2.02012-07-30 14:55:41 -06002015-09-13 12:56:15 -0600ECMDB21392M2MDB001787PyrimidinePyrimidine is a heterocyclic aromatic organic compound similar to benzene and pyridine, containing two nitrogen atoms at positions 1 and 3 of the six-member ring. (Wikipedia) The group of compounds called pyrimidines are heterocyclic, six-membered, nitrogen-containing carbon ring structures, with uracil, cytosine and thymine being the basal structures of ribose-containing nucleosides (uridine, cytidine and thymidine respectively), or deoxyribose-containing deoxynucleosides, and their corresponding ribonucleotides or deoxyribonucleotides. Pyrimidines serve essential functions in metabolism as ribonucleotide bases in RNA (uracil and cytosine), and as deoxyribonucleotide bases in DNA (cytosine and thymine), and are linked by phosphodiester bridges to purine nucleotides in double-stranded DNA. Pyrimidines are synthesized de novo from simple precursors. (PMID 16098809)1,3-Diazabenzene1,3-Diazin1,3-DiazineM-diazineMetadiazineMiazinePYPYRPyrimidinPYRIMIDINEPyrimidine basePyrimidine dimerC4H4N280.08880.037448138pyrimidinepyrimidine25247-63-6C1=CN=CN=C1InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4HCZPWVGJYEJSRLH-UHFFFAOYSA-NLiquidlogp-0.21logs0.77solubility4.70e+02 g/lmelting_point22 oClogp0.05pka_strongest_basic1.58iupacpyrimidineaverage_mass80.088mono_mass80.037448138smilesC1=CN=CN=C1formulaC4H4N2inchiInChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4HinchikeyCZPWVGJYEJSRLH-UHFFFAOYSA-Npolar_surface_area25.78refractivity22.72polarizability7.62rotatable_bond_count0acceptor_count2donor_count0physiological_charge0formal_charge0Purine 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.PW000942ec00240MetabolicMetabolic pathwayseco01100Specdb::CMs16109Specdb::CMs136181Specdb::CMs143915Specdb::NmrOneD1957Specdb::NmrOneD135790Specdb::NmrOneD135791Specdb::NmrOneD135792Specdb::NmrOneD135793Specdb::NmrOneD135794Specdb::NmrOneD135795Specdb::NmrOneD135796Specdb::NmrOneD135797Specdb::NmrOneD135798Specdb::NmrOneD135799Specdb::NmrOneD135800Specdb::NmrOneD135801Specdb::NmrOneD135802Specdb::NmrOneD135803Specdb::NmrOneD135804Specdb::NmrOneD135805Specdb::NmrOneD135806Specdb::NmrOneD135807Specdb::NmrOneD135808Specdb::NmrOneD135809Specdb::MsMs2265Specdb::MsMs2266Specdb::MsMs2267Specdb::MsMs301735Specdb::MsMs301736Specdb::MsMs301737Specdb::MsMs344287Specdb::MsMs344288Specdb::MsMs344289Specdb::MsMs451866Specdb::MsMs2782372Specdb::MsMs2782373Specdb::MsMs2782374Specdb::MsMs2926048Specdb::MsMs2926049Specdb::MsMs2926050Specdb::NmrTwoD1890HMDB0336192608903C0039616898PYRIMIDINE-RINGP1RPyrimidine Loffler, M., Fairbanks, L. D., Zameitat, E., Marinaki, A. M., Simmonds, H. A. (2005). "Pyrimidine pathways in health and disease." Trends Mol Med 11:430-437.16098809http://hmdb.ca/system/metabolites/msds/000/002/942/original/HMDB03361.pdf?1358462116Putative pyrimidine permease rutGP75892RUTG_ECOLIrutGhttp://ecmdb.ca/proteins/P75892.xmlPyrimidine nucleoside + Water <> Ribose + PyrimidineR02172