2.0 2012-05-31 14:05:06 -0600 2015-06-03 15:54:44 -0600 ECMDB04103 M2MDB000611 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate 2-c-methyl-D-erythritol-2,4-cyclodiphosphate is a member of the chemical class known as Organic Pyrophosphates. These are organic compounds containing the pyrophosphate oxoanion, with the structure OP([O-])(=O)OP(O)([O-])=O. 2-C-Methyl-D-erythritol-2,4-cyclodiphosphoric acid ME-2,4cPP MeEry2,4CP C5H10O9P2 276.075 275.980004942 (6S,7R)-7-hydroxy-6-(hydroxymethyl)-6-methyl-2,4-dioxo-1,3,5,2lambda5,4lambda5-trioxadiphosphocane-2,4-bis(olate) (6S,7R)-7-hydroxy-6-(hydroxymethyl)-6-methyl-2,4-dioxo-1,3,5,2lambda5,4lambda5-trioxadiphosphocane-2,4-bis(olate) 143488-44-2 [H][C@@]1(O)COP([O-])(=O)OP([O-])(=O)O[C@@]1(C)CO InChI=1S/C5H12O9P2/c1-5(3-6)4(7)2-12-15(8,9)14-16(10,11)13-5/h4,6-7H,2-3H2,1H3,(H,8,9)(H,10,11)/p-2/t4-,5+/m1/s1 SFRQRNJMIIUYDI-UHNVWZDZSA-L Cytosol logp -1.01 ALOGPS logs -0.76 ALOGPS solubility 5.46e+01 g/l ALOGPS logp -1.8 ChemAxon pka_strongest_acidic 1.83 ChemAxon pka_strongest_basic -3.1 ChemAxon iupac (6S,7R)-7-hydroxy-6-(hydroxymethyl)-6-methyl-2,4-dioxo-1,3,5,2lambda5,4lambda5-trioxadiphosphocane-2,4-bis(olate) ChemAxon average_mass 276.075 ChemAxon mono_mass 275.980004942 ChemAxon smiles [H][C@@]1(O)COP([O-])(=O)OP([O-])(=O)O[C@@]1(C)CO ChemAxon formula C5H10O9P2 ChemAxon inchi InChI=1S/C5H12O9P2/c1-5(3-6)4(7)2-12-15(8,9)14-16(10,11)13-5/h4,6-7H,2-3H2,1H3,(H,8,9)(H,10,11)/p-2/t4-,5+/m1/s1 ChemAxon inchikey SFRQRNJMIIUYDI-UHNVWZDZSA-L ChemAxon polar_surface_area 148.41 ChemAxon refractivity 46.84 ChemAxon polarizability 19.85 ChemAxon rotatable_bond_count 1 ChemAxon acceptor_count 6 ChemAxon donor_count 2 ChemAxon physiological_charge -2 ChemAxon formal_charge -2 ChemAxon Terpenoid backbone biosynthesis ec00900 Metabolic pathways eco01100 Secondary metabolites: isoprenoid biosynthesis (nonmevalonate pathway) The biosynthesis of isoprenoids starts with a D-glyceraldehyde 3-phosphate interacting with a hydrogen ion through a 1-deoxyxylulose-5-phosphate synthase resulting in a carbon dioxide and 1-Deoxy-D-xylulose. The latter compound then interacts with a hydrogen ion through a NADPH driven 1-deoxy-D-xylulose 5-phosphate reductoisomerase resulting in a NADP and a 2-C-methyl-D-erythritol 4-phosphate. The latter compound then interacts with a cytidine triphosphate and a hydrogen ion through a 4-diphosphocytidyl-2C-methyl-D-erythritol synthase resulting in a pyrophosphate and a 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol. The latter compound is then phosphorylated through an ATP driven 4-diphosphocytidyl-2-C-methylerythritol kinase resulting in a release of an ADP, a hydrogen ion and a 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol. The latter compound then interacts with a 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase resulting in the release of a 2-C-methyl-D-erythritol-2,4-cyclodiphosphate resulting in the release of a cytidine monophosphate and 2-C-methyl-D-erythritol-2,4-cyclodiphosphate. The latter compound then interacts with a reduced flavodoxin through a 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase resulting in the release of a water molecule, a hydrogen ion, an oxidized flavodoxin and a 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate. The compound 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate can interact with an NADPH,a hydrogen ion through a 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase resulting in a NADP, a water molecule and either a Dimethylallylpyrophosphate or a Isopentenyl pyrophosphate. These two last compounds can be are isomers that can be produced through a isopentenyl diphosphate isomerase.and then get incorporated into the methylerythritol phosphate and polyisoprenoid biosynthesis pathway PW000975 Metabolic Secondary metabolites: methylerythritol phosphate and polyisoprenoid biosynthesis The biosynthesis of isoprenoids starts with a D-glyceraldehyde 3-phosphate interacting with a hydrogen ion through a 1-deoxyxylulose-5-phosphate synthase resulting in a carbon dioxide and 1-Deoxy-D-xylulose. The latter compound then interacts with a hydrogen ion through a NADPH driven 1-deoxy-D-xylulose 5-phosphate reductoisomerase resulting in a NADP and a 2-C-methyl-D-erythritol 4-phosphate. The latter compound then interacts with a cytidine triphosphate and a hydrogen ion through a 4-diphosphocytidyl-2C-methyl-D-erythritol synthase resulting in a pyrophosphate and a 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol. The latter compound is then phosphorylated through an ATP driven 4-diphosphocytidyl-2-C-methylerythritol kinase resulting in a release