2.02012-05-31 10:25:09 -06002015-09-13 12:56:07 -0600ECMDB00262M2MDB000110ThymineThymine is a nucleobase that is also known as 5-methyluracil. As the name suggests, thymine may be derived by methylation of uracil at the 5th carbon. In RNA, thymine is replaced with uracil. In DNA, thymine (T) binds to adenine (A) via two hydrogen bonds, thus stabilizing the nucleic acid structures. Thymine combined with deoxyribose creates the nucleoside deoxythymidine, when it is combined with ribose it creates the nucleoside thymidine. Thymidine can be phosphorylated with one, two, or three phosphoric acid groups, creating, respectively, TMP, TDP, or TTP2,4-Dihydroxy-5-methylpyrimidine4-Hydroxy-5-methylpyrimidin-2(1H)-one5-Methyl-1,2,3,4-tetrahydropyrimidine-2,4-dione5-Methyl-2,4(1H,3H)-pyrimidinedione5-Methyl-2,4-dihydroxypyrimidine5-Methylpyrimidine-2,4-dione5-MethyluracilThymineC5H6N2O2126.1133126.0429274465-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dionethymine65-71-4CC1=CNC(=O)NC1=OInChI=1S/C5H6N2O2/c1-3-2-6-5(9)7-4(3)8/h2H,1H3,(H2,6,7,8,9)RWQNBRDOKXIBIV-UHFFFAOYSA-NSolidCytosolExtra-organismPeriplasmlogp-0.99logs-1.07solubility1.08e+01 g/lmelting_point320 oClogp-0.46pka_strongest_acidic9.06pka_strongest_basic-5iupac5-methyl-1,2,3,4-tetrahydropyrimidine-2,4-dioneaverage_mass126.1133mono_mass126.042927446smilesCC1=CNC(=O)NC1=OformulaC5H6N2O2inchiInChI=1S/C5H6N2O2/c1-3-2-6-5(9)7-4(3)8/h2H,1H3,(H2,6,7,8,9)inchikeyRWQNBRDOKXIBIV-UHFFFAOYSA-Npolar_surface_area58.2refractivity30.33polarizability11.42rotatable_bond_count0acceptor_count2donor_count2physiological_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.PW000942ec00240MetabolicPantothenate and CoA biosynthesisThe CoA biosynthesis requires compounds from two other pathways: aspartate metabolism and valine biosynthesis. It requires a Beta-Alanine and R-pantoate.
The compound (R)-pantoate is generated in two reactions, as shown by the interaction of alpha-ketoisovaleric acid, 5,10 methylene-THF and water through a 3-methyl-2-oxobutanoate hydroxymethyltransferase resulting in a tetrahydrofolic acid and a 2-dehydropantoate. This compound interacts with hydrogen through a NADPH driven acetohydroxy acid isomeroreductase resulting in the release of NADP and R-pantoate.
On the other hand L-aspartic acid interacts with a hydrogen ion and gets decarboxylated through an Aspartate 1- decarboxylase resulting in a carbon dioxide and a Beta-alanine.
Beta-alanine and R-pantoate interact with an ATP driven pantothenate synthetase resulting in pyrophosphate, AMP, hydrogen ion and pantothenic acid.
Pantothenic acid is phosphorylated through a ATP-driven pantothenate kinase resulting in a ADP, a hydrogen ion and D-4'-Phosphopantothenate. This compound interacts with a CTP and a L-cysteine resulting in a fused 4'-phosphopantothenoylcysteine decarboxylase and phosphopantothenoylcysteine synthetase resulting in a hydrogen ion, a pyrophosphate, a CMP and 4-phosphopantothenoylcysteine.
The latter compound interacts with a hydrogen ion through a fused 4'-phosphopantothenoylcysteine decarboxylase and phosphopantothenoylcysteine synthetase resulting in a carbon dioxide release and a 4-phosphopantetheine. This compound interacts with an ATP, hydrogen ion and an phosphopantetheine adenylyltransferase resulting in a release of pyrophosphate, and dephospho-CoA.
