ECMDB: Ribose-1-phosphate (ECMDB04147) (M2MDB000637)

Identification Taxonomy Physical Properties Biological Properties Spectra Concentrations Links References Enzymes (6)XML

Proteins (1026)

Record Information

Version

2.0

Creation Date

2012-05-31 14:06:32 -0600

Update Date

2015-10-02 02:25:46 -0600

Secondary Accession Numbers

ECMDB04147

Identification

Name:

Ribose-1-phosphate

Description

Ribose 1-phosphate is an intermediate in the metabolism of Pyrimidine and the metabolism of Nicotinate and nicotinamide. It is a substrate for Uridine phosphorylase 2, Phosphoglucomutase, Purine nucleoside phosphorylase and Uridine phosphorylase 1. Ribose 1-phosphate can be formed from guanosine through the action of purine nucleoside phosphorylase. Ribose 1-phosphate can also act as a ribose donor in the synthesis of xanthosine as catalyzed by the same enzyme (purine nucleoside phosphorylase). The presence of guanase, which irreversibly converts guanine to xanthine, affects the overall process of guanosine transformation. The activated ribose moiety in Ribose 1-phosphate which stems from the catabolism of purine nucleosides can be transferred to uracil and, in the presence of ATP, used for the synthesis of pyrimidine nucleotides; therefore, purine nucleosides can act as ribose donors for the salvage of pyrimidine bases. (PMID: 9133638)

Structure

MOL SDF 3D-SDF PDB SMILES InChI View 3D Structure

Synonyms:

α-D-ribofuranose 1-phosphate
α-D-ribofuranose 1-phosphoric acid
α-D-ribose-1P
1-O-Phosphono-D-ribofuranose
A-D-Ribofuranose 1-(dihydrogen phosphate)
a-D-Ribofuranose 1-(dihydrogen phosphoric acid)
a-D-Ribofuranose 1-phosphate
a-D-Ribofuranose 1-phosphoric acid
A-D-Ribose 1-phosphate
a-D-Ribose 1-phosphoric acid
a-D-Ribose-1P
Alpha-D-Ribofuranose 1-(dihydrogen phosphate)
alpha-D-Ribofuranose 1-(dihydrogen phosphoric acid)
Alpha-D-Ribofuranose 1-phosphate
alpha-D-Ribofuranose 1-phosphoric acid
Alpha-D-Ribose 1-phosphate
alpha-D-Ribose 1-phosphoric acid
Alpha-D-Ribose-1P
D-Ribofuranose 1-(dihydrogen phosphate)
D-Ribofuranose 1-(dihydrogen phosphoric acid)
D-Ribofuranose 1-phosphate
D-Ribofuranose 1-phosphoric acid
D-Ribose-1-phosphate
D-Ribose-1-phosphoric acid
D-Ribose-1P
Ribofuranose 1-phosphate
Ribofuranose 1-phosphoric acid
Ribose 1-phosphate
Ribose 1-phosphoric acid
Ribose-1-phosphate
Ribose-1-phosphoric acid
α-D-Ribofuranose 1-(dihydrogen phosphate)
α-D-Ribofuranose 1-(dihydrogen phosphoric acid)
α-D-Ribofuranose 1-phosphate
α-D-Ribofuranose 1-phosphoric acid
α-D-Ribose 1-phosphate
α-D-Ribose 1-phosphoric acid
α-D-Ribose-1P

Chemical Formula:

C₅H₁₁O₈P

Weight:

Average: 230.1098
Monoisotopic: 230.01915384

InChI Key:

YXJDFQJKERBOBM-TXICZTDVSA-N

InChI:

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

CAS number:

14075-00-4

IUPAC Name:

{[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic acid

Traditional IUPAC Name:

ribose 1-phosphate

SMILES:

OC[C@H]1O[C@H](OP(O)(O)=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
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Tetrahydrofuran
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

D-ribose 1-phosphate (CHEBI:16300 )

Physical Properties

State:

Solid

Charge:

-2

Melting point:

Not Available

Experimental Properties:

Property	Value	Source
LogP:	-2.919	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	35.2 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.4	ChemAxon
logS	-0.82	ALOGPS
pKa (Strongest Acidic)	1.16	ChemAxon
pKa (Strongest Basic)	-3	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	18.17 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:

SMPDB Pathways:

PRPP Biosynthesis	PW000909
Pyrimidine metabolism	PW000942
Pyrimidine ribonucleosides degradtion	PW002024
adenine and adenosine salvage I	PW002069
adenine and adenosine salvage II	PW002071
adenosine nucleotides degradation	PW002091
guanine and guanosine salvage	PW002074
purine ribonucleosides degradation	PW002076
pyrimidine ribonucleosides degradation	PW002104

KEGG Pathways:

Drug metabolism - other enzymes ec00983
Metabolic pathways eco01100
Nicotinate and nicotinamide metabolism ec00760
Pentose phosphate pathway ec00030
Purine metabolism ec00230
Pyrimidine metabolism ec00240

EcoCyc Pathways:

PRPP biosynthesis II PWY0-661
adenine and adenosine salvage III PWY-6609
adenine and adenosine salvage V PWY-6611
adenosine nucleotides degradation II SALVADEHYPOX-PWY
guanine and guanosine salvage I PWY-6620
guanosine nucleotides degradation III PWY-6608
purine ribonucleosides degradation to ribose-1-phosphate PWY0-1296
pyrimidine ribonucleosides degradation I PWY0-1295
salvage pathways of pyrimidine ribonucleotides PWY0-163
xanthine and xanthosine salvage SALVPURINE2-PWY

