2.0 2012-05-31 13:49:58 -0600 2015-09-13 15:15:22 -0600 ECMDB01328 M2MDB000339 dTDP-D-Glucose dTDP-D-glucose is a member of the chemical class known as Pyrimidine Nucleotide Sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group. dTDP-D-glucose is a key metabolite in prokaryotes as a precursor for a large number of modified deoxysugars, and these deoxysugars are a major part of various antibiotics, ranging from glycosides to macrolides. (PMID 18051285) DTDP-D-Glucose DTDP-delta-glucose DTDP-Glc DTDP-Glucose dTDP-δ-Glucose DTDPglucose Mono-a-D-glucopyranosyl ester mono-a-delta-Glucopyranosyl ester mono-a-δ-Glucopyranosyl ester Mono-alpha-D-glucopyranosyl ester Mono-alpha-delta-glucopyranosyl ester mono-α-D-Glucopyranosyl ester mono-α-δ-Glucopyranosyl ester P-a-D-Glucopyranosyl ester P-alpha-D-Glucopyranosyl ester P-α-D-Glucopyranosyl ester TDP-D-Glucose TDP-delta-glucose TDP-Glc TDP-Glucose TDP-δ-Glucose TDPG Thymidine 5-(trihydrogen diphosphate) Thymidine 5-(trihydrogen diphosphoric acid) Thymidine 5-diphosphate-D-Glucose Thymidine 5-diphosphate-delta-Glucose Thymidine 5-diphosphate-δ-glucose Thymidine 5-diphosphoric acid-D-glucose Thymidine 5-diphosphoric acid-delta-glucose Thymidine 5-diphosphoric acid-δ-glucose C16H26N2O16P2 564.329 564.075755818 {[hydroxy({[(3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})phosphoryl]oxy}({[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphinic acid dtdp-D-glucose 2196-62-5 CC1=CN([C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)OC3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)O2)C(=O)NC1=O InChI=1S/C16H26N2O16P2/c1-6-3-18(16(25)17-14(6)24)10-2-7(20)9(31-10)5-30-35(26,27)34-36(28,29)33-15-13(23)12(22)11(21)8(4-19)32-15/h3,7-13,15,19-23H,2,4-5H2,1H3,(H,26,27)(H,28,29)(H,17,24,25)/t7-,8+,9+,10+,11+,12-,13+,15?/m0/s1 YSYKRGRSMLTJNL-KFQCIAAJSA-N Cytosol logp -1.21 ALOGPS logs -1.70 ALOGPS solubility 1.12e+01 g/l ALOGPS logp -3.7 ChemAxon pka_strongest_acidic 1.73 ChemAxon pka_strongest_basic -3 ChemAxon iupac {[hydroxy({[(3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy})phosphoryl]oxy}({[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)oxolan-2-yl]methoxy})phosphinic acid ChemAxon average_mass 564.329 ChemAxon mono_mass 564.075755818 ChemAxon smiles CC1=CN([C@H]2C[C@H](O)[C@@H](COP(O)(=O)OP(O)(=O)OC3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)O2)C(=O)NC1=O ChemAxon formula C16H26N2O16P2 ChemAxon inchi InChI=1S/C16H26N2O16P2/c1-6-3-18(16(25)17-14(6)24)10-2-7(20)9(31-10)5-30-35(26,27)34-36(28,29)33-15-13(23)12(22)11(21)8(4-19)32-15/h3,7-13,15,19-23H,2,4-5H2,1H3,(H,26,27)(H,28,29)(H,17,24,25)/t7-,8+,9+,10+,11+,12-,13+,15?/m0/s1 ChemAxon inchikey YSYKRGRSMLTJNL-KFQCIAAJSA-N ChemAxon polar_surface_area 271.31 ChemAxon refractivity 109.3 ChemAxon polarizability 46.61 ChemAxon rotatable_bond_count 9 ChemAxon acceptor_count 13 ChemAxon donor_count 8 ChemAxon physiological_charge -2 ChemAxon formal_charge 0 ChemAxon Starch and sucrose metabolism The metabolism of starch and sucrose begins with D-fructose interacting with a D-glucose in a reversible reaction through a maltodextrin glucosidase resulting in a water molecule and a sucrose. D-fructose is phosphorylated through an ATP driven fructokinase resulting in the release of an ADP, a hydrogen ion and a Beta-D-fructofuranose 6-phosphate. This compound can also be introduced into the cytoplasm through either a mannose PTS permease or a hexose-6-phosphate:phosphate antiporter. The Beta-D-fructofuranose 6-phosphate is isomerized through a phosphoglucose isomerase resulting in a Beta-D-glucose 6-phosphate. This compound can also be incorporated by glucose PTS permease or a hexose-6-phosphate:phosphate antiporter. The beta-D-glucose 6 phosphate can also be produced by a D-glucose being phosphorylated by an ATP-driven glucokinase resulting in a ADP, a hydrogen ion and a Beta-D-glucose 6 phosphate. The beta-D-glucose can produce alpha-D-glucose-1-phosphate by two methods: 1.-Beta-D-glucose is isomerized into an alpha-D-Glucose 6-phosphate and then interacts in a reversible reaction through a phosphoglucomutase-1 resulting in a alpha-D-glucose-1-phosphate. 