ECMDB: beta-D-Ribopyranose (ECMDB20344) (M2MDB001173)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (4)Transporters (4)XML

Proteins (87)

Record Information

Version

2.0

Creation Date

2012-05-31 14:40:08 -0600

Update Date

2015-07-07 11:22:39 -0600

Secondary Accession Numbers

ECMDB20344

Identification

Name:

beta-D-Ribopyranose

Description

Beta-D-ribopyranose is a member of the chemical class known as Pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Ribose 5-phosphate is involved in the pentose phosphate pathway and ribose degradation. The pentose phosphate pathway plays several key roles in metabolism including supply of biosynthetic carbon skeletons and reducing power. (PMID 9546650) Ribose-5-phosphate isomerase A (RpiA) plays an important role in interconverting between ribose-5-phosphate (R5P) and ribulose-5-phosphate in the pentose phosphate pathway and the Calvin cycle. (PMID 19214439). In Escherichia coli, RpiA catalyzes the interconversion of ribose-5-phosphate and ribulose-5-phosphate and is a key enzyme in the pentose phosphate pathway. (PMID 12182339).

Structure

MOL SDF PDB SMILES InChI

Synonyms:

5-(Dihydrogen phosphate)D-Ribose
5-(Dihydrogen phosphoric acid)D-ribose
5-O-Phosphono-D-ribose
b-D-Ribopyranose
D-Ribofuranose, 5-(dihydrogen phosphate)
D-Ribofuranose, 5-(dihydrogen phosphoric acid)
D-Ribose
D-Ribose 5-(dihydrogen phosphate)
D-Ribose 5-(dihydrogen phosphoric acid)
D-Ribose 5-phosphate
D-Ribose 5-phosphoric acid
D-Ribose, 5-(dihydrogen phosphate)
D-Ribose, 5-(dihydrogen phosphoric acid)
D-Ribose-5-P
D-Ribose-5-phosphate
D-Ribose-5-phosphorate
D-Ribose-5-phosphoric acid
Pentose
Ribose
Ribose 5-monophosphate
Ribose 5-monophosphoric acid
Ribose 5-phosphate
Ribose 5-phosphoric acid
Ribose phosphate
Ribose phosphoric acid
Ribose, 5-(dihydrogen phosphate)
Ribose, 5-(dihydrogen phosphoric acid)
Ribose-5-P
Ribose-5-phosphate
Ribose-5-phosphorate
Ribose-5-phosphoric acid
Ribose-5P
β-D-Ribopyranose

Chemical Formula:

C₅H₁₀O₅

Weight:

Average: 150.1299
Monoisotopic: 150.05282343

InChI Key:

SRBFZHDQGSBBOR-TXICZTDVSA-N

InChI:

InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3-,4-,5-/m1/s1

CAS number:

50-69-1

IUPAC Name:

(2R,3R,4R,5R)-oxane-2,3,4,5-tetrol

Traditional IUPAC Name:

β-D-ribopyranose

SMILES:

O[C@@H]1CO[C@@H](O)[C@H](O)[C@@H]1O

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.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

Alternative Parents

Substituents

Pentose monosaccharide
Oxane
Secondary alcohol
Hemiacetal
Oxacycle
Organoheterocyclic compound
Polyol
Hydrocarbon derivative
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

D-ribopyranose (CHEBI:27476 )

Physical Properties

State:

Solid

Charge:

Melting point:

95 °C

Experimental Properties:

Property	Value	Source

Predicted Properties

Property	Value	Source
Water Solubility	1220 g/L	ALOGPS
logP	-2.6	ALOGPS
logP	-2.3	ChemAxon
logS	0.91	ALOGPS
pKa (Strongest Acidic)	11.31	ChemAxon
pKa (Strongest Basic)	-3.5	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	90.15 Å²	ChemAxon
Rotatable Bond Count	0	ChemAxon
Refractivity	29.96 m³·mol⁻¹	ChemAxon
Polarizability	13.39 Å³	ChemAxon
Number of Rings	1	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

Reactions:

beta-D-Ribopyranose <> beta-D-ribofuranose
Adenosine triphosphate + beta-D-Ribopyranose + Water > ADP + Phosphate + beta-D-Ribopyranose + Hydrogen ion
Adenosine triphosphate + beta-D-Ribopyranose + Water > ADP + Phosphate + beta-D-Ribopyranose + Hydrogen ion
beta-D-ribofuranose <> beta-D-Ribopyranose
beta-D-Ribopyranose > beta-D-ribofuranose
beta-D-Ribopyranose + Adenosine triphosphate + Water > ADP + Phosphate + Hydrogen ion

SMPDB Pathways:

Ribose Degradation

PW002102

KEGG Pathways:

ABC transporters ec02010

EcoCyc Pathways:

ribose degradation RIBOKIN-PWY

Concentrations

Concentration	Strain	Media	Growth Status	Growth System	Temperature	Details
260± 21 uM	K12	0.2 g/L NH4Cl, 2.0 g/L (NH4)2SO4, 3.25 g/L KH2PO4, 2.5 g/L K2HPO4, 1.5 g/L NaH2PO4, 0.5 g/L MgSO4; trace substances: 10 mg/L CaCl2, 0.5 mg/L ZnSO4, 0.25 mg/L CuCl2, 0.25 mg/L MnSO4, 0.175 mg/L CoCl2, 0.125 mg/L H3BO3, 2.5 mg/L AlCl3, 0.5 mg/L Na2MoO4, 10	Stationary Phase, glucose limited	Bioreactor, pH controlled, aerated, dilution rate=0.125 L/h	37 oC	PMID: 11488613

Find out more about how we convert literature concentrations.