Concentrations

Concentration	Strain	Media	Growth Status	Growth System	Temperature	Details
1020± 0 uM	K12 NCM3722	Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glycerol	Mid-Log Phase	Shake flask and filter culture	37 oC	PMID: 19561621
686± 0 uM	K12 NCM3722	Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L acetate	Mid-Log Phase	Shake flask and filter culture	37 oC	PMID: 19561621
1320± 0 uM	K12 NCM3722	Gutnick minimal complete medium (4.7 g/L KH2PO4; 13.5 g/L K2HPO4; 1 g/L K2SO4; 0.1 g/L MgSO4-7H2O; 10 mM NH4Cl) with 4 g/L glucose	Mid-Log Phase	Shake flask and filter culture	37 oC	PMID: 19561621

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	splash10-0002-9110000000-add01bb15cc1fd9e2e29	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-014i-2931000000-fe633c386d1b3ab9db9a	View in MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	View in JSpectraViewer
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-0090000000-e2c9f6f60320b17dd479	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-01t9-9250000000-029c27941ed85100b53c	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-9000000000-311ca08c80d0a6c765da	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-9000000000-36d97c26c72c69ab56c6	View in MoNA
LC-MS/MS	LC-MS/MS Spectrum - LC-ESI-QQ , negative	splash10-004i-9000000000-08796c6cb24ecefd9abf	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-9230000000-bf825c0a48e8f3fb1db5	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-9330000000-af34500034734754adda	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0002-9000000000-ea509fab4675ba638745	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-9180000000-4449ca89ca00716d8cef	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9110000000-c74e6f3e6a87ec4b57fb	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-81a191a3e73e8031cb23	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0159-0900000000-6d6c0c7544f77dfb0c41	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00lr-7910000000-9441b177b385255d831b	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4m-9000000000-a9998928687caae44190	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-004i-3090000000-4bb2aedb7cfc3f4c2255	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-e5ae44d04fcc61ba1d70	View in MoNA
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-00ffef4ac2a980d6a310	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:

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
Giorgelli, F., Bottai, C., Mascia, L., Scolozzi, C., Camici, M., Ipata, P. L. (1997). "Recycling of alpha-D-ribose 1-phosphate for nucleoside interconversion." Biochim Biophys Acta 1335:6-22. Pubmed: 9133638
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
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:

Tochikura, Tatsurokuro; Sakai, Takuo; Ogata, Koichi. Ribose 1-phosphate production by fermentation. Jpn. Tokkyo Koho (1969), 3 pp.

Material Safety Data Sheet (MSDS)

Not Available

Links

External Links:

Resource	Link
CHEBI ID	16300
HMDB ID	HMDB01489
Pubchem Compound ID	123732
Kegg ID	C00620
ChemSpider ID	388373
Wikipedia ID	Not Available
BioCyc ID	RIBOSE-1P
EcoCyc ID	RIBOSE-1P
Ligand Expo	RDP

Enzymes

Protein Details

1. Phosphopentomutase

General function:: Involved in catalytic activity
Specific function:: Phosphotransfer between the C1 and C5 carbon atoms of pentose
Gene Name:: deoB
Uniprot ID:: P0A6K6
Molecular weight:: 44370

Reactions

Alpha-D-ribose 1-phosphate = D-ribose 5-phosphate.
2-deoxy-alpha-D-ribose 1-phosphate = 2-deoxy-alpha-D-ribose 5-phosphate.

Protein Details

2. Purine nucleoside phosphorylase deoD-type

General function:: Involved in purine-nucleoside phosphorylase activity
Specific function:: Cleavage of guanosine or inosine to respective bases and sugar-1-phosphate molecules
Gene Name:: deoD
Uniprot ID:: P0ABP8
Molecular weight:: 25950

Reactions

Purine nucleoside + phosphate = purine + alpha-D-ribose 1-phosphate.

Protein Details

3. Uridine phosphorylase

General function:: Involved in transferase activity, transferring pentosyl groups
Specific function:: Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1- phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis
Gene Name:: udp
Uniprot ID:: P12758
Molecular weight:: 27159

Reactions

Uridine + phosphate = uracil + alpha-D-ribose 1-phosphate.

Protein Details

4. 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
Uniprot ID:: P36938
Molecular weight:: 58361

Reactions

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

Protein Details

5. Xanthosine phosphorylase

General function:: Involved in purine-nucleoside phosphorylase activity
Specific function:: The nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the nucleoside molecule, with the formation of the corresponding free bases and pentose-1-phosphate. This protein can degrade all purine nucleosides except adenosine and deoxyadenosine
Gene Name:: xapA
Uniprot ID:: P45563
Molecular weight:: 29834

Protein Details

6. Uncharacterized protein yhfW

General function:: Involved in catalytic activity
Specific function:: Specific function unknown
Gene Name:: yhfW
Uniprot ID:: P45549
Molecular weight:: 44559

Ribose-1-phosphate (ECMDB04147) (M2MDB000637)

Structure for #<Compound:0xa06ade70>

Enzymes

Reactions

Reactions

Reactions

Reactions