND2
Uniprot ID:: P53319
Molecular weight:: 53922.30078

Reactions

6-phospho-D-gluconate + NADP(+) → D-ribulose 5-phosphate + CO(2) + NADPH.

Protein Details

5. 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.

Structure for #<Compound:0xaf5121ec>

Enzymes

Reactions

Reactions

Reactions

Reactions

Reactions