Spectra

Spectra:

Spectrum Type	Description	Splash Key
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-000x-9400000000-f20d1c35a7eeea1609a5	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (4 TMS) - 70eV, Positive	splash10-00g0-9256300000-ae2d57025e3828494249	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0ue9-1900000000-07783f4be8db8a14f6f0	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0f89-1900000000-eebbf905b1ed94cebf13	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0cka-9100000000-9f3469ad5a1c8e425555	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0002-2900000000-3482c4e67045ff82c4f4	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-001j-4900000000-aedd03247641e8491448	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0006-9000000000-b0a8f8b59e745078a05e	View in MoNA
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	View in JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	View in JSpectraViewer

References

References:

Buchholz, A., Takors, R., Wandrey, C. (2001). "Quantification of intracellular metabolites in Escherichia coli K12 using liquid chromatographic-electrospray ionization tandem mass spectrometric techniques." Anal Biochem 295:129-137. Pubmed: 11488613
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
Vijayendran, C., Barsch, A., Friehs, K., Niehaus, K., Becker, A., Flaschel, E. (2008). "Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling." Genome Biol 9:R72. Pubmed: 18402659

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	27476
HMDB ID	HMDB12194
Pubchem Compound ID	441481
Kegg ID	C08353
ChemSpider ID	5575
Wikipedia ID	Not Available
BioCyc ID	CPD0-1110
EcoCyc ID	CPD0-1110
Ligand Expo	RIP

Enzymes

Protein Details

1. Ribose import ATP-binding protein RbsA

General function:: Involved in nucleotide binding
Specific function:: Part of the ABC transporter complex RbsABCD involved in ribose import. Responsible for energy coupling to the transport system
Gene Name:: rbsA
Uniprot ID:: P04983
Molecular weight:: 55041

Reactions

ATP + H(2)O + monosaccharide(Out) = ADP + phosphate + monosaccharide(In).

Protein Details

2. Ribose transport system permease protein rbsC

General function:: Involved in transporter activity
Specific function:: Part of the binding-protein-dependent transport system for ribose. Probably responsible for the translocation of the substrate across the membrane
Gene Name:: rbsC
Uniprot ID:: P0AGI1
Molecular weight:: 33452

Protein Details

3. D-ribose pyranase

General function:: Involved in intramolecular lyase activity
Specific function:: Catalyzes the interconversion of beta-pyran and beta- furan forms of D-ribose. It also catalyzes the conversion between beta-allofuranose and beta-allopyranose
Gene Name:: rbsD
Uniprot ID:: P04982
Molecular weight:: 15292

Reactions

Beta-D-ribopyranose = beta-D-ribofuranose.
Beta-D-allopyranose = beta-D-allofuranose.

Protein Details

4. D-ribose-binding periplasmic protein

General function:: Carbohydrate transport and metabolism
Specific function:: Involved in the high-affinity D-ribose membrane transport system and also serves as the primary chemoreceptor for chemotaxis
Gene Name:: rbsB
Uniprot ID:: P02925
Molecular weight:: 30950

Transporters

Protein Details

1. Ribose import ATP-binding protein RbsA

General function:: Involved in nucleotide binding
Specific function:: Part of the ABC transporter complex RbsABCD involved in ribose import. Responsible for energy coupling to the transport system
Gene Name:: rbsA
Uniprot ID:: P04983
Molecular weight:: 55041

Reactions

ATP + H(2)O + monosaccharide(Out) = ADP + phosphate + monosaccharide(In).

Protein Details

2. Sugar efflux transporter C

General function:: Involved in transmembrane transport
Specific function:: Involved in the efflux of sugars. The physiological role may be the detoxification of non-metabolizable sugar analogs
Gene Name:: setC
Uniprot ID:: P31436
Molecular weight:: 43493

Protein Details

3. Ribose transport system permease protein rbsC

General function:: Involved in transporter activity
Specific function:: Part of the binding-protein-dependent transport system for ribose. Probably responsible for the translocation of the substrate across the membrane
Gene Name:: rbsC
Uniprot ID:: P0AGI1
Molecular weight:: 33452

Protein Details

4. D-ribose-binding periplasmic protein

General function:: Carbohydrate transport and metabolism
Specific function:: Involved in the high-affinity D-ribose membrane transport system and also serves as the primary chemoreceptor for chemotaxis
Gene Name:: rbsB
Uniprot ID:: P02925
Molecular weight:: 30950

beta-D-Ribopyranose (ECMDB20344) (M2MDB001173)

Structure for #<Compound:0xa6449048>

Enzymes

Reactions

Reactions

Transporters

Reactions