2.0 2012-05-31 10:25:29 -0600 2015-09-13 15:15:18 -0600 ECMDB00283 M2MDB000116 Ribose 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. 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 C5H10O5 150.1299 150.05282343 (3R,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol D-ribofuranoside 50-69-1 OC[C@H]1OC(O)[C@H](O)[C@@H]1O InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5?/m1/s1 HMFHBZSHGGEWLO-SOOFDHNKSA-N Cytosol Extra-organism Periplasm logp -2.65 ALOGPS logs 0.85 ALOGPS solubility 1.07e+03 g/l ALOGPS logp -2.3 ChemAxon pka_strongest_acidic 11.31 ChemAxon pka_strongest_basic -3 ChemAxon iupac (3R,4S,5R)-5-(hydroxymethyl)oxolane-2,3,4-triol ChemAxon average_mass 150.1299 ChemAxon mono_mass 150.05282343 ChemAxon smiles OC[C@H]1OC(O)[C@H](O)[C@@H]1O ChemAxon formula C5H10O5 ChemAxon inchi InChI=1S/C5H10O5/c6-1-2-3(7)4(8)5(9)10-2/h2-9H,1H2/t2-,3-,4-,5?/m1/s1 ChemAxon inchikey HMFHBZSHGGEWLO-SOOFDHNKSA-N ChemAxon polar_surface_area 90.15 ChemAxon refractivity 29.96 ChemAxon polarizability 13.68 ChemAxon rotatable_bond_count 1 ChemAxon acceptor_count 5 ChemAxon donor_count 4 ChemAxon physiological_charge 0 ChemAxon formal_charge 0 ChemAxon Pentose phosphate pathway ec00030 Purine metabolism ec00230 Pyrimidine metabolism The metabolism of pyrimidines begins with L-glutamine interacting with water molecule and a hydrogen carbonate through an ATP driven carbamoyl phosphate synthetase resulting in a hydrogen ion, an ADP, a phosphate, an L-glutamic acid and a carbamoyl phosphate. The latter compound interacts with an L-aspartic acid through a aspartate transcarbamylase resulting in a phosphate, a hydrogen ion and a N-carbamoyl-L-aspartate. The latter compound interacts with a hydrogen ion through a dihydroorotase resulting in the release of a water molecule and a 4,5-dihydroorotic acid. This compound interacts with an ubiquinone-1 through a dihydroorotate dehydrogenase, type 2 resulting in a release of an ubiquinol-1 and an orotic acid. The orotic acid then interacts with a phosphoribosyl pyrophosphate through a orotate phosphoribosyltransferase resulting in a pyrophosphate and an orotidylic acid. The latter compound then interacts with a hydrogen ion through an orotidine-5 '-phosphate decarboxylase, resulting in an release of carbon dioxide and an Uridine 5' monophosphate. The Uridine 5' monophosphate process to get phosphorylated by an ATP driven UMP kinase resulting in the release of an ADP and an Uridine 5--diphosphate. Uridine 5-diphosphate can be metabolized in multiple ways in order to produce a Deoxyuridine triphosphate. 1.-Uridine 5-diphosphate interacts with a reduced thioredoxin through a ribonucleoside diphosphate reductase 1 resulting in the release of a water molecule and an oxidized thioredoxin and an dUDP. The dUDP is then phosphorylated by an ATP through a nucleoside diphosphate kinase resulting in the release of an ADP and a DeoxyUridine triphosphate. 2.-Uridine 5-diphosphate interacts with a reduced NrdH glutaredoxin-like protein through a Ribonucleoside-diphosphate reductase 1 resulting in a release of a water molecule, an oxidized NrdH glutaredoxin-like protein and a dUDP. The dUDP is then phosphorylated by an ATP through a nucleoside diphosphate kinase resulting in the release of an ADP and a DeoxyUridine triphosphate. 3.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate. The latter compound interacts with a reduced flavodoxin through ribonucleoside-triphosphate reductase resulting in the release of an oxidized flavodoxin, a water molecule and a Deoxyuridine triphosphate 4.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate The uridine triphosphate interacts with a L-glutamine and a water molecule through an ATP driven CTP synthase resulting in an ADP, a phosphate, a hydrogen ion, an L-glutamic acid and a cytidine triphosphate. The cytidine triphosphate interacts with a reduced flavodoxin through a ribonucleoside-triphosphate reductase resulting in the release of a water molecule, an oxidized flavodoxin and a dCTP. The dCTP interacts with a water molecule and a hydrogen ion through a dCTP deaminase resulting in a release of an ammonium molecule and a Deoxyuridine triphosphate. 