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Pathway Description
Pyrimidine Metabolism
Saccharomyces cerevisiae
Category:
Metabolite Pathway
Sub-Category:
Metabolic
Created: 2016-02-19
Last Updated: 2019-08-14
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.
References
Pyrimidine Metabolism References
Zrenner R, Stitt M, Sonnewald U, Boldt R: Pyrimidine and purine biosynthesis and degradation in plants. Annu Rev Plant Biol. 2006;57:805-36. doi: 10.1146/annurev.arplant.57.032905.105421.
Pubmed: 16669783
Amutha B, Pain D: Nucleoside diphosphate kinase of Saccharomyces cerevisiae, Ynk1p: localization to the mitochondrial intermembrane space. Biochem J. 2003 Mar 15;370(Pt 3):805-15. doi: 10.1042/BJ20021415.
Pubmed: 12472466
Jong AY, Ma JJ: Saccharomyces cerevisiae nucleoside-diphosphate kinase: purification, characterization, and substrate specificity. Arch Biochem Biophys. 1991 Dec;291(2):241-6.
Pubmed: 1659321
Souciet JL, Nagy M, Le Gouar M, Lacroute F, Potier S: Organization of the yeast URA2 gene: identification of a defective dihydroorotase-like domain in the multifunctional carbamoylphosphate synthetase-aspartate transcarbamylase complex. Gene. 1989 Jun 30;79(1):59-70. doi: 10.1016/0378-1119(89)90092-9.
Pubmed: 2570735
Galibert F, Alexandraki D, Baur A, Boles E, Chalwatzis N, Chuat JC, Coster F, Cziepluch C, De Haan M, Domdey H, Durand P, Entian KD, Gatius M, Goffeau A, Grivell LA, Hennemann A, Herbert CJ, Heumann K, Hilger F, Hollenberg CP, Huang ME, Jacq C, Jauniaux JC, Katsoulou C, Karpfinger-Hartl L, et al.: Complete nucleotide sequence of Saccharomyces cerevisiae chromosome X. EMBO J. 1996 May 1;15(9):2031-49.
Pubmed: 8641269
Engel SR, Dietrich FS, Fisk DG, Binkley G, Balakrishnan R, Costanzo MC, Dwight SS, Hitz BC, Karra K, Nash RS, Weng S, Wong ED, Lloyd P, Skrzypek MS, Miyasato SR, Simison M, Cherry JM: The reference genome sequence of Saccharomyces cerevisiae: then and now. G3 (Bethesda). 2014 Mar 20;4(3):389-98. doi: 10.1534/g3.113.008995.
Pubmed: 24374639
Souciet JL, Potier S, Hubert JC, Lacroute F: Nucleotide sequence of the pyrimidine specific carbamoyl phosphate synthetase, a part of the yeast multifunctional protein encoded by the URA2 gene. Mol Gen Genet. 1987 May;207(2-3):314-9. doi: 10.1007/bf00331595.
Pubmed: 3039294
Cziepluch C, Kordes E, Pujol A, Jauniaux JC: Sequencing analysis of a 40.2 kb fragment of yeast chromosome X reveals 19 open reading frames including URA2 (5' end), TRK1, PBS2, SPT10, GCD14, RPE1, PHO86, NCA3, ASF1, CCT7, GZF3, two tRNA genes, three remnant delta elements and a Ty4 transposon. Yeast. 1996 Nov;12(14):1471-4. doi: 10.1002/(SICI)1097-0061(199611)12:14%3C1471::AID-YEA30%3E3.0.CO;2-4.
Pubmed: 8948101
Nagy M, Le Gouar M, Potier S, Souciet JL, Herve G: The primary structure of the aspartate transcarbamylase region of the URA2 gene product in Saccharomyces cerevisiae. Features involved in activity and nuclear localization. J Biol Chem. 1989 May 15;264(14):8366-74.
Pubmed: 2498313
Guyonvarch A, Nguyen-Juilleret M, Hubert JC, Lacroute F: Structure of the Saccharomyces cerevisiae URA4 gene encoding dihydroorotase. Mol Gen Genet. 1988 Apr;212(1):134-41. doi: 10.1007/bf00322456.
