Ribose (PAMDB000116)

IdentificationTaxonomyPhysical PropertiesBiological PropertiesSpectraConcentrationsLinksReferencesEnzymes Transporters
Proteins (3280)
Record Information
Version 1.0
Update Date 1/22/2018 12:54:54 PM
Metabolite IDPAMDB000116
Identification
Name: Ribose
Description:Ribose is a pentose that is actively used in many biological systems usually in its D-form. Ribose constitutes the backbone of RNA, a biopolymer that is the basis of genetic transcription. It is related to deoxyribose, as found in DNA. Once phosphorylated, ribose can become a subunit of ATP, NADH, and several other compounds that are critical to metabolism like the secondary messengers cAMP and cGMP. In cells D-ribose must be phosphorylated before it can be used. Ribokinase catalyzes this reaction by converting D-ribose to D-ribose 5-phosphate.
Structure
Thumb
🔍MOLSDFPDBSMILESInChIView Structure
Synonyms:
  • 5-Methylthio-D-ribose
  • 5-Methylthioribose
  • a-D-Ribose
  • a-D-Ribose-5
  • a-delta-Ribose
  • a-delta-Ribose-5
  • a-δ-Ribose
  • a-δ-Ribose-5
  • Alpha-D-Ribose
  • Alpha-D-Ribose-5
  • Alpha-delta-Ribose
  • Alpha-delta-Ribose-5
  • D-(-)-Ribose
  • D-Ribo-2,3,4,5-tetrahydroxyvaleraldehyde
  • D-Ribose
  • Delta-(-)-Ribose
  • Delta-Ribo-2,3,4,5-tetrahydroxyvaleraldehyde
  • Delta-Ribose
  • MTR
  • Pentose
  • Ribose
  • S-Methyl-5-thio-D-ribofuranose
  • α-D-Ribose
  • α-D-Ribose-5
  • α-δ-Ribose
  • α-δ-Ribose-5
  • δ-(-)-Ribose
  • δ-ribo-2,3,4,5-Tetrahydroxyvaleraldehyde
  • δ-Ribose
Chemical Formula: C5H10O5
Average Molecular Weight: 150.1299
Monoisotopic Molecular Weight: 150.05282343
InChI Key: HMFHBZSHGGEWLO-SOOFDHNKSA-N
InChI:InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5?/m1/s1
CAS number: 50-69-1
IUPAC Name:(3R,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol
Traditional IUPAC Name: D-ribofuranoside
SMILES:OC[C@H]1OC(O)[C@H](O)[C@@H]1O
Chemical Taxonomy
Taxonomy DescriptionThis compound belongs to the class of organic compounds known as monosaccharides. These are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn.
Kingdom Organic compounds
Super ClassOrganooxygen compounds
Class Carbohydrates and carbohydrate conjugates
Sub ClassMonosaccharides
Direct Parent Monosaccharides
Alternative Parents
Substituents
  • Monosaccharide
  • Oxolane
  • Secondary alcohol
  • Polyol
  • Hemiacetal
  • 1,2-diol
  • Oxacycle
  • Organoheterocyclic compound
  • Hydrocarbon derivative
  • Primary alcohol
  • Alcohol
  • Aliphatic heteromonocyclic compound
Molecular Framework Aliphatic heteromonocyclic compounds
External Descriptors
Physical Properties
State: Not Available
Charge:0
Melting point: Not Available
Experimental Properties:
PropertyValueSource
LogP:-2.188PhysProp
Predicted Properties
PropertyValueSource
Water Solubility1070.0 mg/mLALOGPS
logP-2.6ALOGPS
logP-2.3ChemAxon
logS0.85ALOGPS
pKa (Strongest Acidic)11.31ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count4ChemAxon
Polar Surface Area90.15 Å2ChemAxon
Rotatable Bond Count1ChemAxon
Refractivity29.96 m3·mol-1ChemAxon
Polarizability13.68 Å3ChemAxon
Number of Rings1ChemAxon
Bioavailability1ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations: Cytoplasm
Reactions:
Adenosine triphosphate + Water + Ribose > ADP + Hydrogen ion + Phosphate + Ribose
Adenosine triphosphate + Water + Ribose > ADP + Hydrogen ion + Phosphate + Ribose
Cytidine + Water > Cytosine + Ribose
Water + Uridine > Ribose + Uracil
Adenosine + Water > Adenine + Ribose
Water + Inosine > Hypoxanthine + Ribose
Water + Xanthosine > Ribose + Xanthine
Water + D-Ribose-5-phosphate > Phosphate + Ribose
Adenosine triphosphate + Ribose <> ADP + Hydrogen ion + D-Ribose-5-phosphate
Adenosine triphosphate + Ribose <> ADP + D-Ribose-5-phosphate
Guanosine + Water <> Guanine + Ribose
A pyrimidine nucleoside + Water > Ribose + a pyrimidine base
Pyrimidine nucleoside + Water <> Ribose + Pyrimidine
Pathways:
Spectra
Spectra:
Spectrum TypeDescriptionSplash Key
