2.02012-05-31 13:50:34 -06002015-06-03 15:53:57 -0600ECMDB01351M2MDB000350Deoxyribose 1-phosphateDeoxyribose 1-phosphate is an intermediate in the metabolism of Pyrimidine. It is a substrate for Purine nucleoside phosphorylase and Thymidine phosphorylase.2-Deoxy-a-D-ribose 1-phosphate2-Deoxy-a-D-ribose 1-phosphoric acid2-Deoxy-a-delta-ribose 1-phosphate2-Deoxy-a-delta-ribose 1-phosphoric acid2-Deoxy-a-δ-ribose 1-phosphate2-Deoxy-a-δ-ribose 1-phosphoric acid2-Deoxy-alpha-D-ribose 1-phosphate2-Deoxy-alpha-D-ribose 1-phosphoric acid2-Deoxy-alpha-delta-ribose 1-phosphate2-Deoxy-alpha-delta-ribose 1-phosphoric acid2-Deoxy-D-erythro-pentofuranose 1-phosphate2-Deoxy-D-erythro-pentofuranose 1-phosphoric acid2-Deoxy-D-ribose 1-phosphate2-Deoxy-D-ribose 1-phosphoric acid2-Deoxy-D-ribose-1-phosphate2-Deoxy-D-ribose-1-phosphoric acid2-Deoxy-delta-erythro-pentofuranose 1-phosphate2-Deoxy-delta-erythro-pentofuranose 1-phosphoric acid2-Deoxy-delta-ribose 1-phosphate2-Deoxy-delta-ribose 1-phosphoric acid2-Deoxy-delta-ribose-1-phosphate2-Deoxy-delta-ribose-1-phosphoric acid2-Deoxy-α-D-ribose 1-phosphate2-Deoxy-α-D-ribose 1-phosphoric acid2-Deoxy-α-δ-ribose 1-phosphate2-Deoxy-α-δ-ribose 1-phosphoric acid2-Deoxy-δ-erythro-pentofuranose 1-phosphate2-Deoxy-δ-erythro-pentofuranose 1-phosphoric acid2-Deoxy-δ-ribose 1-phosphate2-Deoxy-δ-ribose 1-phosphoric acid2-Deoxy-δ-ribose-1-phosphate2-Deoxy-δ-ribose-1-phosphoric acid2-Deoxyribofuranose 1-phosphate2-Deoxyribofuranose 1-phosphoric acidD-2-Deoxy-ribofuranose 1-phosphateD-2-Deoxy-ribofuranose 1-phosphoric acidDelta-2-Deoxy-ribofuranose 1-phosphatedelta-2-Deoxy-ribofuranose 1-phosphoric acidDeoxy-D-ribose 1-phosphateDeoxy-D-ribose 1-phosphoric acidDeoxyribose 1-phosphateDeoxyribose 1-phosphoric acidDeoxyribose-1-phosphateDeoxyribose-1-phosphoric acidDR1Pδ-2-Deoxy-ribofuranose 1-phosphateδ-2-Deoxy-ribofuranose 1-phosphoric acidC5H11O7P214.1104214.024239218{[(4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic aciddeoxyribose-1-phosphate17210-42-3OC[C@H]1OC(C[C@@H]1O)OP(O)(O)=OInChI=1S/C5H11O7P/c6-2-4-3(7)1-5(11-4)12-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5?/m0/s1KBDKAJNTYKVSEK-PYHARJCCSA-NSolidCytosollogp-2.14logs-0.76solubility3.76e+01 g/llogp-1.5pka_strongest_acidic1.37pka_strongest_basic-3iupac{[(4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic acidaverage_mass214.1104mono_mass214.024239218smilesOC[C@H]1OC(C[C@@H]1O)OP(O)(O)=OformulaC5H11O7PinchiInChI=1S/C5H11O7P/c6-2-4-3(7)1-5(11-4)12-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5?/m0/s1inchikeyKBDKAJNTYKVSEK-PYHARJCCSA-Npolar_surface_area116.45refractivity39.32polarizability17.21rotatable_bond_count3acceptor_count6donor_count4physiological_charge-2formal_charge0Pentose phosphate pathwayec00030Purine metabolismec00230Pyrimidine metabolismThe 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.PW000942ec00240MetabolicDrug metabolism - other enzymesec00983Nicotinate and nicotinamide metabolismec00760Metabolic pathwayseco01100purine deoxyribonucleosides degradationPW002077Metabolicpyrimidine deoxyribonucleosides degradationThe degradation of deoxycytidine starts with deoxycytidine being introduced into the cytosol through either a nupG or nupC symporter.
Once inside, it can can be degrade through water,a hydrogen ion and a deoxycytidien deaminsa resultin in the release of a ammonium and a a deoxyuridine. The deoxyuridine is then degraded through a uracil phosphorylase resulting in the release of a deoxyribose 1-phosphate and a uracil.
