2.0 2012-05-31 13:48:48 -0600 2015-06-03 15:53:53 -0600 ECMDB01271 M2MDB000318 Pseudouridine 5'-phosphate Pseudouridine 5'-phosphate is a member of the chemical class known as Pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. Pseudouridine 5'-phosphate is an intermediate in pseudouridine degradation pathway. In this pathway, pseudouridine is metabolised to uracil. [BiocycPWY-6019] PseudoU5P Pseudouridine 5'-phosphate Pseudouridine 5'-phosphoric acid C9H13N2O9P 324.1813 324.035866536 {[(2R,3S,4R,5S)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid pseudouridine 5'-phosphate 1157-60-4 O[C@H]1[C@@H](O)[C@@H](O[C@@H]1COP(O)(O)=O)C1=CNC(=O)NC1=O InChI=1S/C9H13N2O9P/c12-5-4(2-19-21(16,17)18)20-7(6(5)13)3-1-10-9(15)11-8(3)14/h1,4-7,12-13H,2H2,(H2,16,17,18)(H2,10,11,14,15)/t4-,5-,6-,7+/m1/s1 MOBMOJGXNHLLIR-GBNDHIKLSA-N Solid Cytoplasm Periplasm logp -1.86 ALOGPS logs -1.64 ALOGPS solubility 7.51e+00 g/l ALOGPS logp -3.2 ChemAxon pka_strongest_acidic 1.23 ChemAxon pka_strongest_basic -3.6 ChemAxon iupac {[(2R,3S,4R,5S)-5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}phosphonic acid ChemAxon average_mass 324.1813 ChemAxon mono_mass 324.035866536 ChemAxon smiles O[C@H]1[C@@H](O)[C@@H](O[C@@H]1COP(O)(O)=O)C1=CNC(=O)NC1=O ChemAxon formula C9H13N2O9P ChemAxon inchi InChI=1S/C9H13N2O9P/c12-5-4(2-19-21(16,17)18)20-7(6(5)13)3-1-10-9(15)11-8(3)14/h1,4-7,12-13H,2H2,(H2,16,17,18)(H2,10,11,14,15)/t4-,5-,6-,7+/m1/s1 ChemAxon inchikey MOBMOJGXNHLLIR-GBNDHIKLSA-N ChemAxon polar_surface_area 174.65 ChemAxon refractivity 63.31 ChemAxon polarizability 26.32 ChemAxon rotatable_bond_count 4 ChemAxon acceptor_count 8 ChemAxon donor_count 6 ChemAxon physiological_charge -2 ChemAxon formal_charge 0 ChemAxon 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 Purine degradation Pseudouridine is phosphorylated by interacting with atp and a psuK resulting in the release of an ADP, a hydrogen ion and a pseudouridine 5'-phosphate. The latter compound then reacts with water through a pseudouridine 5'-phosphate glycosidase resulting in the release of a uracil and D-ribofuranose 5-phosphate PW001887 Metabolic Specdb::CMs 3177 Specdb::CMs 38004 Specdb::CMs 163291 Specdb::NmrOneD 9082 Specdb::NmrOneD 9083 Specdb::NmrOneD 9084 Specdb::NmrOneD 9085 Specdb::NmrOneD 9086 Specdb::NmrOneD 9087 Specdb::NmrOneD 9088 Specdb::NmrOneD 9089 Specdb::NmrOneD 9090 Specdb::NmrOneD 9091 Specdb::NmrOneD 9092 Specdb::NmrOneD 9093 Specdb::NmrOneD 9094 Specdb::NmrOneD 9095 Specdb::NmrOneD 9096 Specdb::NmrOneD 9097 Specdb::NmrOneD 9098 Specdb::NmrOneD 9099 Specdb::NmrOneD 9100 Specdb::NmrOneD 9101 Specdb::MsMs 23861 Specdb::MsMs 23862 Specdb::MsMs 23863 Specdb::MsMs 30659 Specdb::MsMs 30660 Specdb::MsMs 30661 Specdb::MsMs 2719494 Specdb::MsMs 2719495 Specdb::MsMs 2719496 Specdb::MsMs 2958633 Specdb::MsMs 2958634 Specdb::MsMs 2958635 HMDB01271 388535 C01168 18116 PSEUDOURIDINE-5-P PSU 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 Charette M, Gray MW: Pseudouridine in RNA: what, where, how, and why. IUBMB Life. 2000 May;49(5):341-51. 10902565 Pseudouridine kinase P30235 PSUK_ECOLI psuK http://ecmdb.ca/proteins/P30235.xml Pseudouridine + Adenosine triphosphate > Hydrogen ion + Pseudouridine 5'-phosphate + ADP PSEUDOURIDINE-KINASE-RXN D-Ribose-5-phosphate + Uracil <> Water + Pseudouridine 5'-phosphate RXN0-5398 Pseudouridine 5'-phosphate + Water > Uracil + D-Ribose-5-phosphate RXN0-5398 Adenosine triphosphate + Pseudouridine > ADP + Pseudouridine 5'-phosphate PSEUDOURIDINE-KINASE-RXN Adenosine triphosphate + Pseudouridine <> ADP + Pseudouridine 5'-phosphate R03315 Pseudouridine + Adenosine triphosphate + Pseudouridine > Pseudouridine 5'-phosphate + Adenosine diphosphate + Hydrogen ion + ADP PW_R005150 Pseudouridine 5'-phosphate + Water > Uracil + D-ribofuranose 5-phosphate + D-ribofuranose 5-phosphate PW_R005151