2.0 2012-05-31 13:55:08 -0600 2015-09-16 14:50:11 -0600 ECMDB02033 M2MDB000431 D-Ribose-5-phosphate 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) &alpha;-D-ribose-5-phosphate &alpha;-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 C5H11O8P 230.1098 230.01915384 {[(2R,3S,4R)-3,4,5-trihydroxyoxolan-2-yl]methoxy}phosphonic acid D-ribofuranose 5-phosphate 4151-19-3 OC1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O 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 KTVPXOYAKDPRHY-SOOFDHNKSA-N Cytosol Extra-organism Periplasm logp -2.07 ALOGPS logs -0.84 ALOGPS solubility 3.36e+01 g/l ALOGPS logp -2.4 ChemAxon pka_strongest_acidic 1.22 ChemAxon pka_strongest_basic -3.7 ChemAxon iupac {[(2R,3S,4R)-3,4,5-trihydroxyoxolan-2-yl]methoxy}phosphonic acid ChemAxon average_mass 230.1098 ChemAxon mono_mass 230.01915384 ChemAxon smiles OC1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O ChemAxon formula C5H11O8P ChemAxon 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 ChemAxon inchikey KTVPXOYAKDPRHY-SOOFDHNKSA-N ChemAxon polar_surface_area 136.68 ChemAxon refractivity 40.83 ChemAxon polarizability 18.21 ChemAxon rotatable_bond_count 3 ChemAxon acceptor_count 7 ChemAxon donor_count 5 ChemAxon physiological_charge -2 ChemAxon formal_charge 0 ChemAxon Pentose phosphate pathway ec00030 Purine metabolism ec00230 Carbon fixation in photosynthetic organisms ec00710 Fructose and mannose metabolism ec00051 Biosynthesis of ansamycins ec01051 Microbial metabolism in diverse environments ec01120 Metabolic pathways eco01100 PRPP Biosynthesis The biosynthesis of phosphoribosyl pyrophosphate begins with a product of the pentose phosphate, D-ribose 5-phosphate interact with a phosphopentomutase resulting in a Ribose 1-phosphate or it can be phosphorylated through an ATP driven ribose-phosphate diphosphokinase resulting in a release of a hydrogen ion, an AMP and a phosphoribosyl pyrophosphate. The latter compound is then involved in the purine nucleotides de novo biosynthesis pathway. Ribose 1-phosphate can interact spontaneously with ATP resulting in a release of hydrogen ion, ADP and a ribose 1,5-biphosphate. The latter compound is then phosphorylated through a ribose 1,5-bisphosphokinase resulting in the release of ADP and phosphoribosyl pyrophosphate. The latter compound is then involved in the purine nucleotides de novo biosynthesis pathway. PW000909 Metabolic Pentose Phosphate PW000893 Metabolic Pyrimidine ribonucleosides degradtion Cytidine and Uridine are transported through their corresponding nucleoside hydrogen symporters . Once cytidine is incorporated into the cytosol, it is deaminated through a reaction with water and a hydrogen ion through a cytidine deaminase resulting in the release of ammonium and uridine. Uridine is then lyase by a phosphate through a uridine phosphorylase resulting in the release of a uracil and a alpha-D-ribose-1-phosphate. This compound is then transformed into an isomer D-ribose 5-phosphate through a alpha-D-ribose 1,5-phosphomutase. This cumpound is then incorporated into the pentose phosphate pathway PW002024 Metabolic adenine and adenosine salvage III Adenosine is first incorporated into the cytosol through either a nupG or a nupC transporter. Once in the cytosol, adenosine is degraded into adenine by reacting with a water and a adenosine nucleosidase, releasing a D-ribofuranose and a adenine. The adenine then reacts with a