2.-Beta-D-glucose interacts with a putative beta-phosphoglucomutase resulting in a Beta-D-glucose 1-phosphate. Beta-D-glucose 1-phosphate can be incorporated into the cytoplasm through a glucose PTS permease. This compound is then isomerized into a Alpha-D-glucose-1-phosphate The beta-D-glucose can cycle back into a D-fructose by first interacting with D-fructose in a reversible reaction through a Polypeptide: predicted glucosyltransferase resulting in the release of a phosphate and a sucrose. The sucrose then interacts in a reversible reaction with a water molecule through a maltodextrin glucosidase resulting in a D-glucose and a D-fructose. Alpha-D-glucose-1-phosphate can produce glycogen in by two different sets of reactions: 1.-Alpha-D-glucose-1-phosphate interacts with a hydrogen ion and an ATP through a glucose-1-phosphate adenylyltransferase resulting in a pyrophosphate and an ADP-glucose. The ADP-glucose then interacts with an amylose through a glycogen synthase resulting in the release of an ADP and an Amylose. The amylose then interacts with 1,4-α-glucan branching enzyme resulting in glycogen 2.- Alpha-D-glucose-1-phosphate interacts with amylose through a maltodextrin phosphorylase resulting in a phosphate and a glycogen. Alpha-D-glucose-1-phosphate can also interacts with UDP-galactose through a galactose-1-phosphate uridylyltransferase resulting in a galactose 1-phosphate and a Uridine diphosphate glucose. The UDP-glucose then interacts with an alpha-D-glucose 6-phosphate through a trehalose-6-phosphate synthase resulting in a uridine 5'-diphosphate, a hydrogen ion and a Trehalose 6- phosphate. The latter compound can also be incorporated into the cytoplasm through a trehalose PTS permease. Trehalose interacts with a water molecule through a trehalose-6-phosphate phosphatase resulting in the release of a phosphate and an alpha,alpha-trehalose.The alpha,alpha-trehalose can also be obtained from glycogen being metabolized through a glycogen debranching enzyme resulting in a the alpha, alpha-trehalose. This compound ca then be hydrated through a cytoplasmic trehalase resulting in the release of an alpha-D-glucose and a beta-d-glucose. Glycogen is then metabolized by reacting with a phosphate through a glycogen phosphorylase resulting in a alpha-D-glucose-1-phosphate and a dextrin. The dextrin is then hydrated through a glycogen phosphorylase-limit dextrin α-1,6-glucohydrolase resulting in the release of a debranched limit dextrin and a maltotetraose. This compound can also be incorporated into the cytoplasm through a maltose ABC transporter. The maltotetraose interacts with a phosphate through a maltodextrin phosphorylase releasing a alpha-D-glucose-1-phosphate and a maltotriose. The maltotriose can also be incorporated through a maltose ABC transporter. The maltotriose can then interact with water through a maltodextrin glucosidase resulting in a D-glucose and a D-maltose. D-maltose can also be incorporated through a maltose ABC transporter The D-maltose can then interact with a maltotriose through a amylomaltase resulting in a maltotetraose and a D-glucose. The D-glucose is then phosphorylated through an ATP driven glucokinase resulting in a hydrogen ion, an ADP and a Beta-D-glucose 6-phosphate PW000941 ec00500 Metabolic Streptomycin biosynthesis ec00521 Polyketide sugar unit biosynthesis ec00523 Biosynthesis of vancomycin group antibiotics ec01055 Metabolic pathways eco01100 Secondary Metabolites: enterobacterial common antigen biosynthesis The biosynthesis of a enterobacterial common antigen can begin with a di-trans,octa-cis-undecaprenyl phosphate interacts with a Uridine diphosphate-N-acetylglucosamine through undecaprenyl-phosphate α-N-acetylglucosaminyl transferase resulting in a N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol and a Uridine 5'-monophosphate. The N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol then reacts with an UDP-ManNAcA from the Amino sugar and nucleotide sugar metabolism pathway. This reaction is metabolized by a UDP-N-acetyl-D-mannosaminuronic