The degradation of thymidine starts with thymidine being introduced into the cytosol through either a nupG or nupC symporter.
Thymidine is then degrades through a phosphorylase resulting in the release of a thymine and a deoxyribose 1-phosphate.PW002063Metabolicsalvage pathways of pyrimidine deoxyribonucleotidesThe pathway begins with the introduction of deoxycytidine into the cytosol, either through a nupG symporter or a nupC symporter. Once inside it is deaminated when reacting with a water molecule, a hydrogen ion and a deoxycytidine deaminase resulting in the release of an ammonium and a deoxyuridine. Deoxyuridine can also be imported through a nupG symporter or a nupC symporter.
Deoxyuridine can react with an ATP through a deoxyuridine kinase resulting in the release of a ADP , a hydrogen ion and a dUMP.
Deoxyuridine can also react with a phosphate through a uracil phosphorylase resulting in the release of a uracil and a deoxy-alpha-D-ribose 1-phosphate. This compound in turn reacts with a thymine through a thymidine phosphorylase resulting in the release of a phosphate and a thymidine. Thymidine in turn reacts with an ATP through a thymidine kinase resulting in a release of an ADP, a hydrogen ion and a dTMP PW002061Metabolicpyrimidine deoxyribonucleosides degradationPWY0-1298purine deoxyribonucleosides degradationPWY0-1297Specdb::CMs3341Specdb::CMs38035Specdb::CMs153463Specdb::NmrOneD255108Specdb::NmrOneD255109Specdb::NmrOneD255110Specdb::NmrOneD255111Specdb::NmrOneD255112Specdb::NmrOneD255113Specdb::NmrOneD255114Specdb::NmrOneD255115Specdb::NmrOneD255116Specdb::NmrOneD255117Specdb::NmrOneD255118Specdb::NmrOneD255119Specdb::NmrOneD255120Specdb::NmrOneD255121Specdb::NmrOneD255122Specdb::NmrOneD255123Specdb::NmrOneD255124Specdb::NmrOneD255125Specdb::NmrOneD255126Specdb::NmrOneD255127Specdb::MsMs27293Specdb::MsMs27294Specdb::MsMs27295Specdb::MsMs33851Specdb::MsMs33852Specdb::MsMs33853Specdb::MsMs2301420Specdb::MsMs2301421Specdb::MsMs2301422Specdb::MsMs3063616Specdb::MsMs3063617Specdb::MsMs3063618HMDB01351439287388420C0067228542DEOXY-D-RIBOSE-1-PHOSPHATEKeseler, 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-D590.21097882Kanehisa, 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-D114.22080510van 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 370:17-25.17765195Winder, 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 80:2939-2948.18331064Holmberg I, Stal P, Hamberg M: Quantitative determination of 8-hydroxy-2'-deoxyguanosine in human urine by isotope dilution mass spectrometry: normal levels in hemochromatosis. Free Radic Biol Med. 1999 Jan;26(1-2):129-35.9890648Thymidine phosphorylaseP07650TYPH_ECOLIdeoAhttp://ecmdb.ca/proteins/P07650.xmlPhosphopentomutaseP0A6K6DEOB_ECOLIdeoBhttp://ecmdb.ca/proteins/P0A6K6.xmlPurine nucleoside phosphorylase deoD-typeP0ABP8DEOD_ECOLIdeoDhttp://ecmdb.ca/proteins/P0ABP8.xmlUridine phosphorylaseP12758UDP_ECOLIudphttp://ecmdb.ca/proteins/P12758.xmlXanthosine phosphorylaseP45563XAPA_ECOLIxapAhttp://ecmdb.ca/proteins/P45563.xmlDeoxyinosine + Phosphate <> Deoxyribose 1-phosphate + HypoxanthineR02748Deoxyguanosine + Phosphate <> Deoxyribose 1-phosphate + GuanineR01969Deoxyuridine + Phosphate <> Deoxyribose 1-phosphate + UracilR02484Phosphate + Thymidine <> Deoxyribose 1-phosphate + ThymineR01570Deoxyribose 1-phosphate <> Deoxyribose 5-phosphateR02749D-PPENTOMUT-RXNDeoxyadenosine + Phosphate <> Deoxyribose 1-phosphate + AdenineR025575-FU + Deoxyribose 1-phosphate <> 5-Fluorodeoxyuridine + PhosphateR08230Purine nucleoside + Phosphate + Purine deoxyribonucleoside <> Purine + Ribose-1-phosphate + Deoxyribose 1-phosphateR08368 Deoxyribose 1-phosphate > Deoxyribose 5-phosphatePW_R006071Deoxyuridine + Phosphate > Uracil + Deoxyribose 1-phosphatePW_R006018Deoxyribose 1-phosphate + Thymine > Phosphate + ThymidinePW_R006019Deoxyadenosine + Phosphate > Adenine + Deoxyribose 1-phosphatePW_R006069