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-0udi-0920000000-c414574c94624914be8cView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-0fk9-9831000000-d0b33cef6c46219ea9a8View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-0udi-0920000000-e3647dbf79b8733c3bfdView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-0udi-0921000000-e8a202c64cf867b21cefView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-0udi-0920000000-272c588a02a550b79c74View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-0ldi-0941000000-999cd264e51df6d784b4View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS)splash10-0udi-0910000000-54f42f17ff952d787b86View in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies)splash10-0uxr-0920000000-d29b5079ba0fde220b0dView in MoNA
GC-MSGC-MS Spectrum - GC-EI-TOF (Pegasus III TOF-MS system, Leco; GC 6890, Agilent Technologies) (4 TMS; 1 MEOX)splash10-0fk9-8920000000-71080ebc024c820bf8fdView in MoNA
GC-MSGC-MS Spectrum - GC-MSNot Available
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 10V, Positive (Annotated)splash10-014r-4900000000-76daa3235c9f82ef4f5aView in MoNA
LC-MS/MSLC-MS/MS Spectrum - Quattro_QQQ 25V, Positive (Annotated)splash10-000i-9100000000-b44f013dcb4efe64039dView in MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, PositiveNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, NegativeNot Available
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, NegativeNot Available
1D NMR1H NMR SpectrumNot Available
2D NMR[1H,13C] 2D NMR SpectrumNot Available
References
References:
  • Abe H, Tanuma S: Properties of poly(ADP-ribose) glycohydrolase purified from pig testis nuclei. Arch Biochem Biophys. 1996 Dec 1;336(1):139-46. Pubmed: 8951044
  • Alexy T, Toth A, Marton Z, Horvath B, Koltai K, Feher G, Kesmarky G, Kalai T, Hideg K, Sumegi B, Toth K: Inhibition of ADP-evoked platelet aggregation by selected poly(ADP-ribose) polymerase inhibitors. J Cardiovasc Pharmacol. 2004 Mar;43(3):423-31. Pubmed: 15076227
  • Augustin A, Muller-Steffner H, Schuber F: Molecular cloning and functional expression of bovine spleen ecto-NAD+ glycohydrolase: structural identity with human CD38. Biochem J. 2000 Jan 1;345 Pt 1:43-52. Pubmed: 10600637
  • Boros LG, Steinkamp MP, Fleming JC, Lee WN, Cascante M, Neufeld EJ: Defective RNA ribose synthesis in fibroblasts from patients with thiamine-responsive megaloblastic anemia (TRMA). Blood. 2003 Nov 15;102(10):3556-61. Epub 2003 Jul 31. Pubmed: 12893755
  • Carloto A, Costas MJ, Cameselle JC, McLennan AG, Ribeiro JM: The specific, submicromolar-Km ADP-ribose pyrophosphatase purified from human placenta is enzymically indistinguishable from recombinant NUDT9 protein, including a selectivity for Mn2+ as activating cation and increase in Km for ADP-ribose, both elicited by H2O2. Biochim Biophys Acta. 2006 Oct;1760(10):1545-51. Epub 2006 Jun 9. Pubmed: 16860484
  • Cheng C, Zochodne DW: Sensory neurons with activated caspase-3 survive long-term experimental diabetes. Diabetes. 2003 Sep;52(9):2363-71. Pubmed: 12941777
  • Dancis J, Lee J, Mendoza S, Liebes L: Nucleoside transport by perfused human placenta. Placenta. 1993 Sep-Oct;14(5):547-54. Pubmed: 8290494
  • Dhanoa TS, Housner JA: Ribose: more than a simple sugar? Curr Sports Med Rep. 2007 Jul;6(4):254-7. Pubmed: 17618002
  • Dodd SL, Johnson CA, Fernholz K, St Cyr JA: The role of ribose in human skeletal muscle metabolism. Med Hypotheses. 2004;62(5):819-24. Pubmed: 15082114
  • Drel VR, Pacher P, Stevens MJ, Obrosova IG: Aldose reductase inhibition counteracts nitrosative stress and poly(ADP-ribose) polymerase activation in diabetic rat kidney and high-glucose-exposed human mesangial cells. Free Radic Biol Med. 2006 Apr 15;40(8):1454-65. Epub 2006 Jan 31. Pubmed: 16631535
  • Genovese T, Mazzon E, Di Paola R, Muia C, Crisafulli C, Caputi AP, Cuzzocrea S: ROLE OF ENDOGENOUS AND EXOGENOUS LIGANDS FOR THE PEROXISOME PROLIFERATOR-ACTIVATED RECEPTOR alpha IN THE DEVELOPMENT OF BLEOMYCIN-INDUCED LUNG INJURY. Shock. 2005 Dec;24(6):547-55. Pubmed: 16317386
  • Jacobson EL, Giacomoni PU, Roberts MJ, Wondrak GT, Jacobson MK: Optimizing the energy status of skin cells during solar radiation. J Photochem Photobiol B. 2001 Oct;63(1-3):141-7. Pubmed: 11684461
  • Jiang Q, Wong J, Fyrst H, Saba JD, Ames BN: gamma-Tocopherol or combinations of vitamin E forms induce cell death in human prostate cancer cells by interrupting sphingolipid synthesis. Proc Natl Acad Sci U S A. 2004 Dec 21;101(51):17825-30. Epub 2004 Dec 13. Pubmed: 15596715