acid transferase resulting in a uridine 5' diphosphate, a hydrogen ion and a Undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate-4-acetamido-4,6-dideoxy-D-galactose pyrophosphate. Glucose 1 phosphate can be metabolize by interacting with a hydrogen ion and a thymidine 5-triphosphate by either reacting with a dTDP-glucose pyrophosphorylase or a dTDP-glucose pyrophosphorylase 2 resulting in the release of a pyrophosphate and a dTDP-D-glucose. The latter compound is then dehydrated through an dTDP-glucose 4,6-dehydratase 2 resulting in water and dTDP-4-dehydro-6-deoxy-D-glucose. The latter compound interacts with L-glutamic acid through a dTDP-4-dehydro-6-deoxy-D-glucose transaminase resulting in the release of oxoglutaric acid and dTDP-thomosamine. The latter compound interacts with acetyl-coa through a dTDP-fucosamine acetyltransferase resulting in a Coenzyme A, a hydrogen Ion and a TDP-Fuc4NAc. Undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate-4-acetamido-4,6-dideoxy-D-galactose pyrophosphate then interacts with a TDP--Fuc4NAc through a 4-acetamido-4,6-dideoxy-D-galactose transferase resulting in a hydrogen ion, a dTDP and a Undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate-4-acetamido-4,6-dideoxy-D-galactose pyrophosphate. This compound is then transported through a protein wzxE into the periplasmic space so that it can be incorporated into the outer membrane Enterobacterial common antigen (ECA) is an outer membrane glycolipid common to all members of Enterobacteriaceae. ECA is a unique cell surface antigen that can be found in the outer leaflet of the outer membrane. The carbohydrate portion consists of N-acetyl-glucosamine, N-acetyl-D-mannosaminuronic acid and 4-acetamido-4,6-dideoxy-D-galactose. These amino sugars form trisaccharide repeat units which are part of linear heteropolysaccharide chains. PW000959 Metabolic Secondary Metabolites: enterobacterial common antigen biosynthesis 2 The biosynthesis of a enterobacterial common antigen can begin with a di-trans,octa-cis-undecaprenyl phosphate interacts with a Uridine diphosphate-N-acetylglucosamine through undecaprenyl-phosphate α-N-acetylglucosaminyl transferase resulting in a N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol and a Uridine 5'-monophosphate. The N-acetyl-α-D-glucosaminyl-diphospho-ditrans,octacis-undecaprenol then reacts with an UDP-ManNAcA from the Amino sugar and nucleotide sugar metabolism pathway. This reaction is metabolized by a UDP-N-acetyl-D-mannosaminuronic acid transferase resulting in a uridine 5' diphosphate, a hydrogen ion and a Undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate-4-acetamido-4,6-dideoxy-D-galactose pyrophosphate. Glucose 1 phosphate can be metabolize by interacting with a hydrogen ion and a thymidine 5-triphosphate by either reacting with a dTDP-glucose pyrophosphorylase or a dTDP-glucose pyrophosphorylase 2 resulting in the release of a pyrophosphate and a dTDP-D-glucose. The latter compound is then dehydrated through an dTDP-glucose 4,6-dehydratase 2 resulting in water and dTDP-4-dehydro-6-deoxy-D-glucose. The latter compound interacts with L-glutamic acid through a dTDP-4-dehydro-6-deoxy-D-glucose transaminase resulting in the release of oxoglutaric acid and dTDP-thomosamine. The latter compound interacts with acetyl-coa through a dTDP-fucosamine acetyltransferase resulting in a Coenzyme A, a hydrogen Ion and a TDP-Fuc4NAc. Undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate-4-acetamido-4,6-dideoxy-D-galactose pyrophosphate then interacts with a TDP--Fuc4NAc through a 4-acetamido-4,6-dideoxy-D-galactose transferase resulting in a hydrogen ion, a dTDP and a Undecaprenyl N-acetyl-glucosaminyl-N-acetyl-mannosaminuronate-4-acetamido-4,6-dideoxy-D-galactose pyrophosphate. This compound is then transported through a protein wzxE into the periplasmic space so that it can be incorporated into the outer membrane Enterobacterial common antigen (ECA) is an outer membrane glycolipid common to all members of Enterobacteriaceae. ECA is a unique cell surface antigen that can be found