PRPP through a adenine phosphoribosyltransferase resulting in the release of a pyrophosphate and an AMP PW002072 Metabolic purine ribonucleosides degradation Purine ribonucleoside degradation leads to the production of alpha-D-ribose-1-phosphate. Xanthosine is transported into the cytosol through a xapB. Once in the cytosol xanthosine interacts with phosphate through a xanthosine phosphorylase resulting in the release of a xanthine and a alpha-D-ribose-1-phosphate. Adenosine is transported through a nupC or a nupG transporter, once inside the cytosol it can either react with a phosphate through a adenosine phosphorylase resultin in the release of a adenine and an alpha-D-ribose-1-phosphate. Adenosine reacts with water and hydrogen ion through a adenosine deaminase resulting in the release of ammonium and inosine. Inosine reacts with phosphate through a inosine phosphorylase resulting in the release of a hypoxanthine and an alpha-D-ribose-1-phosphate. Guanosine reacts with a phosphate through a guanosine phosphorylase resulting in the release of a guanine and a alpha-D-ribose-1-phosphate. PW002076 Metabolic Ribose Degradation D-ribose, which can serve as a total source of carbon and energy for E. coli, enters the cell via a high-affinity ABC transport system and hence in unphosphorylated form. The crystal structure of the periplasmic ribose binding protein of the ribose ABC transporter showed it to bind (and thus presumably to facilitate transport of) β-D-ribopyranose. ribose pyranase accelerates the conversion between the pyranose and furanose forms of β-D-ribose. Interconversion of the α- and β-anomers of D-ribofuranose is fast and spontaneous. ribokinase then converts it to D-ribose 5-phosphate, an intermediate of the pentose phosphate pathway, and hence it flows through the pathways of central metabolism to satisfy the cell's need for precursor metabolites, reducing power, and metabolic energy. (EcoCyc) PW002102 Metabolic pyrimidine ribonucleosides degradation The degradation of pyrimidine ribonucleosides starts with either cytidine or uridine being transported into the cytosol. Cytidine is transported into the cytosol through an nupG transporter. Once inside the cytosol, it can be degraded into uridine by reacting with water and ahydrogen ion through a cytidine deaminase resulting in the release of ammonium and uridine. Uridine is transported into the cytosol through a nupG. Once in the cytosol , uridine can be degrade by reacting with phosphate through a uridine phosphorylase resulting in the release of an alpha-D-ribose-1-phosphate and a uracil. The alpha-D-ribose-1-phosphate reacts with an alpha-d-ribose 1,5-phosphomutase resulting in the release of a D-ribose 5-phosphate which can be incorporated into the pentose phosphate pathway. PW002104 Metabolic purine ribonucleosides degradation to ribose-1-phosphate PWY0-1296 adenosine nucleotides degradation III PWY-6617 PRPP biosynthesis I PWY0-662 NAD salvage pathway I PYRIDNUCSAL-PWY pyrimidine ribonucleosides degradation I PWY0-1295 pentose phosphate pathway (non-oxidative branch) NONOXIPENT-PWY PRPP biosynthesis II PWY0-661 ribose degradation RIBOKIN-PWY Specdb::CMs 762 Specdb::CMs 763 Specdb::CMs 764 Specdb::CMs 765 Specdb::CMs 3226 Specdb::CMs 30351 Specdb::CMs 30352 Specdb::CMs 30784 Specdb::CMs 30785 Specdb::CMs 38120 Specdb::NmrOneD 1731 Specdb::NmrOneD 318711 Specdb::NmrOneD 318712 Specdb::NmrOneD 318713 Specdb::NmrOneD 