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D-Ribulose 1,5-bisphosphate (M2MDB000993)

Record Information
Version2.0
Creation Date2012-05-31 14:29:53 -0600
Update Date2015-06-03 17:19:24 -0600
Secondary Accession Numbers
  • ECMDB20145
Identification
Name:D-Ribulose 1,5-bisphosphate
DescriptionD-ribulose 1,5-bisphosphate is a member of the chemical class known as Pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. D-Ribulose 1,5-bisphosphate is invovled in the Calvin reductive pentose phosphate cycle. The Calvin Cycle is the primary conduit for the fixation of carbon dioxide into the biosphere; ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO) catalyzes the rate-limiting fixation step. (PMID 16423843) Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is the key enzyme of the Calvin reductive pentose phosphate cycle. (PMID 19557347)
Structure
Thumb
MOLSDFPDBSMILESInChI
Synonyms:
  • 1-(2-Carboxyphenylamino)-1-deoxy-D-ribulose-5-P
  • 1-(2-Carboxyphenylamino)-1-deoxy-D-ribulose-5-phosphate
  • 1-(2-carboxyphenylamino)-1-Deoxy-D-ribulose-5-phosphoric acid
  • 1-(O-Carboxyphenylamino)-1'-deoxyribulose-5'-P
  • D-Ribulose 1,5-bisphosphoric acid
  • D-Ribulose-1,5-bisphosphate
  • D-Ribulose-1,5-bisphosphoric acid
  • D-Ribulose-1,5-diphosphate
  • D-Ribulose-1,5-diphosphoric acid
  • D-Ribulose-1,5-P2
  • D-RIBULOSE-15-P2
  • Ribulose 1,5-bisphosphate
  • Ribulose 1,5-bisphosphoric acid
Chemical Formula:C5H12O11P2
Weight:Average: 310.0897
Monoisotopic: 309.98548425
InChI Key:YAHZABJORDUQGO-NQXXGFSBSA-N
InChI:InChI=1S/C5H12O11P2/c6-3(1-15-17(9,10)11)5(8)4(7)2-16-18(12,13)14/h3,5-6,8H,1-2H2,(H2,9,10,11)(H2,12,13,14)/t3-,5-/m1/s1
CAS number:24218-00-6
IUPAC Name:{[(3R,4R)-3,4-dihydroxy-2-oxo-5-(phosphonooxy)pentyl]oxy}phosphonic acid
Traditional IUPAC Name:ribulose-1,5-bisphosphate
SMILES:[H][C@@](O)(COP(O)(O)=O)[C@@]([H])(O)C(=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.
KingdomOrganic compounds
Super ClassOrganic oxygen compounds
ClassOrganooxygen compounds
Sub ClassCarbohydrates and carbohydrate conjugates
Direct ParentPentose phosphates
Alternative Parents
Substituents
  • Pentose-5-phosphate
  • Pentose phosphate
  • Glycerone phosphate
  • Monosaccharide phosphate
  • Monoalkyl phosphate
  • Acyloin
  • Beta-hydroxy ketone
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Alpha-hydroxy ketone
  • Ketone
  • 1,2-diol
  • Secondary alcohol
  • Carbonyl group
  • Hydrocarbon derivative
  • Alcohol
  • Organic oxide
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
State:Not Available
Charge:-4
Melting point:Not Available
Experimental Properties:
PropertyValueSource
Predicted Properties
PropertyValueSource
Water Solubility12.1 g/LALOGPS
logP-1.5ALOGPS
logP-2.9ChemAxon
logS-1.4ALOGPS
pKa (Strongest Acidic)1ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area191.05 ŲChemAxon
Rotatable Bond Count8ChemAxon
Refractivity53.35 m³·mol⁻¹ChemAxon
Polarizability22.44 ųChemAxon
Number of Rings0ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations:Cytoplasm
Reactions:
Adenosine triphosphate + D-Ribulose 5-phosphate + D-Ribulose 5-phosphate <> ADP + D-Ribulose 1,5-bisphosphate
Adenosine triphosphate + D-Ribulose 5-phosphate > ADP + D-Ribulose 1,5-bisphosphate
SMPDB Pathways:Not Available
KEGG Pathways:
  • Carbon fixation in photosynthetic organisms ec00710
  • Glyoxylate and dicarboxylate metabolism ec00630
  • Metabolic pathways eco01100
  • Microbial metabolism in diverse environments ec01120
EcoCyc Pathways:
Concentrations
Not Available
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (TMS_5_14) - 70eV, PositiveNot AvailableView in JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-2579000000-fbc5c6119d86387b2f73View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-01oy-3920000000-1811e2b9e48fea5e80e3View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-000e-7900000000-8ca190f0a83b8980a14dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0690-5903000000-7025841546ddccf5e740View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9200000000-b471c4ad5a440e20b6f6View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-f8fe0193a700880773c5View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-03di-0049000000-911dc648500311e364ddView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-0002-9300000000-45c5b700a3591afb8243View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-0002-9100000000-e3ddc6e1d7052a75e316View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0a4i-0009000000-fb37007c75b47c9fa5c9View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-004i-9000000000-58536175e56faf7df2f4View in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-87feca0b926518ec212bView in MoNA
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR13C NMR SpectrumNot AvailableView in JSpectraViewer
1D NMR1H NMR SpectrumNot AvailableView in JSpectraViewer
References
References:
  • 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
  • Lee, J. H., Park, D. O., Park, S. W., Hwang, E. H., Oh, J. I., Kim, Y. M. (2009). "Expression and regulation of ribulose 1,5-bisphosphate carboxylase/oxygenase genes in Mycobacterium sp. strain JC1 DSM 3803." J Microbiol 47:297-307. Pubmed: 19557347
  • Parikh, M. R., Greene, D. N., Woods, K. K., Matsumura, I. (2006). "Directed evolution of RuBisCO hypermorphs through genetic selection in engineered E.coli." Protein Eng Des Sel 19:113-119. Pubmed: 16423843
Synthesis Reference:Not Available
Material Safety Data Sheet (MSDS)Not Available
External Links:
ResourceLink
CHEBI ID16710
HMDB IDHMDB0304322
Pubchem Compound ID1192
Kegg IDC01182
ChemSpider ID1155
Wikipedia IDRibulose-1,5-bisphosphate
BioCyc IDCARBOXYPHENYLAMINO-DEOXYRIBULOSE-P
EcoCyc IDCARBOXYPHENYLAMINO-DEOXYRIBULOSE-P
Ligand ExpoRUB

Enzymes

Protein Details
1. Probable phosphoribulokinase
General function:
Involved in ATP binding
Specific function:
ATP + D-ribulose 5-phosphate = ADP + D- ribulose 1,5-bisphosphate
Gene Name:
prkB
Uniprot ID:
P0AEX5
Molecular weight:
32344
Reactions
ATP + D-ribulose 5-phosphate = ADP + D-ribulose 1,5-bisphosphate.