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Chemical Compound Review

D-ribose     (2R,3R,4R)-2,3,4,5- tetrahydroxypentanal

Synonyms: Ribose, D-, AG-C-85362, AG-F-70659, CHEBI:47014, ANW-31099, ...
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Disease relevance of D-ribose


High impact information on D-ribose

  • PARP-1, an enzyme that catalyzes the attachment of ADP ribose units to target proteins, plays at least two important roles in transcription regulation [6].
  • This discovery implies that most snoRNAs function in targeting nucleotide modification in rRNA: ribose methylation for the box C/D snoRNAs and psi formation for the ACA snoRNAs [7].
  • Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs [8].
  • Translocation of polypeptides is a late event relative to extent of elongation, occurring only after maltose-binding protein has reached molecular weight 33,000 (80% of its entire length) and after ribose-binding protein has been fully elongated (molecular weight 29,000) [9].
  • These trg mutants are indistinguishable from their parent in tactic response to other attractants, swimming pattern, growth rates, and transport of ribose and galactose [1].

Chemical compound and disease context of D-ribose


Biological context of D-ribose

  • Sos does not impede the binding sites for the base and the ribose of GTP or GDP, so the Ras-Sos complex adopts a structure that allows nucleotide release and rebinding [15].
  • One candidate pathway is DNA damage leading to activation of the nuclear enzyme, poly(ADP-ribose) polymerase (PARP), which catalyzes attachment of ADP ribose units from NAD to nuclear proteins following DNA damage [16].
  • Surprisingly, this partition of aaRS in two classes is found to be strongly correlated on the functional level with the acylation occurring either on the 2' OH (class I) or 3' OH (class II) of the ribose of the last nucleotide of tRNA [17].
  • Late after induction, translocation of beta-lactamase was impaired; this may be an indirect effect of heat shock, however, because translocation of ribose binding protein or of the porin, OmpA, was unaffected [18].
  • The aminoacylation of synthetic tDNAs demonstrates that the ribose backbone of a tRNA is not absolutely required for tRNA aminoacylation [19].

Anatomical context of D-ribose


Associations of D-ribose with other chemical compounds


Gene context of D-ribose

  • The C and D box-containing snoRNAs are associated with fibrillarin, and most of them function as guide RNAs in site-specific ribose methylation of rRNAs [29].
  • MKP-1 was also found to inhibit other biochemical events associated with apoptosis, including activation of caspase-3 and the proteolytic cleavage of the caspase-3 substrate, poly(ADP ribose) polymerase [30].
  • It includes the 3' terminus of rbsB (the gene for ribose-binding protein) and the entire rbsK gene, encoding ribokinase [31].
  • Further analyses of the mutants revealed that the rbsK (ribokinase) and rbsD (function unknown) genes are involved in the ribose transport through PtsG, indicating that the phosphorylation of ribose is not mediated by PtsG and that some unknown metabolic function mediated by RbsD is required [32].
  • Transaldolase regulates redox-dependent apoptosis through controlling NADPH and ribose 5-phosphate production via the pentose phosphate pathway [33].

