2.0 2012-05-31 13:51:28 -0600 2015-09-17 15:41:11 -0600 ECMDB01391 M2MDB000366 GDP-4-Dehydro-6-L-deoxygalactose GDP-4-dehydro-6-L-deoxygalactose is a member of the chemical class known as Purine Nucleotide Sugars. These are purine nucleotides bound to a saccharide derivative through the terminal phosphate group. GDP-6-deoxy-D-talose biosynthetic pathway involve the enzyme GDP-4-keto-6-deoxy-D-mannose-3-dehydratase, which catalyzes the third step in colitose production, which is the removal of the hydroxyl group at C3' of GDP-4-keto-6-deoxymannose. (PMID 16943443) GDP-4-Dehydro-6-deoxy-D-talose GDP-4-Dehydro-6-L-deoxygalactose GDP-4-Keto-6-deoxy-D-mannose GDP-4-Keto-6-deoxymannose GDP-4-Keto-6-L-deoxygalactose GDP-4-Oxo-6-deoxy-D-mannose GDP-4-Oxo-6-deoxymannose GDP-DDMan C16H23N5O15P2 587.3258 587.066588115 [({[3,4-dihydroxy-5-(6-hydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy][(3,4-dihydroxy-6-methyl-5-oxooxan-2-yl)oxy]phosphinic acid {[3,4-dihydroxy-5-(6-hydroxy-2-imino-3H-purin-9-yl)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(3,4-dihydroxy-6-methyl-5-oxooxan-2-yl)oxyphosphinic acid C[C@@H]1OC(OP(O)(=O)OP(O)(=O)OCC2O[C@H]([C@H](O)[C@@H]2O)N2C=NC3=C2N=C(N)NC3=O)[C@@H](O)[C@H](O)C1=O InChI=1S/C16H23N5O15P2/c1-4-7(22)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)21-3-18-6-12(21)19-16(17)20-13(6)27/h3-5,8-11,14-15,23-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)/t4-,5?,8+,9+,10+,11-,14+,15?/m0/s1 PNHLMHWWFOPQLK-GTXIGXBOSA-N Cytoplasm Periplasm logp -1.28 ALOGPS logs -1.97 ALOGPS solubility 6.35e+00 g/l ALOGPS logp -3.6 ChemAxon pka_strongest_acidic 1.74 ChemAxon pka_strongest_basic 4.94 ChemAxon iupac [({[3,4-dihydroxy-5-(6-hydroxy-2-imino-3,9-dihydro-2H-purin-9-yl)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy][(3,4-dihydroxy-6-methyl-5-oxooxan-2-yl)oxy]phosphinic acid ChemAxon average_mass 587.3258 ChemAxon mono_mass 587.066588115 ChemAxon smiles C[C@@H]1OC(OP(O)(=O)OP(O)(=O)OCC2O[C@H]([C@H](O)[C@@H]2O)N2C=NC3=C2N=C(N)NC3=O)[C@@H](O)[C@H](O)C1=O ChemAxon formula C16H23N5O15P2 ChemAxon inchi InChI=1S/C16H23N5O15P2/c1-4-7(22)9(24)11(26)15(33-4)35-38(30,31)36-37(28,29)32-2-5-8(23)10(25)14(34-5)21-3-18-6-12(21)19-16(17)20-13(6)27/h3-5,8-11,14-15,23-26H,2H2,1H3,(H,28,29)(H,30,31)(H3,17,19,20,27)/t4-,5?,8+,9+,10+,11-,14+,15?/m0/s1 ChemAxon inchikey PNHLMHWWFOPQLK-GTXIGXBOSA-N ChemAxon polar_surface_area 305.03 ChemAxon refractivity 126.78 ChemAxon polarizability 49.89 ChemAxon rotatable_bond_count 8 ChemAxon acceptor_count 16 ChemAxon donor_count 9 ChemAxon physiological_charge -2 ChemAxon formal_charge 0 ChemAxon Fructose and mannose metabolism ec00051 Amino sugar and nucleotide sugar metabolism ec00520 Amino sugar and nucleotide sugar metabolism II The synthesis of amino sugars and nucleotide sugars starts with the phosphorylation of N-Acetylmuramic acid (MurNac) through its transport from the periplasmic space to the cytoplasm. Once in the cytoplasm, MurNac and water undergo a reversible reaction through a N-acetylmuramic acid 6-phosphate etherase, producing a D-lactic acid and N-Acetyl-D-Glucosamine 6-phosphate. This latter compound can also be introduced into the cytoplasm through a phosphorylating PTS permase in the inner membrane that allows for the transport of N-Acetyl-D-glucosamine from the periplasmic space. N-Acetyl-D-Glucosamine 6-phosphate can also be obtained from chitin dependent reactions. Chitin is hydrated through a bifunctional chitinase to produce chitobiose. This in turn gets hydrated by a beta-hexosaminidase to produce N-acetyl-D-glucosamine. The latter undergoes an atp dependent phosphorylation leading to the production of N-Acetyl-D-Glucosamine 6-phosphate. N-Acetyl-D-Glucosamine 6-phosphate is then be deacetylated in order to produce Glucosamine 6-phosphate through a N-acetylglucosamine-6-phosphate deacetylase. This compound is then deaminased into Beta-D-fructofuranose 6-phosphate through a glucosamine-6-phosphate deaminase. The beta-D-fructofuranose 6 -phosphate is isomerized in a reversible reaction into an alpha-D-mannose 6-phosphate. This compound can also be introduced into the cell from the periplasmic space through a mannose PTS permease that phosphorylates an alpha-D-mannose. Alpha-D-mannose 6-phosphate undergoes a reversible reaction through a phosphomannomutase to produce an alpha-D-mannose 1-phosphate. The alpha-D-mannose 1-phosphate enters the nucleotide sugar metabolism through a reaction with GTP producing a GDP-mannose and releasing a pyrophosphate, all through a mannose-1-phosphate guanylyltransferase. GDP-mannose is then dehydrated to produce GDP-4-dehydro-6-deoxy-alpha-D-mannose through a GDP-mannose 4,6-dehydratase. This compound is then used to synthesize GDP-Beta-L-fucose through a NADPH dependent GDP-L-fucose synthase. Alpha-D-glucose is introduced into the cytoplasm through a glucose PTS permease, which phosphorylates the compound in order to produce an alpha-D-glucose 6-phosphate. This compound is then modified through a phosphoglucomutase 1 to yield alpha-D-glucose 1-phosphate. This compound can either be adenylated to produce ADP-glucose or uridylylated to produce galactose 1-phosphate through glucose-1-phosphate adenyllyltransferase and galactose-1-phosphate uridylyltransferase respectively. PW000887 Metabolic Specdb::MsMs 26657 Specdb::MsMs 26658 Specdb::MsMs 26659 Specdb::MsMs 33215 Specdb::MsMs 33216 Specdb::MsMs 33217 HMDB01391 711 C01222 16955 GDP-4-DEHYDRO-6-L-DEOXYGALACTOSE 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 Cook, P. D., Thoden, J. B., Holden, H. M. (2006). "The structure of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: a unique coenzyme B6-dependent enzyme." Protein Sci 15:2093-2106. 16943443 GDP-mannose 4,6-dehydratase P0AC88 GM4D_ECOLI gmd http://ecmdb.ca/proteins/P0AC88.xml GDP-L-fucose synthase P32055 FCL_ECOLI fcl http://ecmdb.ca/proteins/P32055.xml Guanosine diphosphate mannose > GDP-4-Dehydro-6-L-deoxygalactose + GDP-4-Dehydro-6-L-deoxygalactose PW_R005171