Dephospho-CoA reacts with an ATP driven dephospho-CoA kinase resulting in a ADP , a hydrogen ion and a Coenzyme A.
. The latter is converted into (R)-4'-phosphopantothenate is two steps, involving a β-alanine ligase and a kinase. In most organsims the ligase acts before the kinase (EC 6.3.2.1, pantoate—β-alanine ligase (AMP-forming) followed by EC 2.7.1.33, pantothenate kinase, as described in phosphopantothenate biosynthesis I and phosphopantothenate biosynthesis II. However, in archaea the order is reversed, and EC 2.7.1.169, pantoate kinase acts before EC 6.3.2.36, 4-phosphopantoate—β-alanine ligase, as described in phosphopantothenate biosynthesis III.
The kinases are feedback inhibited by CoA itself, accounting for the primary regulatory mechanism of CoA biosynthesis. The addition of L-cysteine to (R)-4'-phosphopantothenate, resulting in the formation of R-4'-phosphopantothenoyl-L-cysteine (PPC), is followed by decarboxylation of PPC to 4'-phosphopantetheine. The ultimate reaction is catalyzed by EC 2.7.1.24, dephospho-CoA kinase, which converts 4'-phosphopantetheine to CoA. All enzymes of this pathway are essential for growth.
The reactions in the biosynthetic route towards CoA are identical in most organisms, although there are differences in the functionality of the involved enzymes. In plants every step is catalyzed by single monofunctional enzymes, whereas in bacteria and mammals bifunctional enzymes are often employed [Rubio06].PW000828ec00770MetabolicDrug metabolism - other enzymesec00983beta-Alanine metabolismThe Beta-Alanine Metabolism starts with a product of Aspartate metabolism. Aspartate is decarboxylated by aspartate 1-decarboxylase, releasing carbon dioxide and Beta-alanine. Beta alanine is then metabolized through a pantothenate synthetase resulting in Pantothenic acid undergoes phosphorylation through a ATP driven pantothenate kinase, resulting in D-4-phosphopantothenate.
Pantothenate (vitamin B5) is the universal precursor for the synthesis of the 4'-phosphopantetheine moiety of coenzyme A and acyl carrier protein. Only plants and microorganismscan synthesize pantothenate de novo - animals require a dietary supplement. The enzymes of this pathway are therefore considered to be antimicrobial drug targets.PW000896ec00410MetabolicMetabolic pathwayseco01100pyrimidine 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 PW002061Metabolicsalvage pathways of pyrimidine deoxyribonucleotidesPWY0-181pyrimidine deoxyribonucleosides degradationPWY0-1298Specdb::CMs502Specdb::CMs503Specdb::CMs504Specdb::CMs1108Specdb::CMs3444Specdb::CMs29559Specdb::CMs30235Specdb::CMs30700Specdb::CMs30936Specdb::CMs31107Specdb::CMs32328Specdb::CMs137189Specdb::CMs144923Specdb::EiMs1326Specdb::NmrOneD1222Specdb::NmrOneD1297Specdb::NmrOneD2565Specdb::NmrOneD3262Specdb::NmrOneD6322Specdb::NmrOneD6323Specdb::NmrOneD6324Specdb::NmrOneD6325Specdb::NmrOneD6326Specdb::NmrOneD6327Specdb::NmrOneD6328Specdb::NmrOneD6329Specdb::NmrOneD6330Specdb::NmrOneD6331Specdb::NmrOneD6332Specdb::NmrOneD6333Specdb::NmrOneD6334Specdb::NmrOneD6335Specdb::NmrOneD6336Specdb::NmrOneD6337Specdb::NmrOneD6338Specdb::NmrOneD6339Specdb::NmrOneD6340Specdb::NmrOneD6341Specdb::NmrOneD166498Specdb::MsMs3806Specdb::MsMs3807Specdb::MsMs3808Specdb::MsMs3809Specdb::MsMs3810Specdb::MsMs3821Specdb::MsMs438500Specdb::MsMs438501Specdb::MsMs438502Specdb::MsMs438503Specdb::MsMs438504Specdb::MsMs439112Specdb::MsMs2235168Specdb::MsMs2254674Specdb::MsMs2255916Specdb::MsMs454Specdb::MsMs455Specdb::MsMs456Specdb::MsMs3805Specdb::MsMs3811Specdb::MsMs3812Specdb::MsMs3813Specdb::MsMs3814Specdb::MsMs3815Specdb::MsMs3819Specdb::NmrTwoD1245HMDB0026211351103C0017817821THYMINETDRThymineKeseler, 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-D114.22080510Vijayendran, C., Barsch, A., Friehs, K., Niehaus, K., Becker, A., Flaschel, E. (2008). "Perceiving molecular evolution processes in Escherichia coli by comprehensive metabolite and gene expression profiling." Genome Biol 9:R72.18402659van 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 80:2939-2948.18331064Sreekumar A, Poisson LM, Rajendiran TM, Khan AP, Cao Q, Yu J, Laxman B, Mehra R, Lonigro RJ, Li Y, Nyati MK, Ahsan A, Kalyana-Sundaram S, Han B, Cao X, Byun J, Omenn GS, Ghosh D, Pennathur S, Alexander DC, Berger A, Shuster JR, Wei JT, Varambally S, Beecher C, Chinnaiyan AM: Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression. Nature. 2009 Feb 12;457(7231):910-4.19212411Eells JT, Spector R: Purine and pyrimidine base and nucleoside concentrations in human cerebrospinal fluid and plasma. Neurochem Res. 1983 Nov;8(11):1451-7.6656991Hofmann U, Schwab M, Seefried S, Marx C, Zanger UM, Eichelbaum M, Murdter TE: Sensitive method for the quantification of urinary pyrimidine metabolites in healthy adults by gas chromatography-tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2003 Jul 5;791(1-2):371-80.12798197van Lenthe H, van Kuilenburg AB, Ito T, Bootsma AH, van Cruchten A, Wada Y, van Gennip AH: Defects in pyrimidine degradation identified by HPLC-electrospray tandem mass spectrometry of urine specimens or urine-soaked filter paper strips. Clin Chem. 2000 Dec;46(12):1916-22.11106323Allgayer H, Kolb M, Stuber V, Kruis W: Effects of bile acids on base hydroxylation in a model of human colonic mucosal DNA. Cancer Detect Prev. 2002;26(1):85-9.12088208Goukassian D, Gad F, Yaar M, Eller MS, Nehal US, Gilchrest BA: Mechanisms and implications of the age-associated decrease in DNA repair capacity. FASEB J. 2000 Jul;14(10):1325-34.10877825Wassberg C, Backvall H, Diffey B, Ponten F, Berne B: Enhanced epidermal ultraviolet responses in chronically sun-exposed skin are dependent on previous sun exposure. Acta Derm Venereol. 2003;83(4):254-61.12926795Schilsky RL, O'Laughlin K, Ratain MJ: Phase I clinical and pharmacological study of thymidine (NSC 21548) and cis-diamminedichloroplatinum(II) in patients with advanced cancer. Cancer Res. 1986 Aug;46(8):4184-8.3731086Maskell R, Okubadejo OA, Payne RH, Pead L: Human infections with thymine-requiring bacteria. J Med Microbiol. 1978 Feb;11(1):33-45.621731Ling G, Chadwick CA, Berne B, Potten CS, Ponten J, Ponten F: Epidermal p53 response and repair of thymine dimers in human skin after a single dose of ultraviolet radiation: effects of photoprotection. 