2.02012-07-30 14:55:41 -06002015-09-13 15:15:32 -0600ECMDB21388M2MDB001783PseudouridinePseudouridine is the C-glycoside isomer of the nucleoside uridine, and it is the most prevalent of the over one hundred different modified nucleosides found in RNA. Pseudouridine is found in all species and in all classes of RNA except mRNA. It is formed by enzymes called pseudouridine synthases, which post-transcriptionally isomerize specific uridine residues in RNA (Wikipedia).(1S)-1,4-anhydro-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitol5-(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl-1H-pyrimidine-2,4-dione5-(b-D-Ribofuranosyl)uracil5-(b-delta-Ribofuranosyl)uracil5-(b-δ-Ribofuranosyl)uracil5-(beta-D-ribofuranosyl)uracil5-(β-D-Ribofuranosyl)uracil5-b-D-ribofuranosyl-Uracil5-b-delta-Ribofuranosyl-uracil5-b-δ-Ribofuranosyl-uracil5-beta-delta-ribofuranosyl-Uracil5-Ribosyluracil5-β-δ-Ribofuranosyl-uracilB-D-Pseudouridineb-delta-PseudouridineB-Pseudouridineb-δ-PseudouridineBeta-delta-PseudouridineBeta-PseudouridinePPseudouridine CPsi-uridineY-Uridineβ-Pseudouridineβ-δ-PseudouridineC9H12N2O6244.2014244.0695361265-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dioneβ-pseudouridine1445-07-4OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C1=CNC(=O)NC1=OInChI=1S/C9H12N2O6/c12-2-4-5(13)6(14)7(17-4)3-1-10-9(16)11-8(3)15/h1,4-7,12-14H,2H2,(H2,10,11,15,16)/t4-,5-,6-,7+/m1/s1PTJWIQPHWPFNBW-GBNDHIKLSA-NSolidCytoplasmlogp-2.01logs-0.58solubility6.38e+01 g/llogp-3.1pka_strongest_acidic8.66pka_strongest_basic-3iupac5-[(2S,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,2,3,4-tetrahydropyrimidine-2,4-dioneaverage_mass244.2014mono_mass244.069536126smilesOC[C@H]1O[C@H]([C@H](O)[C@@H]1O)C1=CNC(=O)NC1=OformulaC9H12N2O6inchiInChI=1S/C9H12N2O6/c12-2-4-5(13)6(14)7(17-4)3-1-10-9(16)11-8(3)15/h1,4-7,12-14H,2H2,(H2,10,11,15,16)/t4-,5-,6-,7+/m1/s1inchikeyPTJWIQPHWPFNBW-GBNDHIKLSA-Npolar_surface_area128.12refractivity52.44polarizability21.79rotatable_bond_count2acceptor_count6donor_count5physiological_charge0formal_charge0Pyrimidine 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.PW000942ec00240MetabolicPurine degradationPseudouridine 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-phosphatePW001887MetabolicSpecdb::CMs3193Specdb::CMs37754Specdb::CMs131415Specdb::CMs139149Specdb::CMs1074989Specdb::CMs1074991Specdb::CMs1074992Specdb::CMs1074994Specdb::CMs1074996Specdb::CMs1074998Specdb::CMs1074999Specdb::CMs1075001Specdb::CMs1075003Specdb::CMs1075005Specdb::CMs1075007Specdb::CMs1075008Specdb::CMs1075010Specdb::CMs1075012Specdb::CMs1075013Specdb::CMs1075015Specdb::CMs1075017Specdb::CMs1075019Specdb::CMs1075021Specdb::CMs1075022Specdb::CMs1075024Specdb::NmrOneD1533Specdb::NmrOneD145290Specdb::NmrOneD145291Specdb::NmrOneD145292Specdb::NmrOneD145293Specdb::NmrOneD145294Specdb::NmrOneD145295Specdb::NmrOneD145296Specdb::NmrOneD145297Specdb::NmrOneD145298Specdb::NmrOneD145299Specdb::NmrOneD145300Specdb::NmrOneD145301Specdb::NmrOneD145302Specdb::NmrOneD145303Specdb::NmrOneD145304Specdb::NmrOneD145305Specdb::NmrOneD145306Specdb::NmrOneD145307Specdb::NmrOneD145308Specdb::NmrOneD145309Specdb::MsMs27470Specdb::MsMs27471Specdb::MsMs27472Specdb::MsMs34028Specdb::MsMs34029Specdb::MsMs34030Specdb::MsMs438664Specdb::MsMs1470934Specdb::MsMs1470935Specdb::MsMs1470936Specdb::MsMs2231836Specdb::MsMs2232383Specdb::MsMs2236609Specdb::MsMs2236750Specdb::MsMs2245020Specdb::MsMs2245111Specdb::MsMs2247123Specdb::MsMs2247156Specdb::MsMs2249122Specdb::MsMs2249277Specdb::MsMs2251095Specdb::MsMs2251298Specdb::MsMs2252989Specdb::MsMs2253464Specdb::MsMs2255113HMDB007671504714319C0206717802CPD-497PseudouridineLee SH, Jung BH, Kim SY, Chung BC: A rapid and sensitive method for quantitation of nucleosides in human urine using liquid chromatography/mass spectrometry with direct urine injection. Rapid Commun Mass Spectrom. 2004;18(9):973-7.15116424Shoemaker JD, Elliott WH: Automated screening of urine samples for carbohydrates, organic and amino acids after treatment with urease. J Chromatogr. 1991 Jan 2;562(1-2):125-38.2026685Uziel M, Smith LH, Taylor SA: Modified nucleosides in urine: selective removal and analysis. Clin Chem. 1976 Sep;22(9):1451-5.954194Bernert JT Jr, Bell CJ, Guntupalli J, Hannon WH: Pseudouridine is unsuitable as an endogenous renal clearance marker. Clin Chem. 1988 Jun;34(6):1011-7.3378317Woodcock TM, Chou TC, Tan CT, Sternberg SS, Philips FS, Young CW, Burchenal JH: Biochemical, pharmacological, and phase I clinical evaluation of pseudoisocytidine. Cancer Res. 1980 Nov;40(11):4243-9.7471064Colonna A, Russo T, Esposito F, Salvatore F, Cimino F: Determination of pseudouridine and other nucleosides in human blood serum by high-performance liquid chromatography. Anal Biochem. 1983 Apr 1;130(1):19-26.6869800Mak TW, Ho SS, Ho CS, Jones MG, Lai CK, Lam CW: Pleural fluid pseudouridine in malignant and benign pleural effusions. Ann Clin Biochem. 1998 Jan;35 ( Pt 1):94-8.9463745anessian, Stephen; Machaalani, Roger. A highly stereo-controlled and efficient synthesis of a- and b-pseudouridines. Tetrahedron Letters (2003), 44(45), 8321-8323.Pseudouridine kinaseP30235PSUK_ECOLIpsuKhttp://ecmdb.ca/proteins/P30235.xmlPutative pseudouridine transporterP33024PSUT_ECOLIpsuThttp://ecmdb.ca/proteins/P33024.xmlPseudouridine + Adenosine triphosphate > Hydrogen ion + Pseudouridine 5'-phosphate + ADPPSEUDOURIDINE-KINASE-RXNAdenosine triphosphate + Pseudouridine > ADP + Pseudouridine 5'-phosphatePSEUDOURIDINE-KINASE-RXNAdenosine triphosphate + Pseudouridine <> ADP + Pseudouridine 5'-phosphateR03315 Pseudouridine + Adenosine triphosphate + Pseudouridine > Pseudouridine 5'-phosphate + Adenosine diphosphate + Hydrogen ion + ADPPW_R005150