2.0 2012-05-31 13:03:12 -0600 2015-09-17 15:41:07 -0600 ECMDB01000 M2MDB000221 dUDP dUDP is a member of the chemical class known as Pyrimidine 2'-deoxyribonucleoside Diphosphates. These are pyrimidine nucleotides with a diphosphate group linked to the ribose moiety lacking an hydroxyl group at position 2. Deoxyuridine Diphosphate (dUDP) dUDP is a deoxyribonucleotide made from UDP in the reaction catalyzed by ribonucleotide reductase, as follows: UDP + NADPH <=> dUDP + NADP+ (http://www.pearsonhighered.com/mathews/molex/dudp.htm) 2'-Deoxyuridine-5'-diphosphate 2'-Deoxyuridine-5'-diphosphoric acid Deoxyuridine-diphosphate Deoxyuridine-diphosphoric acid DUDP C9H14N2O11P2 388.1618 388.007282324 [({[5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid deoxyuridine-5'-diphosphate O[C@H]1C[C@@H](O[C@@H]1COP(O)(=O)OP(O)(O)=O)N1C=CC(=O)NC1=O InChI=1S/C9H14N2O11P2/c12-5-3-8(11-2-1-7(13)10-9(11)14)21-6(5)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,18,19)(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1 QHWZTVCCBMIIKE-SHYZEUOFSA-N Cytosol logp -0.99 ALOGPS logs -1.68 ALOGPS solubility 8.03e+00 g/l ALOGPS logp -2.1 ChemAxon pka_strongest_acidic 1.77 ChemAxon pka_strongest_basic -3.2 ChemAxon iupac [({[5-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-3-hydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy]phosphonic acid ChemAxon average_mass 388.1618 ChemAxon mono_mass 388.007282324 ChemAxon smiles O[C@H]1C[C@@H](O[C@@H]1COP(O)(=O)OP(O)(O)=O)N1C=CC(=O)NC1=O ChemAxon formula C9H14N2O11P2 ChemAxon inchi InChI=1S/C9H14N2O11P2/c12-5-3-8(11-2-1-7(13)10-9(11)14)21-6(5)4-20-24(18,19)22-23(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,18,19)(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1 ChemAxon inchikey QHWZTVCCBMIIKE-SHYZEUOFSA-N ChemAxon polar_surface_area 192.16 ChemAxon refractivity 72.8 ChemAxon polarizability 30.47 ChemAxon rotatable_bond_count 6 ChemAxon acceptor_count 9 ChemAxon donor_count 5 ChemAxon physiological_charge -2 ChemAxon formal_charge 0 ChemAxon Pyrimidine metabolism 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. PW000942 ec00240 Metabolic pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis I PWY0-166 Specdb::MsMs 23510 Specdb::MsMs 23511 Specdb::MsMs 23512 Specdb::MsMs 30308 Specdb::MsMs 30309 Specdb::MsMs 30310 HMDB01000 667 C01346 DUDP Keseler, 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. 21097882 van 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. 17765195 Ribonucleoside-diphosphate reductase 1 subunit alpha P00452 RIR1_ECOLI nrdA http://ecmdb.ca/proteins/P00452.xml Thymidylate kinase P0A720 KTHY_ECOLI tmk http://ecmdb.ca/proteins/P0A720.xml Nucleoside diphosphate kinase P0A763 NDK_ECOLI ndk http://ecmdb.ca/proteins/P0A763.xml Uridine kinase P0A8F4 URK_ECOLI udk http://ecmdb.ca/proteins/P0A8F4.xml Thioredoxin-2 P0AGG4 THIO2_ECOLI trxC http://ecmdb.ca/proteins/P0AGG4.xml Anaerobic ribonucleoside-triphosphate reductase P28903 NRDD_ECOLI nrdD http://ecmdb.ca/proteins/P28903.xml Ribonucleoside-diphosphate reductase 2 subunit beta P37146 RIR4_ECOLI nrdF http://ecmdb.ca/proteins/P37146.xml Ribonucleoside-diphosphate reductase 2 subunit alpha P39452 RIR3_ECOLI nrdE http://ecmdb.ca/proteins/P39452.xml Adenylate kinase P69441 KAD_ECOLI adk http://ecmdb.ca/proteins/P69441.xml Ribonucleoside-diphosphate reductase 1 subunit beta P69924 RIR2_ECOLI nrdB http://ecmdb.ca/proteins/P69924.xml Glutaredoxin-4 P0AC69 GLRX4_ECOLI grxD http://ecmdb.ca/proteins/P0AC69.xml Glutaredoxin-3 P0AC62 GLRX3_ECOLI grxC http://ecmdb.ca/proteins/P0AC62.xml Glutaredoxin-2 P0AC59 GLRX2_ECOLI grxB http://ecmdb.ca/proteins/P0AC59.xml Glutaredoxin-1 P68688 GLRX1_ECOLI grxA http://ecmdb.ca/proteins/P68688.xml Thioredoxin-1 P0AA25 THIO_ECOLI trxA http://ecmdb.ca/proteins/P0AA25.xml Nucleoside diphosphate kinase P0A763 NDK_ECOLI ndk http://ecmdb.ca/proteins/P0A763.xml Reduced Thioredoxin + Uridine 5'-diphosphate > dUDP + Water + Oxidized Thioredoxin glutaredoxin + Uridine 5'-diphosphate > dUDP + glutaredoxin + Water Adenosine triphosphate + dUDP <> ADP + Deoxyuridine triphosphate R02331 DUDPKIN-RXN dUDP + Adenosine triphosphate > Deoxyuridine triphosphate + ADP DUDPKIN-RXN dUDP + Adenosine triphosphate + dUDP > Adenosine diphosphate + Deoxyuridine triphosphate + ADP PW_R003538 Uridine 5'-diphosphate + reduced thioredoxin + Uridine 5'-diphosphate oxidized thioredoxin + Water + dUDP + dUDP PW_R003537 Adenosine triphosphate + dUMP <> ADP + dUDP