318714 Specdb::NmrOneD 318715 Specdb::NmrOneD 318716 Specdb::NmrOneD 318717 Specdb::NmrOneD 318718 Specdb::NmrOneD 318719 Specdb::NmrOneD 318720 Specdb::NmrOneD 318721 Specdb::NmrOneD 318722 Specdb::NmrOneD 318723 Specdb::NmrOneD 318724 Specdb::NmrOneD 318725 Specdb::NmrOneD 318726 Specdb::NmrOneD 318727 Specdb::NmrOneD 318728 Specdb::NmrOneD 318729 Specdb::NmrOneD 318730 Specdb::MsMs 1649 Specdb::MsMs 1650 Specdb::MsMs 5395 Specdb::MsMs 5396 Specdb::MsMs 5397 Specdb::MsMs 5398 Specdb::MsMs 5403 Specdb::MsMs 179718 Specdb::MsMs 179719 Specdb::MsMs 179720 Specdb::MsMs 182052 Specdb::MsMs 182053 Specdb::MsMs 182054 Specdb::MsMs 438832 Specdb::MsMs 438833 Specdb::MsMs 438834 Specdb::MsMs 439063 Specdb::NmrTwoD 1083 Specdb::NmrTwoD 1672 HMDB01548 388313 C00117 17797 RIBOSE-5P D-ribose-5-P 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. 21097882 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. 22080510 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. 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. 18331064 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. 19561621 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. 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. 6699001 http://hmdb.ca/system/metabolites/msds/000/001/402/original/HMDB01548.pdf?1358461502 Phosphopentomutase P0A6K6 DEOB_ECOLI deoB http://ecmdb.ca/proteins/P0A6K6.xml Ribose-phosphate pyrophosphokinase P0A717 KPRS_ECOLI prs http://ecmdb.ca/proteins/P0A717.xml Ribose-5-phosphate isomerase A P0A7Z0 RPIA_ECOLI rpiA http://ecmdb.ca/proteins/P0A7Z0.xml Ribokinase P0A9J6 RBSK_ECOLI rbsK http://ecmdb.ca/proteins/P0A9J6.xml AMP nucleosidase P0AE12 AMN_ECOLI amn http://ecmdb.ca/proteins/P0AE12.xml Class B acid phosphatase P0AE22 APHA_ECOLI aphA http://ecmdb.ca/proteins/P0AE22.xml Transketolase 1 P27302 TKT1_ECOLI tktA http://ecmdb.ca/proteins/P27302.xml Transketolase 2 P33570 TKT2_ECOLI tktB http://ecmdb.ca/proteins/P33570.xml Phosphoglucomutase P36938 PGM_ECOLI pgm http://ecmdb.ca/proteins/P36938.xml Ribose-5-phosphate isomerase B P37351 RPIB_ECOLI rpiB http://ecmdb.ca/proteins/P37351.xml Sugar phosphatase supH P75792 SUPH_ECOLI supH http://ecmdb.ca/proteins/P75792.xml ADP-ribose pyrophosphatase Q93K97 ADPP_ECOLI nudF http://ecmdb.ca/proteins/Q93K97.xml ADP compounds hydrolase nudE P45799 NUDE_ECOLI nudE http://ecmdb.ca/proteins/P45799.xml Uncharacterized protein yhfW P45549 YHFW_ECOLI yhfW http://ecmdb.ca/proteins/P45549.xml Outer membrane protein N P77747 OMPN_ECOLI ompN http://ecmdb.ca/proteins/P77747.xml Outer membrane pore protein E P02932 PHOE_ECOLI phoE http://ecmdb.ca/proteins/P02932.xml Outer membrane protein F P02931 OMPF_ECOLI ompF http://ecmdb.ca/proteins/P02931.xml Outer membrane protein C P06996 OMPC_ECOLI ompC http://ecmdb.ca/proteins/P06996.xml D-Ribose-5-phosphate <> D-Ribulose 5-phosphate R01056 RIB5PISOM-RXN D-Ribose-5-phosphate + Xylulose 5-phosphate <> D-Glyceraldehyde 3-phosphate + D-Sedoheptulose 7-phosphate 1TRANSKETO-RXN Ribose-1-phosphate <> D-Ribose-5-phosphate PPENTOMUT-RXN Adenosine diphosphate ribose + Water <> Adenosine monophosphate +2 Hydrogen ion + D-Ribose-5-phosphate R01054 RXN0-1441 Water + D-Ribose-5-phosphate > Phosphate + Ribose Adenosine triphosphate + D-Ribose-5-phosphate <> Adenosine monophosphate + Hydrogen ion + Phosphoribosyl pyrophosphate R01049 PRPPSYN-RXN Adenosine monophosphate + Water <> Adenine + D-Ribose-5-phosphate R00182 