2.02012-05-31 10:26:02 -06002015-09-13 12:56:07 -0600ECMDB00300M2MDB000126UracilUracil is a common naturally occurring pyrimidine found in RNA, it base pairs with adenine and is replaced by thymine in DNA. Methylation of uracil produces thymine. Uracil serves as allosteric regulator and coenzyme for many important biochemical reactions. Uracil is also involved in the biosynthesis of polysaccharides and the transportation of sugars containing aldehydes. In E. coli, uracil catabolism is regulated by the amount of metabolically available nitrogen. (PMID: 4567228)2,4-Dihydroxypyrimidine2,4-Dioxopyrimidine2,4-Pyrimidinediol2,4-PyrimidinedioneHybar XPirodPyrodUracilC4H4N2O2112.0868112.0272773821,2,3,4-tetrahydropyrimidine-2,4-dioneuracil66-22-8O=C1NC=CC(=O)N1InChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)ISAKRJDGNUQOIC-UHFFFAOYSA-NSolidCytosolExtra-organismPeriplasmlogp-1.20logs-0.63solubility2.65e+01 g/lmelting_point330 oClogp-0.86pka_strongest_acidic8.8pka_strongest_basic-5.5iupac1,2,3,4-tetrahydropyrimidine-2,4-dioneaverage_mass112.0868mono_mass112.027277382smilesO=C1NC=CC(=O)N1formulaC4H4N2O2inchiInChI=1S/C4H4N2O2/c7-3-1-2-5-4(8)6-3/h1-2H,(H2,5,6,7,8)inchikeyISAKRJDGNUQOIC-UHFFFAOYSA-Npolar_surface_area58.2refractivity25.97polarizability9.37rotatable_bond_count0acceptor_count2donor_count2physiological_charge0formal_charge0Arginine and proline metabolismec00330Pyrimidine 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 pathwayseco01100Purine 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-phosphatePW001887MetabolicPyrimidine ribonucleosides degradtionCytidine and Uridine are transported through their corresponding nucleoside hydrogen symporters . Once cytidine is incorporated into the cytosol, it is deaminated through a reaction with water and a hydrogen ion through a cytidine deaminase resulting in the release of ammonium and uridine.
Uridine is then lyase by a phosphate through a uridine phosphorylase resulting in the release of a uracil and a alpha-D-ribose-1-phosphate. This compound is then transformed into an isomer D-ribose 5-phosphate through a alpha-D-ribose 1,5-phosphomutase. This cumpound is then incorporated into the pentose phosphate pathway
PW002024MetabolicUracil degradation IIIPW002026Metabolicpyrimidine 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 PW002061Metabolicpyrimidine ribonucleosides degradationThe degradation of pyrimidine ribonucleosides starts with either cytidine or uridine being transported into the cytosol.
Cytidine is transported into the cytosol through an nupG transporter. Once inside the cytosol, it can be degraded into uridine by reacting with water and ahydrogen ion through a cytidine deaminase resulting in the release of ammonium and uridine.