5.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate The uridine triphosphate interacts with a L-glutamine and a water molecule through an ATP driven CTP synthase resulting in an ADP, a phosphate, a hydrogen ion, an L-glutamic acid and a cytidine triphosphate. The cytidine triphosphate then interacts spontaneously with a water molecule resulting in the release of a phosphate, a hydrogen ion and a CDP. The CDP then interacts with a reduced NrdH glutaredoxin-like protein through a ribonucleoside-diphosphate reductase 2 resulting in the release of a water molecule, an oxidized NrdH glutaredoxin-like protein and a dCDP. The dCDP is then phosphorylated through an ATP driven nucleoside diphosphate kinase resulting in an ADP and a dCTP. The dCTP interacts with a water molecule and a hydrogen ion through a dCTP deaminase resulting in a release of an ammonium molecule and a Deoxyuridine triphosphate. 6.-Uridine 5-diphosphate is phosphorylated by an ATP-driven nucleoside diphosphate kinase resulting in an ADP and an Uridinetriphosphate The uridine triphosphate interacts with a L-glutamine and a water molecule through an ATP driven CTP synthase resulting in an ADP, a phosphate, a hydrogen ion, an L-glutamic acid and a cytidine triphosphate. The cytidine triphosphate then interacts spontaneously with a water molecule resulting in the release of a phosphate, a hydrogen ion and a CDP. The CDP interacts with a reduced thioredoxin through a ribonucleoside diphosphate reductase 1 resulting in a release of a water molecule, an oxidized thioredoxin and a dCDP. The dCDP is then phosphorylated through an ATP driven nucleoside diphosphate kinase resulting in an ADP and a dCTP. The dCTP interacts with a water molecule and a hydrogen ion through a dCTP deaminase resulting in a release of an ammonium molecule and a Deoxyuridine triphosphate. The deoxyuridine triphosphate then interacts with a water molecule through a nucleoside triphosphate pyrophosphohydrolase resulting in a release of a hydrogen ion, a phosphate and a dUMP. The dUMP then interacts with a methenyltetrahydrofolate through a thymidylate synthase resulting in a dihydrofolic acid and a 5-thymidylic acid. Then 5-thymidylic acid is then phosphorylated through a nucleoside diphosphate kinase resulting in the release of an ADP and thymidine 5'-triphosphate. PW000942 ec00240 Metabolic ABC transporters ec02010 Bacterial chemotaxis ec02030 Metabolic pathways eco01100 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 <i>S</i>-methyl-5'-thioadenosine degradation IV PWY0-1391 Specdb::CMs 512 Specdb::CMs 513 Specdb::CMs 514 Specdb::CMs 515 Specdb::CMs 516 Specdb::CMs 517 Specdb::CMs 518 Specdb::CMs 519 Specdb::CMs 520 Specdb::CMs 3093 Specdb::CMs 30182 Specdb::CMs 30272 Specdb::CMs 30273 Specdb::CMs 30274 Specdb::CMs 30275 Specdb::CMs 30276 Specdb::CMs 30277 Specdb::CMs 30528 Specdb::CMs 30775 Specdb::CMs 37401 Specdb::CMs 168746 Specdb::CMs 1056715 Specdb::CMs 1056717 Specdb::CMs 1056719 Specdb::CMs 1056721 Specdb::NmrOneD 1311 Specdb::NmrOneD 143290 Specdb::NmrOneD 143291 Specdb::NmrOneD 143292 Specdb::NmrOneD 143293 Specdb::NmrOneD 143294 Specdb::NmrOneD 143295 Specdb::NmrOneD 143296 Specdb::NmrOneD 143297 Specdb::NmrOneD 143298 Specdb::NmrOneD 143299 Specdb::NmrOneD 143300 Specdb::NmrOneD 143301 Specdb::NmrOneD 143302 Specdb::NmrOneD 143303 Specdb::NmrOneD 143304 Specdb::NmrOneD 143305 Specdb::NmrOneD 143306 Specdb::NmrOneD 143307 Specdb::NmrOneD 143308 Specdb::NmrOneD 143309 Specdb::MsMs 481 Specdb::MsMs 482 Specdb::MsMs 179481 Specdb::MsMs 179482 Specdb::MsMs 179483 Specdb::MsMs 181809 Specdb::MsMs 181810 Specdb::MsMs 181811 Specdb::MsMs 2236312 Specdb::MsMs 2237049 Specdb::MsMs 2238484 Specdb::MsMs 2239120 Specdb::MsMs 2240571 Specdb::MsMs 2241111 Specdb::MsMs 2242643 Specdb::MsMs 2243233 Specdb::MsMs 2251535 Specdb::MsMs 2362058 Specdb::MsMs 2362059 Specdb::MsMs 2362060 Specdb::MsMs 2599739 Specdb::MsMs 2599740 Specdb::MsMs 2599741 Specdb::NmrTwoD 1254 HMDB00283 5575 C00121 Ribose Keseler, I. 