P. aeruginosa Metabolome Database: D-Ribose-5-phosphate (PAMDB000431)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes Transporters

Proteins (3280)

Record Information

Version

1.0

Update Date

1/22/2018 11:54:54 AM

Metabolite ID

PAMDB000431

Identification

Name:

D-Ribose-5-phosphate

Description:

D-ribose-5-phosphate 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 both a product and an intermediate of the pentose phosphate pathway. The last step of the oxidative reactions in the pentose phosphate pathway is the production of ribulose-5-phosphate. Ribulose-5-phosphate can reversibly isomerize to ribose-5-phosphate. Ribulose-5-phosphate can alternatively undergo a series of isomerizations as well as transaldolations and transketolations that result in the production of other pentoses phosphates as well as fructose 6-phosphate and glyceraldehyde-3-phosphate (both intermediates in glycolysis). The enzyme ribose-phosphate diphosphokinase converts ribose-5-phosphate into phosphoribosyl pyrophosphate. (WikiPedia)

Structure

🔍MOL SDF PDB SMILES InChI View Structure

Synonyms:

α-D-ribose-5-phosphate
α-D-ribose-5-phosphoric acid
a-D-Ribose-5-phosphate
a-D-Ribose-5-phosphoric acid
Alpha-D-Ribose-5-phosphate
alpha-D-Ribose-5-phosphoric acid
D-Ribose 5'-phosphate
D-Ribose 5'-phosphoric acid
D-Ribose 5-phosphate
D-Ribose 5-phosphoric acid
D-ribose-5-P
D-Ribose-5-phosphorate
D-Ribose-5-phosphoric acid
R5P
Ribose 5-phosphate
Ribose 5-phosphoric acid
Ribose-5-P
Ribose-5-phosphate
Ribose-5-phosphorate
Ribose-5-phosphoric acid
Ribose-5P
α-D-Ribose-5-phosphate
α-D-Ribose-5-phosphoric acid

Chemical Formula:

C₅H₁₁O₈P

Average Molecular Weight:

230.1098

Monoisotopic Molecular Weight:

230.01915384

InChI Key:

KTVPXOYAKDPRHY-SOOFDHNKSA-N

InChI:

InChI=1S/C5H11O8P/c6-3-2(1-12-14(9,10)11)13-5(8)4(3)7/h2-8H,1H2,(H2,9,10,11)/t2-,3-,4-,5?/m1/s1

CAS number:

4151-19-3

IUPAC Name:

{[(2R,3S,4R)-3,4,5-trihydroxyoxolan-2-yl]methoxy}phosphonic acid

Traditional IUPAC Name:

D-ribofuranose 5-phosphate

SMILES:

OC1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O

Chemical Taxonomy

Taxonomy Description

This compound belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.

Kingdom

Organic compounds

Super Class

Organooxygen compounds

Class

Carbohydrates and carbohydrate conjugates

Sub Class

Monosaccharides

Direct Parent

Monosaccharide phosphates

Alternative Parents

Substituents

Monosaccharide phosphate
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Organic phosphate
Oxolane
Secondary alcohol
Polyol
Hemiacetal
1,2-diol
Oxacycle
Organoheterocyclic compound
Hydrocarbon derivative
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

D-ribose 5-phosphate (CHEBI:52742 )

Physical Properties

State:

Not Available

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source
LogP:	-2.919	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	33.6 mg/mL	ALOGPS
logP	-2.1	ALOGPS
logP	-2.4	ChemAxon
logS	-0.84	ALOGPS
pKa (Strongest Acidic)	1.22	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	136.68 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	40.83 m³·mol^-1	ChemAxon
Polarizability	18.35 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:

D-Ribose-5-phosphate + Uracil <> Water + Pseudouridine 5'-phosphate
Xylulose 5-phosphate + D-Ribose-5-phosphate + Xylulose 5-phosphate <> D-Sedoheptulose 7-phosphate + D-Glyceraldehyde 3-phosphate + D-Sedoheptulose 7-phosphate + D-Glyceraldehyde 3-phosphate

More...

Pathways:

Biosynthesis of ansamycins pae01051
Carbon fixation in photosynthetic organisms pae00710
Fructose and mannose metabolism pae00051
Metabolic pathways pae01100
Microbial metabolism in diverse environments pae01120
Pentose phosphate pathway pae00030
Purine metabolism pae00230

Spectra

Spectra:

Spectrum Type	Description	Splash Key
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)	splash10-014j-1942000000-8c3468eabd202324a3ae	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS)	splash10-0fr2-1943000000-b5d1468f33c224a23bd3	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS; 1 MEOX)	splash10-00di-9532000000-693524b08b2ccd6179c5	View in MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (5 TMS; 1 MEOX)	splash10-00di-9421000000-dbcd94d0a73f35716059	View in MoNA
GC-MS	GC-MS Spectrum - GC-MS	Not Available
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)	splash10-0002-9320000000-7f3d980d223a6b9f5f3f	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)	splash10-0002-9000000000-a5df0614f5cbd8b55405	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-056r-0090700000-ea86961dacc666b5fc7d	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0002-9100000000-6cbb3e84820a37a47fbb	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-004i-0090000000-10949588537786dbae1e	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-ITFT (LTQ Orbitrap XL, Thermo Scientfic) , Negative	splash10-0a4i-0000900000-10d8b4fd09ed514cc12e	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QTOF (UPLC Q-Tof Premier, Waters) , Negative	splash10-002b-9000000000-49264a7584727750bd70	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	Not Available
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	Not Available
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	Not Available
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	Not Available
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	Not Available
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	Not Available
1D NMR	1H NMR Spectrum	Not Available
2D NMR	[1H,1H] 2D NMR Spectrum	Not Available
2D NMR	[1H,13C] 2D NMR Spectrum	Not Available