Uridine is transported into the cytosol through a nupG. Once in the cytosol , uridine can be degrade by reacting with phosphate through a uridine phosphorylase resulting in the release of an alpha-D-ribose-1-phosphate and a uracil. The alpha-D-ribose-1-phosphate reacts with an alpha-d-ribose 1,5-phosphomutase resulting in the release of a D-ribose 5-phosphate which can be incorporated into the pentose phosphate pathway.PW002104Metabolicsalvage pathways of pyrimidine deoxyribonucleotidesPWY0-181pyrimidine deoxyribonucleosides degradationPWY0-1298uracil degradation IIIPWY0-1471salvage pathways of pyrimidine ribonucleotidesPWY0-163pyrimidine ribonucleosides degradation IPWY0-1295Specdb::CMs529Specdb::CMs530Specdb::CMs1056Specdb::CMs3073Specdb::CMs29052Specdb::CMs29557Specdb::CMs30706Specdb::CMs30824Specdb::CMs31120Specdb::CMs31804Specdb::CMs168787Specdb::EiMs430Specdb::NmrOneD1229Specdb::NmrOneD1321Specdb::NmrOneD2568Specdb::NmrOneD3264Specdb::NmrOneD4763Specdb::NmrOneD143410Specdb::NmrOneD143411Specdb::NmrOneD143412Specdb::NmrOneD143413Specdb::NmrOneD143414Specdb::NmrOneD143415Specdb::NmrOneD143416Specdb::NmrOneD143417Specdb::NmrOneD143418Specdb::NmrOneD143419Specdb::NmrOneD143420Specdb::NmrOneD143421Specdb::NmrOneD143422Specdb::NmrOneD143423Specdb::NmrOneD143424Specdb::NmrOneD143425Specdb::NmrOneD143426Specdb::NmrOneD143427Specdb::NmrOneD143428Specdb::NmrOneD143429Specdb::MsMs510Specdb::MsMs511Specdb::MsMs512Specdb::MsMs3964Specdb::MsMs3965Specdb::MsMs3966Specdb::MsMs3967Specdb::MsMs3968Specdb::MsMs3969Specdb::MsMs3970Specdb::MsMs3973Specdb::MsMs3974Specdb::MsMs20012Specdb::MsMs20013Specdb::MsMs20014Specdb::MsMs21563Specdb::MsMs21564Specdb::MsMs21565Specdb::MsMs438568Specdb::MsMs438569Specdb::MsMs438570Specdb::MsMs438571Specdb::MsMs438572Specdb::MsMs439025Specdb::MsMs440041Specdb::NmrTwoD1017Specdb::NmrTwoD1263HMDB0030011741141C0010617568URACILURAUracilKeseler, 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). 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Journal of the American Pharmaceutical Association (1912-1977) (1955), 44 545-50.http://hmdb.ca/system/metabolites/msds/000/000/219/original/HMDB00300.pdf?1358896161Thymidine phosphorylaseP07650TYPH_ECOLIdeoAhttp://ecmdb.ca/proteins/P07650.xmlUracil phosphoribosyltransferaseP0A8F0UPP_ECOLIupphttp://ecmdb.ca/proteins/P0A8F0.xmlPurine nucleoside phosphorylase deoD-typeP0ABP8DEOD_ECOLIdeoDhttp://ecmdb.ca/proteins/P0ABP8.xmlUridine phosphorylaseP12758UDP_ECOLIudphttp://ecmdb.ca/proteins/P12758.xmlNon-specific ribonucleoside hydrolase rihCP22564RIHC_ECOLIrihChttp://ecmdb.ca/proteins/P22564.xmlCytosine deaminaseP25524CODA_ECOLIcodAhttp://ecmdb.ca/proteins/P25524.xmlPyrimidine-specific ribonucleoside hydrolase rihBP33022RIHB_ECOLIrihBhttp://ecmdb.ca/proteins/P33022.xmlPyrimidine-specific ribonucleoside hydrolase rihAP41409RIHA_ECOLIrihAhttp://ecmdb.ca/proteins/P41409.xmlPutative flavin reductase rutFP75893RUTF_ECOLIrutFhttp://ecmdb.ca/proteins/P75893.xmlUncharacterized protein yeiAP25889YEIA_ECOLIyeiAhttp://ecmdb.ca/proteins/P25889.xmlPutative monooxygenase rutAP75898RUTA_ECOLIrutAhttp://ecmdb.ca/proteins/P75898.xmlUncharacterized oxidoreductase yeiTP76440YEIT_ECOLIyeiThttp://ecmdb.ca/proteins/P76440.xmlUracil permeaseP0AGM7URAA_ECOLIuraAhttp://ecmdb.ca/proteins/P0AGM7.xmlPutative pyrimidine permease rutGP75892RUTG_ECOLIrutGhttp://ecmdb.ca/proteins/P75892.