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J Chromatogr B Analyt Technol Biomed Life Sci. 2004 May 25;804(2):435-9.15081940Castro-Gago M, Camina F, Lojo S, Rodriguez-Segade S, Rodriguez-Nunez A: Concentrations of purine nucleotides and purine and pyrimidine bases in cerebrospinal fluid of neurologically healthy children. Eur J Clin Chem Clin Biochem. 1992 Nov;30(11):761-5.1489848Placzek M, Gaube S, Kerkmann U, Gilbertz KP, Herzinger T, Haen E, Przybilla B: Ultraviolet B-induced DNA damage in human epidermis is modified by the antioxidants ascorbic acid and D-alpha-tocopherol. J Invest Dermatol. 2005 Feb;124(2):304-7.15675947Thienpont LM, Van Landuyt KG, Stockl D, Saeyens W, De Keukeleire D, De Leenheer AP: Evaluation of 2-iminoimidazolidin-4-one and thymine as respective internal standards for normal-phase and reversed-phase high-performance liquid chromatographic determination of creatinine in human serum. J Chromatogr B Biomed Appl. 1995 Mar 10;665(1):63-9.7795802Rodriguez Ortner E, Hayes RB, Weissfeld J, Gelmann EP: Effect of homeodomain protein NKX3.1 R52C polymorphism on prostate gland size. Urology. 2006 Feb;67(2):311-5. Epub 2006 Jan 25.16442598Antille C, Tran C, Sorg O, Carraux P, Didierjean L, Saurat JH: Vitamin A exerts a photoprotective action in skin by absorbing ultraviolet B radiation. J Invest Dermatol. 2003 Nov;121(5):1163-7.14708621Zhang, Shi-Ying; Wu, Da-Jun; Zhang, Yan-Ping. Synthesis of thymine. Zhongguo Yiyao Gongye Zazhi (1999), 30(7), 325.http://hmdb.ca/system/metabolites/msds/000/000/193/original/HMDB00262.pdf?1358896049Thymidine phosphorylaseP07650TYPH_ECOLIdeoAhttp://ecmdb.ca/proteins/P07650.xmlCytosine deaminaseP25524CODA_ECOLIcodAhttp://ecmdb.ca/proteins/P25524.xmlUncharacterized protein yeiAP25889YEIA_ECOLIyeiAhttp://ecmdb.ca/proteins/P25889.xmlPutative monooxygenase rutAP75898RUTA_ECOLIrutAhttp://ecmdb.ca/proteins/P75898.xmlUncharacterized oxidoreductase yeiTP76440YEIT_ECOLIyeiThttp://ecmdb.ca/proteins/P76440.xmlOuter membrane protein NP77747OMPN_ECOLIompNhttp://ecmdb.ca/proteins/P77747.xmlOuter membrane pore protein EP02932PHOE_ECOLIphoEhttp://ecmdb.ca/proteins/P02932.xmlOuter membrane protein FP02931OMPF_ECOLIompFhttp://ecmdb.ca/proteins/P02931.xmlOuter membrane protein CP06996OMPC_ECOLIompChttp://ecmdb.ca/proteins/P06996.xmlPhosphate + Thymidine <> Deoxyribose 1-phosphate + ThymineR015705-Methylcytosine + Water <> Thymine + AmmoniaR01411Thymine + Oxygen + FMNH > (<i>Z</i>)-2-methylureidoacrylate peracid + Flavin Mononucleotide + Hydrogen ionRXN-12886Dihydrothymine + NAD <> Thymine + NADH + Hydrogen ionRXN0-6565Thymidine + Phosphate <> deoxyribose-1-phosphate + ThymineTHYM-PHOSPH-RXNDihydrothymine + NAD > Thymine + NADHRXN0-6565Thymine + FMNH(2) + Oxygen > (Z)-2-Methyl-ureidoacrylate peracid + Flavin Mononucleotide + WaterThymidine + Inorganic phosphate > Thymine + 2-deoxy-alpha-D-ribose 1-phosphateDihydrouracil + NAD + Dihydrothymine <> Uracil + NADH + Hydrogen ion + ThymineR00977 Uracil + FMNH + Oxygen + Thymine <> Ureidoacrylate peracid + Flavin Mononucleotide + (Z)-2-Methyl-ureidoacrylate peracidR09936 Deoxyribose 1-phosphate + Thymine > Phosphate + ThymidinePW_R0060195 5-Methylcytosine + Water <> Thymine + Ammonia