References

References:

Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli." Nat Chem Biol 5:593-599. Pubmed: 19561621
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
Nakayama Y, Kinoshita A, Tomita M: Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition. Theor Biol Med Model. 2005 May 9;2(1):18. Pubmed: 15882454
Pilz RB, Willis RC, Boss GR: The influence of ribose 5-phosphate availability on purine synthesis of cultured human lymphoblasts and mitogen-stimulated lymphocytes. J Biol Chem. 1984 Mar 10;259(5):2927-35. Pubmed: 6699001
van der Werf, M. J., Overkamp, K. M., Muilwijk, B., Coulier, L., Hankemeier, T. (2007). "Microbial metabolomics: toward a platform with full metabolome coverage." Anal Biochem 370:17-25. Pubmed: 17765195
Winder, C. L., Dunn, W. B., Schuler, S., Broadhurst, D., Jarvis, R., Stephens, G. M., Goodacre, R. (2008). "Global metabolic profiling of Escherichia coli cultures: an evaluation of methods for quenching and extraction of intracellular metabolites." Anal Chem 80:2939-2948. Pubmed: 18331064

Synthesis Reference:

Not Available

Material Safety Data Sheet (MSDS)

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Links

External Links:

Resource	Link
CHEBI ID	17797
HMDB ID	HMDB01548
Pubchem Compound ID	439167
Kegg ID	C00117
ChemSpider ID	388313
Wikipedia	D-ribose-5-P
BioCyc ID	RIBOSE-5P
EcoCyc ID	RIBOSE-5P

Enzymes

Protein Details

• Ribose-phosphate pyrophosphokinase

General function:: Involved in magnesium ion binding
Specific function:: ATP + D-ribose 5-phosphate = AMP + 5-phospho- alpha-D-ribose 1-diphosphate
Gene Name:: prs
Locus Tag:: PA4670
Molecular weight:: 34 kDa

Reactions

ATP + D-ribose 5-phosphate = AMP + 5-phospho-alpha-D-ribose 1-diphosphate.

Protein Details

• Ribose-5-phosphate isomerase A

General function:: Involved in ribose-5-phosphate isomerase activity
Specific function:: D-ribose 5-phosphate = D-ribulose 5-phosphate
Gene Name:: rpiA
Locus Tag:: PA0330
Molecular weight:: 23.7 kDa

Reactions

D-ribose 5-phosphate = D-ribulose 5-phosphate.

Protein Details

• Ribokinase

General function:: Involved in phosphotransferase activity, alcohol group as acceptor
Specific function:: ATP + D-ribose = ADP + D-ribose 5-phosphate
Gene Name:: rbsK
Locus Tag:: PA1950
Molecular weight:: 31.8 kDa

Reactions

ATP + D-ribose = ADP + D-ribose 5-phosphate.

Protein Details

• AMP nucleosidase

General function:: Involved in catalytic activity
Specific function:: Involved in regulation of AMP concentrations
Gene Name:: amn
Locus Tag:: PA3970
Molecular weight:: 56.2 kDa

Reactions

AMP + H(2)O = D-ribose 5-phosphate + adenine.

Protein Details

• Class B acid phosphatase

General function:: Involved in acid phosphatase activity
Specific function:: Dephosphorylates several organic phosphomonoesters and catalyzes the transfer of low-energy phosphate groups from phosphomonoesters to hydroxyl groups of various organic compounds. Preferentially acts on aryl phosphoesters. Might function as a broad-spectrum dephosphorylating enzyme able to scavenge both 3'- and 5'-nucleotides and also additional organic phosphomonoesters
Gene Name:: aphA
Locus Tag:: PA1409
Molecular weight:: 38 kDa

Reactions

A phosphate monoester + H(2)O = an alcohol + phosphate.

Protein Details

• Transketolase 1

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:: tktA
Locus Tag:: PA0548
Molecular weight:: 72.2 kDa

Reactions

Sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-ribose 5-phosphate + D-xylulose 5-phosphate.

Protein Details

• Phosphoglucomutase

General function:: Involved in intramolecular transferase activity, phosphotransferases
Specific function:: This enzyme participates in both the breakdown and synthesis of glucose
Gene Name:: pgm
Locus Tag:: PA5131
Molecular weight:: 55.6 kDa

Reactions

Alpha-D-glucose 1-phosphate = alpha-D-glucose 6-phosphate.

Protein Details

• ADP-ribose pyrophosphatase

General function:: Involved in hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
Specific function:: Acts on ADP-mannose and ADP-glucose as well as ADP- ribose. Prevents glycogen biosynthesis. The reaction catalyzed by this enzyme is a limiting step of the gluconeogenic process
Gene Name:: nudF
Locus Tag:: PA4971
Molecular weight:: 23.1 kDa

Reactions

ADP-ribose + H(2)O = AMP + D-ribose 5-phosphate.

D-Ribose-5-phosphate (PAMDB000431)

Structure for D-Ribose-5-phosphate (PAMDB000431)

Enzymes

Reactions

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Transporters