  • 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
  • McNealy T, Frey M, Trojan L, Knoll T, Alken P, Michel MS: Intrinsic presence of poly (ADP-ribose) is significantly increased in malignant prostate compared to benign prostate cell lines. Anticancer Res. 2003 Mar-Apr;23(2B):1473-8. Pubmed: 12820412
  • Okamoto H: The Reg gene family and Reg proteins: with special attention to the regeneration of pancreatic beta-cells. J Hepatobiliary Pancreat Surg. 1999;6(3):254-62. Pubmed: 10526060
  • Quadrilatero J, Rush JW: Increased DNA fragmentation and altered apoptotic protein levels in skeletal muscle of spontaneously hypertensive rats. J Appl Physiol. 2006 Oct;101(4):1149-61. Epub 2006 Jun 15. Pubmed: 16778006
  • Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4. Pubmed: 19212411
  • Szabo E, Virag L, Bakondi E, Gyure L, Hasko G, Bai P, Hunyadi J, Gergely P, Szabo C: Peroxynitrite production, DNA breakage, and poly(ADP-ribose) polymerase activation in a mouse model of oxazolone-induced contact hypersensitivity. J Invest Dermatol. 2001 Jul;117(1):74-80. Pubmed: 11442752
  • Takeda Y, Usukura M, Yoneda T, Oda N, Ito Y, Mabuchi H: The expression of messenger RNA for ADP-ribosyl cyclase in aldosterone-producing adenomas. Clin Endocrinol (Oxf). 2005 Apr;62(4):504-8. Pubmed: 15807884
  • Tamagno E, Parola M, Bardini P, Piccini A, Borghi R, Guglielmotto M, Santoro G, Davit A, Danni O, Smith MA, Perry G, Tabaton M: Beta-site APP cleaving enzyme up-regulation induced by 4-hydroxynonenal is mediated by stress-activated protein kinases pathways. J Neurochem. 2005 Feb;92(3):628-36. Pubmed: 15659232
  • Thomas D, Yang H, Boffa DJ, Ding R, Sharma VK, Lagman M, Li B, Hering B, Mohanakumar T, Lakey J, Kapur S, Hancock WW, Suthanthiran M: Proapoptotic Bax is hyperexpressed in isolated human islets compared with antiapoptotic Bcl-2. Transplantation. 2002 Dec 15;74(11):1489-96. Pubmed: 12490780
  • Toth O, Szabo C, Kecskes M, Poto L, Nagy A, Losonczy H: In vitro effect of the potent poly(ADP-ribose) polymerase (PARP) inhibitor INO-1001 alone and in combination with aspirin, eptifibatide, tirofiban, enoxaparin or alteplase on haemostatic parameters. Life Sci. 2006 Jun 20;79(4):317-23. Epub 2006 Feb 9. Pubmed: 16480745
  • 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
  • Wall KA, Klis M, Kornet J, Coyle D, Ame JC, Jacobson MK, Slama JT: Inhibition of the intrinsic NAD+ glycohydrolase activity of CD38 by carbocyclic NAD analogues. Biochem J. 1998 Nov 1;335 ( Pt 3):631-6. Pubmed: 9794804
  • 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
  • Wurzer G, Herceg Z, Wesierska-Gadek J: Increased resistance to anticancer therapy of mouse cells lacking the poly(ADP-ribose) polymerase attributable to up-regulation of the multidrug resistance gene product P-glycoprotein. Cancer Res. 2000 Aug 1;60(15):4238-44. Pubmed: 10945636
Synthesis Reference: Park, Yong-Cheol; Choi, Jin-Ho; Bennett, George N.; Seo, Jin-Ho. Characterization of D-ribose biosynthesis in Bacillus subtilis JY200 deficient in transketolase gene. Journal of Biotechnology (2006), 121(4), 508-516.
Material Safety Data Sheet (MSDS) Download (PDF)
External Links:
ResourceLink
CHEBI ID47013
HMDB IDHMDB00283
Pubchem Compound ID5779
Kegg IDC00121
ChemSpider ID5575
WikipediaRibose
BioCyc IDNot Available

Enzymes

Protein Details
• 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
Locus Tag:
PA1947
Molecular weight:
55.8 kDa
Reactions
ATP + H(2)O + monosaccharide(Out) = ADP + phosphate + monosaccharide(In).
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
• 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
• 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
Locus Tag:
PA1948
Molecular weight:
34 kDa
Protein Details
• 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
Locus Tag:
PA1946
Molecular weight:
33.9 kDa

Transporters

Protein Details
• 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
Locus Tag:
PA1947
Molecular weight:
55.8 kDa
Reactions
ATP + H(2)O + monosaccharide(Out) = ADP + phosphate + monosaccharide(In).
Protein Details
• 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
Locus Tag:
PA1948
Molecular weight:
34 kDa
Protein Details
• 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
Locus Tag:
PA1946
Molecular weight:
33.9 kDa