of an ADP, a hydrogen ion and a 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol. The latter compound then interacts with a 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase resulting in the release of a 2-C-methyl-D-erythritol-2,4-cyclodiphosphate resulting in the release of a cytidine monophosphate and 2-C-methyl-D-erythritol-2,4-cyclodiphosphate. The latter compound then interacts with a reduced flavodoxin through a 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate synthase resulting in the release of a water molecule, a hydrogen ion, an oxidized flavodoxin and a 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate. The compound 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate can interact with an NADPH,a hydrogen ion through a 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase resulting in a NADP, a water molecule and either a Dimethylallylpyrophosphate or a Isopentenyl pyrophosphate. These two last compounds can be are isomers that can be produced through a isopentenyl diphosphate isomerase. Dimethylallylpyrophosphate interacts with the isopentenyl pyrophosphate through a geranyl diphosphate synthase / farnesyl diphosphate synthase resulting in a pyrophosphate and a geranyl--PP. The latter compound interacts with a Isopentenyl pyrophosphate through a geranyl diphosphate synthase / farnesyl diphosphate synthase resulting in the release of a pyrophosphate and a farnesyl pyrophosphate. The latter compound interacts with isopentenyl pyrophosphate either through a undecaprenyl diphosphate synthase resulting in a release of a pyrophosphate and a di-trans,octa-cis-undecaprenyl diphosphate or through a octaprenyl diphosphate synthase resulting in a pyrophosphate and an octaprenyl diphosphate PW000958 Metabolic methylerythritol phosphate pathway NONMEVIPP-PWY Specdb::NmrOneD 288415 Specdb::NmrOneD 288416 Specdb::NmrOneD 288417 Specdb::NmrOneD 288418 Specdb::NmrOneD 288419 Specdb::NmrOneD 288420 Specdb::NmrOneD 288421 Specdb::NmrOneD 288422 Specdb::NmrOneD 288423 Specdb::NmrOneD 288424 Specdb::NmrOneD 288425 Specdb::NmrOneD 288426 Specdb::NmrOneD 288427 Specdb::NmrOneD 288428 Specdb::NmrOneD 288429 Specdb::NmrOneD 288430 Specdb::NmrOneD 288431 Specdb::NmrOneD 288432 Specdb::NmrOneD 288433 Specdb::NmrOneD 288434 Specdb::MsMs 28304 Specdb::MsMs 28305 Specdb::MsMs 28306 Specdb::MsMs 34862 Specdb::MsMs 34863 Specdb::MsMs 34864 21605869 10241147 C11453 18425 2C-METH-D-ERYTHRITOL-CYCLODIPHOSPHATE 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 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 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase P62617 ISPF_ECOLI ispF http://ecmdb.ca/proteins/P62617.xml 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase P62620 ISPG_ECOLI ispG http://ecmdb.ca/proteins/P62620.xml Flavodoxin-2 P0ABY4 FLAW_ECOLI fldB http://ecmdb.ca/proteins/P0ABY4.xml Flavodoxin-1 P61949 FLAV_ECOLI fldA http://ecmdb.ca/proteins/P61949.xml 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + 2 Flavodoxin reduced + Hydrogen ion >2 flavodoxin semi oxidized + 1-Hydroxy-2-methyl-2-butenyl 4-diphosphate + Water 2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol <> 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + Cytidine monophosphate R05637 RXN0-302 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + 2 Reduced ferredoxin + Oxidized ferredoxin <> 1-Hydroxy-2-methyl-2-butenyl 4-diphosphate + Water +2 Oxidized ferredoxin + Reduced ferredoxin R08689 2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol > Cytidine monophosphate + 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate RXN0-302 1-Hydroxy-2-methyl-2-butenyl 4-diphosphate + Water + Oxidized-ferredoxins < 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + Hydrogen ion + Reduced-ferredoxins RXN0-882 2-phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol + 2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol > Cytidine monophosphate + 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + Cytidine monophosphate PW_R003691 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + a reduced flavodoxin > Water + Hydrogen ion + an oxidized flavodoxin + 1-Hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate PW_R003692 2 2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol <>2 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + Cytidine monophosphate 2 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + 2 Reduced ferredoxin + Oxidized ferredoxin <> 1-Hydroxy-2-methyl-2-butenyl 4-diphosphate + Water 2 2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol <>2 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + Cytidine monophosphate