AMP-NUCLEOSID-RXN Adenosine triphosphate + Ribose <> ADP + Hydrogen ion + D-Ribose-5-phosphate R01051 Adenosine triphosphate + D-Ribose-5-phosphate <> Adenosine monophosphate + Phosphoribosyl pyrophosphate R01049 Adenosine triphosphate + Ribose <> ADP + D-Ribose-5-phosphate R01051 Adenosine diphosphate ribose + Water <> Adenosine monophosphate + D-Ribose-5-phosphate R01054 D-Ribose-5-phosphate <> D-Ribulose 5-phosphate R01056 alpha-D-Ribose 1-phosphate + Ribose-1-phosphate <> D-Ribose-5-phosphate R01057 Sedoheptulose 7-phosphate + D-Glyceraldehyde 3-phosphate + D-Sedoheptulose 7-phosphate <> D-Ribose-5-phosphate + Xylulose 5-phosphate R01641 Aminofructose 6-phosphate + D-Ribose-5-phosphate <> Iminoerythrose 4-phosphate + Sedoheptulose 7-phosphate R06590 D-Sedoheptulose 7-phosphate + D-Glyceraldehyde 3-phosphate <> D-Ribose-5-phosphate + Xylulose 5-phosphate 1TRANSKETO-RXN Water + Adenosine monophosphate > D-Ribose-5-phosphate + Adenine AMP-NUCLEOSID-RXN Water + Nicotinamide ribotide <> Hydrogen ion + D-Ribose-5-phosphate + Niacinamide NMNNUCLEOSID-RXN D-ribose + Adenosine triphosphate > Hydrogen ion + D-Ribose-5-phosphate + ADP RIBOKIN-RXN Adenosine diphosphate ribose + Water > Hydrogen ion + Adenosine monophosphate + D-Ribose-5-phosphate RXN0-1441 D-Ribose-5-phosphate + Uracil <> Water + Pseudouridine 5'-phosphate RXN0-5398 Adenosine diphosphate ribose + Water > Adenosine monophosphate + D-Ribose-5-phosphate Ribose-1-phosphate > D-Ribose-5-phosphate Adenosine triphosphate + D-Ribose-5-phosphate > Adenosine monophosphate + Phosphoribosyl pyrophosphate Pseudouridine 5'-phosphate + Water > Uracil + D-Ribose-5-phosphate RXN0-5398 Adenosine triphosphate + Ribose > ADP + D-Ribose-5-phosphate D-Ribose-5-phosphate > D-Ribulose 5-phosphate Sedoheptulose 7-phosphate + D-Glyceraldehyde 3-phosphate > D-Ribose-5-phosphate + Xylulose 5-phosphate D-Ribulose 5-phosphate <> D-Ribose-5-phosphate PW_R003342 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 PW_R003345 D-Ribose-5-phosphate + Adenosine triphosphate > Hydrogen ion + Adenosine monophosphate + Phosphoribosyl pyrophosphate PW_R003406 D-Ribose-5-phosphate > Ribose-1-phosphate PW_R003407 Ribose + Adenosine triphosphate > D-Ribose-5-phosphate + ADP + Hydrogen ion PW_R006131 D-Ribose-5-phosphate <> D-Ribulose 5-phosphate Adenosine triphosphate + Ribose <> ADP + Hydrogen ion + D-Ribose-5-phosphate Adenosine monophosphate + Water <> Adenine + D-Ribose-5-phosphate Adenosine triphosphate + D-Ribose-5-phosphate <> Adenosine monophosphate + Hydrogen ion + Phosphoribosyl pyrophosphate Adenosine diphosphate ribose + Water <> Adenosine monophosphate +2 Hydrogen ion + D-Ribose-5-phosphate D-Ribose-5-phosphate <> D-Ribulose 5-phosphate Adenosine triphosphate + Ribose <> ADP + Hydrogen ion + D-Ribose-5-phosphate 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 Shake flask and filter culture 1020.0 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 4080000 0 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. 19561621 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 Shake flask and filter culture 686.0 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 2744000 0 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. 19561621 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 Shake flask and filter culture 1320.0 uM 0.0 37 oC K12 NCM3722 Mid-Log Phase 5280000 0 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. 19561621