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Journal of Biotechnology (2006), 121(4), 508-516. http://hmdb.ca/system/metabolites/msds/000/000/205/original/HMDB00283.pdf?1358894050 Ribose import ATP-binding protein RbsA P04983 RBSA_ECOLI rbsA http://ecmdb.ca/proteins/P04983.xml Ribokinase P0A9J6 RBSK_ECOLI rbsK http://ecmdb.ca/proteins/P0A9J6.xml Class B acid phosphatase P0AE22 APHA_ECOLI aphA http://ecmdb.ca/proteins/P0AE22.xml Non-specific ribonucleoside hydrolase rihC P22564 RIHC_ECOLI rihC http://ecmdb.ca/proteins/P22564.xml D-allose import ATP-binding protein AlsA P32721 ALSA_ECOLI alsA http://ecmdb.ca/proteins/P32721.xml Pyrimidine-specific ribonucleoside hydrolase rihB P33022 RIHB_ECOLI rihB http://ecmdb.ca/proteins/P33022.xml Sugar phosphatase supH P75792 SUPH_ECOLI supH http://ecmdb.ca/proteins/P75792.xml Uncharacterized ABC transporter ATP-binding protein ytfR Q6BEX0 YTFR_ECOLI ytfR http://ecmdb.ca/proteins/Q6BEX0.xml Inner membrane ABC transporter permease protein yjfF P37772 YJFF_ECOLI yjfF http://ecmdb.ca/proteins/P37772.xml ABC transporter periplasmic-binding protein ytfQ P39325 YTFQ_ECOLI ytfQ http://ecmdb.ca/proteins/P39325.xml Inner membrane ABC transporter permease protein ytfT P39328 YTFT_ECOLI ytfT http://ecmdb.ca/proteins/P39328.xml Ribose transport system permease protein rbsC P0AGI1 RBSC_ECOLI rbsC http://ecmdb.ca/proteins/P0AGI1.xml D-allose transport system permease protein AlsC P32720 ALSC_ECOLI alsC http://ecmdb.ca/proteins/P32720.xml D-ribose pyranase P04982 RBSD_ECOLI rbsD http://ecmdb.ca/proteins/P04982.xml Pyrimidine-specific ribonucleoside hydrolase rihA P41409 RIHA_ECOLI rihA http://ecmdb.ca/proteins/P41409.xml D-allose-binding periplasmic protein P39265 ALSB_ECOLI alsB http://ecmdb.ca/proteins/P39265.xml D-ribose-binding periplasmic protein P02925 RBSB_ECOLI rbsB http://ecmdb.ca/proteins/P02925.xml Ribose import ATP-binding protein RbsA P04983 RBSA_ECOLI rbsA http://ecmdb.ca/proteins/P04983.xml D-allose import ATP-binding protein AlsA P32721 ALSA_ECOLI alsA http://ecmdb.ca/proteins/P32721.xml Uncharacterized ABC transporter ATP-binding protein ytfR Q6BEX0 YTFR_ECOLI ytfR http://ecmdb.ca/proteins/Q6BEX0.xml Inner membrane ABC transporter permease protein yjfF P37772 YJFF_ECOLI yjfF http://ecmdb.ca/proteins/P37772.xml ABC transporter periplasmic-binding protein ytfQ P39325 YTFQ_ECOLI ytfQ http://ecmdb.ca/proteins/P39325.xml Inner membrane ABC transporter permease protein ytfT P39328 YTFT_ECOLI ytfT http://ecmdb.ca/proteins/P39328.xml Ribose transport system permease protein rbsC P0AGI1 RBSC_ECOLI rbsC http://ecmdb.ca/proteins/P0AGI1.xml D-allose transport system permease protein AlsC P32720 ALSC_ECOLI alsC http://ecmdb.ca/proteins/P32720.xml D-allose-binding periplasmic protein P39265 ALSB_ECOLI alsB http://ecmdb.ca/proteins/P39265.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 D-ribose-binding periplasmic protein P02925 RBSB_ECOLI rbsB http://ecmdb.ca/proteins/P02925.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 Adenosine triphosphate + Water + Ribose > ADP + Hydrogen ion + Phosphate + Ribose Adenosine triphosphate + Water + Ribose > ADP + Hydrogen ion + Phosphate + Ribose Cytidine + Water > Cytosine + Ribose R02137 Water + Uridine > Ribose + Uracil Adenosine + Water > Adenine + Ribose R01245 Water + Inosine > Hypoxanthine + Ribose R01770 Water + Xanthosine > Ribose + Xanthine Water + D-Ribose-5-phosphate > Phosphate + Ribose Adenosine triphosphate + Ribose <> ADP + Hydrogen ion + D-Ribose-5-phosphate R01051 Adenosine triphosphate + Ribose <> ADP + D-Ribose-5-phosphate R01051 Adenosine + Water <> Adenine + Ribose R01245 Guanosine + Water <> Guanine + Ribose R01677 Inosine + Water <> Hypoxanthine + Ribose R01770 Cytidine + Water <> Cytosine + Ribose R02137 Adenosine triphosphate + Ribose > ADP + D-Ribose-5-phosphate A pyrimidine nucleoside + Water > Ribose + a pyrimidine base Pyrimidine nucleoside + Water <> Ribose + Pyrimidine R02172 Ribose + Adenosine triphosphate > D-Ribose-5-phosphate + ADP + Hydrogen ion PW_R006131 Adenosine triphosphate + Ribose <> ADP + Hydrogen ion + D-Ribose-5-phosphate Adenosine triphosphate + Ribose <> ADP + Hydrogen ion + D-Ribose-5-phosphate