in the outer leaflet of the outer membrane. The carbohydrate portion consists of N-acetyl-glucosamine, N-acetyl-D-mannosaminuronic acid and 4-acetamido-4,6-dideoxy-D-galactose. These amino sugars form trisaccharide repeat units which are part of linear heteropolysaccharide chains. PW002045 Metabolic O-antigen building blocks biosynthesis Lipopolysaccharide (LPS), a major outer membrane component, is composed of three domains: Lipid A; the core, which is an oligosaccharide consisting of an inner and outer region; and a distal repeating unit known as O-antigen. E. coli K12 is capable of producing an O-antigen when all the rfb genes are intact. The O-antigen is part of the lipopolysaccharide and is attached to the lipid A-core component, which is separately synthesized. The O-antigen is a repeat unit composed of four sugars: glucose, N-acetylglucosamine, galactose and rhamnose. This pathway depicts the synthesis of three of these sugars. UDP-galactose is transformed from its pyranose form to its furanose form. dTTP glucose-1-phosphate is derivatized to dTDP-rhamnose. Fructose-6-phosphate gains an amino group, incorporates an acetate moiety and then acquires a nucleoside diphosphate resulting in UDP-N-acetyl-D-glucosamine.(EcoCyc) PW002089 Metabolic enterobacterial common antigen biosynthesis ECASYN-PWY dTDP-L-rhamnose biosynthesis I DTDPRHAMSYN-PWY Specdb::CMs 25749 Specdb::CMs 38025 Specdb::NmrOneD 286015 Specdb::NmrOneD 286016 Specdb::NmrOneD 286017 Specdb::NmrOneD 286018 Specdb::NmrOneD 286019 Specdb::NmrOneD 286020 Specdb::NmrOneD 286021 Specdb::NmrOneD 286022 Specdb::NmrOneD 286023 Specdb::NmrOneD 286024 Specdb::NmrOneD 286025 Specdb::NmrOneD 286026 Specdb::NmrOneD 286027 Specdb::NmrOneD 286028 Specdb::NmrOneD 286029 Specdb::NmrOneD 286030 Specdb::NmrOneD 286031 Specdb::NmrOneD 286032 Specdb::NmrOneD 286033 Specdb::NmrOneD 286034 Specdb::MsMs 25352 Specdb::MsMs 25353 Specdb::MsMs 25354 Specdb::MsMs 31910 Specdb::MsMs 31911 Specdb::MsMs 31912 HMDB01328 439324 388455 C00842 15700 DTDP-D-GLUCOSE 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 Kanehisa, 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. 22080510 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 Winder, 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. 18331064 Han, J. M., Kim, S. M., Lee, H. J., Yoo, J. C. (2007). "Cloning and expression of glucose-1-phosphate thymidylyltransferase gene (schS6) from Streptomyces sp. SCC-2136." J Microbiol Biotechnol 17:685-690. 18051285 Goncalves, Ruth J. Thymidine diphosphate glucose and biosynthesis of glucosides in wheat germ. I. Enzymologia (1963), 26(5), 287-93. UDP-glucose 4-epimerase P09147 GALE_ECOLI galE http://ecmdb.ca/proteins/P09147.xml dTDP-glucose 4,6-dehydratase 2 P27830 RMLB2_ECOLI rffG http://ecmdb.ca/proteins/P27830.xml Glucose-1-phosphate thymidylyltransferase 1 P37744 RMLA1_ECOLI rmlA1 http://ecmdb.ca/proteins/P37744.xml dTDP-glucose 4,6-dehydratase 1 P37759 RMLB1_ECOLI rfbB http://ecmdb.ca/proteins/P37759.xml Glucose-1-phosphate thymidylyltransferase 2 P61887 RMLA2_ECOLI rmlA2 http://ecmdb.ca/proteins/P61887.xml Thymidine 5'-triphosphate + Glucose 1-phosphate + Hydrogen ion <> dTDP-D-Glucose + Pyrophosphate R02328 DTDPGLUCOSEPP-RXN dTDP-D-Glucose <> 4,6-Dideoxy-4-oxo-dTDP-D-glucose + Water R06513 DTDPGLUCDEHYDRAT-RXN Thymidine 5'-triphosphate + Glucose 1-phosphate <> Pyrophosphate + dTDP-D-Glucose R02328 dTDP-D-Glucose <> dTDP-D-Galactose R02984 dTDP-D-Glucose > dTDP-4-dehydro-6-deoxy-D-glucose + Water PW_R003705 Thymidine 5'-triphosphate + Hydrogen ion + Glucose 1-phosphate > Pyrophosphate + dTDP-D-Glucose PW_R003706 Alpha-D-glucose 1-phosphate + Thymidine 5'-triphosphate + Hydrogen ion > Pyrophosphate + dTDP-D-Glucose PW_R005999 dTDP-D-Glucose > Water + 4,6-Dideoxy-4-oxo-dTDP-D-glucose PW_R006002 α-D-glucose 1-phosphate + Thymidine 5'-triphosphate + Hydrogen ion > dTDP-D-Glucose + Pyrophosphate PW_R006096 dTDP-D-Glucose <> dTDP-D-Galactose dTDP-D-Glucose <>4 4,6-Dideoxy-4-oxo-dTDP-D-glucose + Water Thymidine 5'-triphosphate + Glucose 1-phosphate + Hydrogen ion <> dTDP-D-Glucose + Pyrophosphate