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.xmlHydrogen ion + NADH + Oxygen + Uracil > NAD + Ureidoacrylate peracidDihydrouracil + NAD <> Hydrogen ion + NADH + UracilDIHYDROURACIL-DEHYDROGENASE-NAD+-RXNWater + Uridine > Ribose + UracilDeoxyuridine + Phosphate <> Deoxyribose 1-phosphate + UracilR02484Cytosine + Hydrogen ion + Water > Ammonium + UracilPhosphoribosyl pyrophosphate + Uracil <> Pyrophosphate + Uridine 5'-monophosphateR00966URACIL-PRIBOSYLTRANS-RXNPhosphate + Uridine <> Ribose-1-phosphate + UracilURPHOS-RXNUridine 5'-monophosphate + Pyrophosphate <> Uracil + Phosphoribosyl pyrophosphateR00966Cytosine + Water <> Uracil + AmmoniaR00974CYTDEAM-RXNUridine + Phosphate <> Uracil + alpha-D-Ribose 1-phosphate + Ribose-1-phosphateR01876Uracil + FMNH + Oxygen <> Ureidoacrylate peracid + Flavin MononucleotideR09936RXN0-6444Deoxyuridine + Phosphate <> deoxyribose-1-phosphate + UracilURA-PHOSPH-RXNWater + Cytosine > Ammonia + UracilCYTDEAM-RXND-Ribose-5-phosphate + Uracil <> Water + Pseudouridine 5'-phosphateRXN0-5398Uracil + Oxygen + FMNH > Hydrogen ion + Ureidoacrylate peracid + Flavin MononucleotideRXN0-6444Pyrophosphate + Uridine 5'-monophosphate < Phosphoribosyl pyrophosphate + UracilURACIL-PRIBOSYLTRANS-RXNUridine + Water > D-ribose + UracilURIDINE-NUCLEOSIDASE-RXNDihydrouracil + NAD > Uracil + NADHPseudouridine 5'-phosphate + Water > Uracil + D-Ribose-5-phosphateRXN0-5398Uracil + FMNH(2) + Oxygen > Ureidoacrylate peracid + Flavin Mononucleotide + WaterUridine + Inorganic phosphate > Uracil + Ribose-1-phosphateUridine 5'-monophosphate + Pyrophosphate > Uracil + Phosphoribosyl pyrophosphateDihydrouracil + NAD + Dihydrothymine <> Uracil + NADH + Hydrogen ion + ThymineR00977 Uracil + FMNH + Oxygen + Thymine <> Ureidoacrylate peracid + Flavin Mononucleotide + (Z)-2-Methyl-ureidoacrylate peracidR09936 Pseudouridine 5'-phosphate + Water > Uracil + D-ribofuranose 5-phosphate + D-ribofuranose 5-phosphatePW_R005151Uracil + FMNH2 + Oxygen > Ureidoacrylate peracid + Flavin Mononucleotide + Hydrogen ion + PeroxyaminoacrylatePW_R005905Uridine + Phosphate > Uracil + Ribose-1-phosphatePW_R005898Deoxyuridine + Phosphate > Uracil + Deoxyribose 1-phosphatePW_R006018Cytosine + Water <> Uracil + AmmoniaPhosphoribosyl pyrophosphate + Uracil <> Pyrophosphate + Uridine 5'-monophosphateCytosine + Water <> Uracil + AmmoniaPhosphoribosyl pyrophosphate + Uracil <> Pyrophosphate + Uridine 5'-monophosphateLuria-Bertani (LB) mediaShake flask1013.0uMtrue99.037 oCBL21 DE3Stationary phase cultures (overnight culture)4052000396000Lin, Z., Johnson, L. C., Weissbach, H., Brot, N., Lively, M. O., Lowther, W. T. (2007). "Free methionine-(R)-sulfoxide reductase from Escherichia coli reveals a new GAF domain function." Proc Natl Acad Sci U S A 104:9597-9602.17535911