Analytical, diagnostic and therapeutic context of D-ribose


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  2. Mechanism of RNA polymerase II--specific initiation of transcription in vitro: ATP requirement and uncapped runoff transcripts. Bunick, D., Zandomeni, R., Ackerman, S., Weinmann, R. Cell (1982) [Pubmed]
  3. Glycation-dependent, reactive oxygen species-mediated suppression of the insulin gene promoter activity in HIT cells. Matsuoka, T., Kajimoto, Y., Watada, H., Kaneto, H., Kishimoto, M., Umayahara, Y., Fujitani, Y., Kamada, T., Kawamori, R., Yamasaki, Y. J. Clin. Invest. (1997) [Pubmed]
  4. Inhibition of the activity of poly(ADP ribose) synthetase reduces ischemia-reperfusion injury in the heart and skeletal muscle. Thiemermann, C., Bowes, J., Myint, F.P., Vane, J.R. Proc. Natl. Acad. Sci. U.S.A. (1997) [Pubmed]
  5. Crystal structure of the catalytic domain of Pseudomonas exotoxin A complexed with a nicotinamide adenine dinucleotide analog: implications for the activation process and for ADP ribosylation. Li, M., Dyda, F., Benhar, I., Pastan, I., Davies, D.R. Proc. Natl. Acad. Sci. U.S.A. (1996) [Pubmed]
  6. PARP goes transcription. Kraus, W.L., Lis, J.T. Cell (2003) [Pubmed]
  7. Small nucleolar RNAs direct site-specific synthesis of pseudouridine in ribosomal RNA. Ni, J., Tien, A.L., Fournier, M.J. Cell (1997) [Pubmed]
  8. Site-specific ribose methylation of preribosomal RNA: a novel function for small nucleolar RNAs. Kiss-László, Z., Henry, Y., Bachellerie, J.P., Caizergues-Ferrer, M., Kiss, T. Cell (1996) [Pubmed]
  9. Translocation of domains of nascent periplasmic proteins across the cytoplasmic membrane is independent of elongation. Randall, L.L. Cell (1983) [Pubmed]
  10. Modulation of folding pathways of exported proteins by the leader sequence. Park, S., Liu, G., Topping, T.B., Cover, W.H., Randall, L.L. Science (1988) [Pubmed]
  11. Defining the enzyme binding domain of a ribonuclease III processing signal. Ethylation interference and hydroxyl radical footprinting using catalytically inactive RNase III mutants. Li, H., Nicholson, A.W. EMBO J. (1996) [Pubmed]
  12. Identification of a methyl-accepting chemotaxis protein for the ribose and galactose chemoreceptors of Escherichia coli. Kondoh, H., Ball, C.B., Adler, J. Proc. Natl. Acad. Sci. U.S.A. (1979) [Pubmed]
  13. Human immunodeficiency virus type 1 (HIV-1) strains selected for resistance against the HIV-1-specific [2',5'-bis-O-(tert-butyldimethylsilyl)-3'-spiro- 5''-(4''-amino-1'',2''-oxathiole-2'',2''-dioxide)]-beta-D-pentofurano syl (TSAO) nucleoside analogues retain sensitivity to HIV-1-specific nonnucleoside inhibitors. Balzarini, J., Karlsson, A., Vandamme, A.M., Pérez-Pérez, M.J., Zhang, H., Vrang, L., Oberg, B., Bäckbro, K., Unge, T., San-Félix, A. Proc. Natl. Acad. Sci. U.S.A. (1993) [Pubmed]
  14. Enhanced poly(adenosine diphosphate ribose) polymerase activity and gene expression in Ewing's sarcoma cells. Prasad, S.C., Thraves, P.J., Bhatia, K.G., Smulson, M.E., Dritschilo, A. Cancer Res. (1990) [Pubmed]
  15. The structural basis of the activation of Ras by Sos. Boriack-Sjodin, P.A., Margarit, S.M., Bar-Sagi, D., Kuriyan, J. Nature (1998) [Pubmed]
  16. Poly(ADP-ribose) polymerase gene disruption renders mice resistant to cerebral ischemia. Eliasson, M.J., Sampei, K., Mandir, A.S., Hurn, P.D., Traystman, R.J., Bao, J., Pieper, A., Wang, Z.Q., Dawson, T.M., Snyder, S.H., Dawson, V.L. Nat. Med. (1997) [Pubmed]
  17. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Eriani, G., Delarue, M., Poch, O., Gangloff, J., Moras, D. Nature (1990) [Pubmed]
  18. An E. coli ribonucleoprotein containing 4.5S RNA resembles mammalian signal recognition particle. Poritz, M.A., Bernstein, H.D., Strub, K., Zopf, D., Wilhelm, H., Walter, P. Science (1990) [Pubmed]
  19. Aminoacylation of synthetic DNAs corresponding to Escherichia coli phenylalanine and lysine tRNAs. Khan, A.S., Roe, B.A. Science (1988) [Pubmed]