Pubmed: 2897615
Johnston M, Hillier L, Riles L, Albermann K, Andre B, Ansorge W, Benes V, Bruckner M, Delius H, Dubois E, Dusterhoft A, Entian KD, Floeth M, Goffeau A, Hebling U, Heumann K, Heuss-Neitzel D, Hilbert H, Hilger F, Kleine K, Kotter P, Louis EJ, Messenguy F, Mewes HW, Hoheisel JD, et al.: The nucleotide sequence of Saccharomyces cerevisiae chromosome XII. Nature. 1997 May 29;387(6632 Suppl):87-90.
Pubmed: 9169871
de Montigny J, Kern L, Hubert JC, Lacroute F: Cloning and sequencing of URA10, a second gene encoding orotate phosphoribosyl transferase in Saccharomyces cerevisiae. Curr Genet. 1990 Feb;17(2):105-11.
Pubmed: 2182197
Hohmann S, Van Dijck P, Luyten K, Thevelein JM: The byp1-3 allele of the Saccharomyces cerevisiae GGS1/TPS1 gene and its multi-copy suppressor tRNA(GLN) (CAG): Ggs1/Tps1 protein levels restraining growth on fermentable sugars and trehalose accumulation. Curr Genet. 1994 Oct;26(4):295-301.
Pubmed: 7882422
Bowman S, Churcher C, Badcock K, Brown D, Chillingworth T, Connor R, Dedman K, Devlin K, Gentles S, Hamlin N, Hunt S, Jagels K, Lye G, Moule S, Odell C, Pearson D, Rajandream M, Rice P, Skelton J, Walsh S, Whitehead S, Barrell B: The nucleotide sequence of Saccharomyces cerevisiae chromosome XIII. Nature. 1997 May 29;387(6632 Suppl):90-3.
Pubmed: 9169872
Dietrich FS, Mulligan J, Hennessy K, Yelton MA, Allen E, Araujo R, Aviles E, Berno A, Brennan T, Carpenter J, Chen E, Cherry JM, Chung E, Duncan M, Guzman E, Hartzell G, Hunicke-Smith S, Hyman RW, Kayser A, Komp C, Lashkari D, Lew H, Lin D, Mosedale D, Davis RW, et al.: The nucleotide sequence of Saccharomyces cerevisiae chromosome V. Nature. 1997 May 29;387(6632 Suppl):78-81.
Pubmed: 9169868
Elledge SJ, Davis RW: Two genes differentially regulated in the cell cycle and by DNA-damaging agents encode alternative regulatory subunits of ribonucleotide reductase. Genes Dev. 1990 May;4(5):740-51. doi: 10.1101/gad.4.5.740.
Pubmed: 2199320
Wang PJ, Chabes A, Casagrande R, Tian XC, Thelander L, Huffaker TC: Rnr4p, a novel ribonucleotide reductase small-subunit protein. Mol Cell Biol. 1997 Oct;17(10):6114-21. doi: 10.1128/mcb.17.10.6114.
Pubmed: 9315671
Tettelin H, Agostoni Carbone ML, Albermann K, Albers M, Arroyo J, Backes U, Barreiros T, Bertani I, Bjourson AJ, Bruckner M, Bruschi CV, Carignani G, Castagnoli L, Cerdan E, Clemente ML, Coblenz A, Coglievina M, Coissac E, Defoor E, Del Bino S, Delius H, Delneri D, de Wergifosse P, Dujon B, Kleine K, et al.: The nucleotide sequence of Saccharomyces cerevisiae chromosome VII. Nature. 1997 May 29;387(6632 Suppl):81-4.
Pubmed: 9169869
Poon PP, Storms RK: Thymidylate synthase is localized to the nuclear periphery in the yeast Saccharomyces cerevisiae. J Biol Chem. 1994 Mar 18;269(11):8341-7.
Pubmed: 8132557
Taylor GR, Lagosky PA, Storms RK, Haynes RH: Molecular characterization of the cell cycle-regulated thymidylate synthase gene of Saccharomyces cerevisiae. J Biol Chem. 1987 Apr 15;262(11):5298-307.
Pubmed: 3031048
Valens M, Bohn C, Daignan-Fornier B, Dang VD, Bolotin-Fukuhara M: The sequence of a 54.7 kb fragment of yeast chromosome XV reveals the presence of two tRNAs and 24 new open reading frames. Yeast. 1997 Mar 30;13(4):379-90. doi: 10.1002/(SICI)1097-0061(19970330)13:4<379::AID-YEA85>3.0.CO;2-G.
Pubmed: 9133743
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