2.02012-05-31 14:05:06 -06002015-06-03 15:54:44 -0600ECMDB04103M2MDB0006112-C-Methyl-D-erythritol-2,4-cyclodiphosphate2-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 acidME-2,4cPPMeEry2,4CPC5H10O9P2276.075275.980004942(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)COInChI=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/s1SFRQRNJMIIUYDI-UHNVWZDZSA-LCytosollogp-1.01logs-0.76solubility5.46e+01 g/llogp-1.8pka_strongest_acidic1.83pka_strongest_basic-3.1iupac(6S,7R)-7-hydroxy-6-(hydroxymethyl)-6-methyl-2,4-dioxo-1,3,5,2lambda5,4lambda5-trioxadiphosphocane-2,4-bis(olate)average_mass276.075mono_mass275.980004942smiles[H][C@@]1(O)COP([O-])(=O)OP([O-])(=O)O[C@@]1(C)COformulaC5H10O9P2inchiInChI=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/s1inchikeySFRQRNJMIIUYDI-UHNVWZDZSA-Lpolar_surface_area148.41refractivity46.84polarizability19.85rotatable_bond_count1acceptor_count6donor_count2physiological_charge-2formal_charge-2Terpenoid backbone biosynthesisec00900Metabolic pathwayseco01100Secondary 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 pathwayPW000975MetabolicSecondary metabolites: methylerythritol phosphate and polyisoprenoid biosynthesisThe 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 diphosphatePW000958Metabolicmethylerythritol phosphate pathwayNONMEVIPP-PWYSpecdb::NmrOneD288415Specdb::NmrOneD288416Specdb::NmrOneD288417Specdb::NmrOneD288418Specdb::NmrOneD288419Specdb::NmrOneD288420Specdb::NmrOneD288421Specdb::NmrOneD288422Specdb::NmrOneD288423Specdb::NmrOneD288424Specdb::NmrOneD288425Specdb::NmrOneD288426Specdb::NmrOneD288427Specdb::NmrOneD288428Specdb::NmrOneD288429Specdb::NmrOneD288430Specdb::NmrOneD288431Specdb::NmrOneD288432Specdb::NmrOneD288433Specdb::NmrOneD288434Specdb::MsMs28304Specdb::MsMs28305Specdb::MsMs28306Specdb::MsMs34862Specdb::MsMs34863Specdb::MsMs348642160586910241147C11453184252C-METH-D-ERYTHRITOL-CYCLODIPHOSPHATEKeseler, 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-D114.22080510Winder, 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 80:2939-2948.183310642-C-methyl-D-erythritol 2,4-cyclodiphosphate synthaseP62617ISPF_ECOLIispFhttp://ecmdb.ca/proteins/P62617.xml4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthaseP62620ISPG_ECOLIispGhttp://ecmdb.ca/proteins/P62620.xmlFlavodoxin-2P0ABY4FLAW_ECOLIfldBhttp://ecmdb.ca/proteins/P0ABY4.xmlFlavodoxin-1P61949FLAV_ECOLIfldAhttp://ecmdb.ca/proteins/P61949.xml2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + 2 Flavodoxin reduced + Hydrogen ion >2 flavodoxin semi oxidized + 1-Hydroxy-2-methyl-2-butenyl 4-diphosphate + Water2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol <> 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + Cytidine monophosphateR05637RXN0-3022-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 ferredoxinR086892-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol > Cytidine monophosphate + 2-C-Methyl-D-erythritol-2,4-cyclodiphosphateRXN0-3021-Hydroxy-2-methyl-2-butenyl 4-diphosphate + Water + Oxidized-ferredoxins < 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + Hydrogen ion + Reduced-ferredoxinsRXN0-8822-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 monophosphatePW_R0036912-C-Methyl-D-erythritol-2,4-cyclodiphosphate + a reduced flavodoxin > Water + Hydrogen ion + an oxidized flavodoxin + 1-Hydroxy-2-methyl-2-(E)-butenyl 4-diphosphatePW_R0036922 2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol <>2 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + Cytidine monophosphate2 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + 2 Reduced ferredoxin + Oxidized ferredoxin <> 1-Hydroxy-2-methyl-2-butenyl 4-diphosphate + Water2 2-Phospho-4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol <>2 2-C-Methyl-D-erythritol-2,4-cyclodiphosphate + Cytidine monophosphate