  20. Ribose metabolism and nucleic acid synthesis in normal and glucose-6-phosphate dehydrogenase-deficient human erythrocytes infected with Plasmodium falciparum. Roth, E.F., Ruprecht, R.M., Schulman, S., Vanderberg, J., Olson, J.A. J. Clin. Invest. (1986) [Pubmed]
  21. Effects of ribose on exercise-induced ischaemia in stable coronary artery disease. Pliml, W., von Arnim, T., Stäblein, A., Hofmann, H., Zimmer, H.G., Erdmann, E. Lancet (1992) [Pubmed]
  22. A signal sequence mutant defective in export of ribose-binding protein and a corresponding pseudorevertant isolated without imposed selection. Iida, A., Groarke, J.M., Park, S., Thom, J., Zabicky, J.H., Hazelbauer, G.L., Randall, L.L. EMBO J. (1985) [Pubmed]
  23. Prevention of tumorigenesis of oncogene-transformed rat fibroblasts with DNA site inhibitors of poly(ADP ribose) polymerase. Tseng, A., Lee, W.M., Jakobovits, E.B., Kirsten, E., Hakam, A., McLick, J., Buki, K., Kun, E. Proc. Natl. Acad. Sci. U.S.A. (1987) [Pubmed]
  24. Structure of poly(adenosine diphosphate ribose): identification of 2'-[1''-ribosyl-2''-(or 3''-)(1'''-ribosyl)]adenosine-5',5'',5'''-tris(phosphate) as a branch linkage. Miwa, M., Saikawa, N., Yamaizumi, Z., Nishimura, S., Sugimura, T. Proc. Natl. Acad. Sci. U.S.A. (1979) [Pubmed]
  25. Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs. Holbrook, S.R., Cheong, C., Tinoco, I., Kim, S.H. Nature (1991) [Pubmed]
  26. Ribose intervention in the cardiac pentose phosphate pathway is not species-specific. Zimmer, H.G., Ibel, H., Suchner, U., Schad, H. Science (1984) [Pubmed]
  27. Effects of naturally occurring sugars on Ehrlich ascites tumor growth in mice. Gonzalez, F., Amos, H. J. Natl. Cancer Inst. (1977) [Pubmed]
  28. Arabidopsis POLYOL TRANSPORTER5, a new member of the monosaccharide transporter-like superfamily, mediates H+-Symport of numerous substrates, including myo-inositol, glycerol, and ribose. Klepek, Y.S., Geiger, D., Stadler, R., Klebl, F., Landouar-Arsivaud, L., Lemoine, R., Hedrich, R., Sauer, N. Plant Cell (2005) [Pubmed]
  29. A small nucleolar RNP protein is required for pseudouridylation of eukaryotic ribosomal RNAs. Bousquet-Antonelli, C., Henry, Y., G'elugne, J.P., Caizergues-Ferrer, M., Kiss, T. EMBO J. (1997) [Pubmed]
  30. Conditional expression of mitogen-activated protein kinase phosphatase-1, MKP-1, is cytoprotective against UV-induced apoptosis. Franklin, C.C., Srikanth, S., Kraft, A.S. Proc. Natl. Acad. Sci. U.S.A. (1998) [Pubmed]
  31. Ribokinase from Escherichia coli K12. Nucleotide sequence and overexpression of the rbsK gene and purification of ribokinase. Hope, J.N., Bell, A.W., Hermodson, M.A., Groarke, J.M. J. Biol. Chem. (1986) [Pubmed]
  32. A mutated PtsG, the glucose transporter, allows uptake of D-ribose. Oh, H., Park, Y., Park, C. J. Biol. Chem. (1999) [Pubmed]
  33. ZNF143 mediates basal and tissue-specific expression of human transaldolase. Grossman, C.E., Qian, Y., Banki, K., Perl, A. J. Biol. Chem. (2004) [Pubmed]
  34. Influence of ribose, adenosine, and "AICAR" on the rate of myocardial adenosine triphosphate synthesis during reperfusion after coronary artery occlusion in the dog. Mauser, M., Hoffmeister, H.M., Nienaber, C., Schaper, W. Circ. Res. (1985) [Pubmed]
  35. Ribose. An oxidation product of glucose 6-phosphate in microsomal fraction. Hino, Y., Minakami, S. J. Biol. Chem. (1983) [Pubmed]
  36. Accumulation of advanced glycation end products as a molecular mechanism for aging as a risk factor in osteoarthritis. DeGroot, J., Verzijl, N., Wenting-van Wijk, M.J., Jacobs, K.M., Van El, B., Van Roermund, P.M., Bank, R.A., Bijlsma, J.W., TeKoppele, J.M., Lafeber, F.P. Arthritis Rheum. (2004) [Pubmed]
  37. Purification, crystallization, and properties of D-ribose isomerase from Mycobacterium smegmatis. Izumori, K., Rees, A.W., Elbein, A.D. J. Biol. Chem. (1975) [Pubmed]
  38. Nucleotide sequence of U-2 ribonucleic acid. The sequence of the 5'-terminal oligonucleotide. Ro-Choi, T.S., Choi, Y.C., Henning, D., McCloskey, J., Busch, H. J. Biol. Chem. (1975) [Pubmed]
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