2.0 2012-05-31 13:49:08 -0600 2015-09-13 12:56:10 -0600 ECMDB01285 M2MDB000324 Geranyl-PP Geranyl diphosphate is regarded as a key intermediate in the steroid, isoprene and terpene biosynthesis pathways and is used by organisms in the biosynthesis of farnesyl pyrophosphate, geranylgeranyl pyrophosphate, cholesterol, terpenes and terpenoids. (wikipedia). In E.coli, geranyl diphosphate synthase (GPPS) catalyzes the condensation of dimethylallyl diphosphate (DMAPP) and isopentenyl diphosphate (IPP) to form geranyl diphosphate. Geranyl pyrophosphate is an intermediate in the HMG-CoA reductase pathway used by organisms in the biosynthesis of terpenes and terpenoids. (Wikipedia) ω,E-geranyl diphosphate ω,e-geranyl diphosphoric acid (2E)-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate (2E)-3,7-Dimethylocta-2,6-dien-1-yl trihydrogen diphosphoric acid Geranyl diphosphate Geranyl diphosphoric acid Geranyl pyrophosphate Geranyl pyrophosphoric acid Geranyl-diphosphate Geranyl-diphosphoric acid Geranyl-PP Geranyl-pyrophosphate Geranyl-pyrophosphoric acid GPP Monoterpenyl diphosphate Monoterpenyl diphosphoric acid Neryl diphosphate Neryl diphosphoric acid Omega,E-geranyl diphosphate Omega,e-geranyl diphosphoric acid Trans-Geranyl pyrophosphate trans-Geranyl pyrophosphoric acid C10H20O7P2 314.2091 314.068426018 [({[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acid geranyl diphosphate 763-10-0 CC(C)=CCC\C(C)=C\CO[P@@](=O)(O)OP(=O)(O)O InChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)/b10-7+ GVVPGTZRZFNKDS-JXMROGBWSA-N Solid Cytosol logp 1.63 ALOGPS logs -2.54 ALOGPS solubility 9.02e-01 g/l ALOGPS logp 1.96 ChemAxon pka_strongest_acidic 1.77 ChemAxon iupac [({[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acid ChemAxon average_mass 314.2091 ChemAxon mono_mass 314.068426018 ChemAxon smiles CC(C)=CCC\C(C)=C\CO[P@@](=O)(O)OP(=O)(O)O ChemAxon formula C10H20O7P2 ChemAxon inchi InChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)/b10-7+ ChemAxon inchikey GVVPGTZRZFNKDS-JXMROGBWSA-N ChemAxon polar_surface_area 113.29 ChemAxon refractivity 72.93 ChemAxon polarizability 28.52 ChemAxon rotatable_bond_count 8 ChemAxon acceptor_count 5 ChemAxon donor_count 3 ChemAxon physiological_charge -2 ChemAxon formal_charge 0 ChemAxon Ubiquinone and other terpenoid-quinone biosynthesis ec00130 Terpenoid backbone biosynthesis ec00900 Metabolic pathways eco01100 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 <i>trans, trans</i>-farnesyl diphosphate biosynthesis PWY-5123 Specdb::CMs 3098 Specdb::CMs 132354 Specdb::CMs 140088 Specdb::NmrOneD 279698 Specdb::NmrOneD 279699 Specdb::NmrOneD 279700 Specdb::NmrOneD 279701 Specdb::NmrOneD 279702 Specdb::NmrOneD 279703 Specdb::NmrOneD 279704 Specdb::NmrOneD 279705 Specdb::NmrOneD 279706 Specdb::NmrOneD 279707 Specdb::NmrOneD 279708 Specdb::NmrOneD 279709 Specdb::NmrOneD 279710 Specdb::NmrOneD 279711 Specdb::NmrOneD 279712 Specdb::NmrOneD 279713 Specdb::NmrOneD 279714 Specdb::NmrOneD 279715 Specdb::NmrOneD 279716 Specdb::NmrOneD 279717 Specdb::MsMs 23015 Specdb::MsMs 23016 Specdb::MsMs 23017 Specdb::MsMs 29813 Specdb::MsMs 29814 Specdb::MsMs 29815 Specdb::MsMs 1471813 Specdb::MsMs 1471814 Specdb::MsMs 1471815 Specdb::MsMs 1471816 Specdb::MsMs 1471817 Specdb::MsMs 1471818 Specdb::MsMs 1471819 Specdb::MsMs 1471820 Specdb::MsMs 1471821 Specdb::MsMs 1471822 Specdb::MsMs 1471823 Specdb::MsMs 1471824 Specdb::MsMs 1471825 Specdb::MsMs 1471826 Specdb::MsMs 1471827 Specdb::MsMs 1471828 Specdb::MsMs 1471829 Specdb::MsMs 1471830 Specdb::MsMs 1471831 HMDB01285 445995 393471 C05847 17211 GERANYL-PP GPP Geranyl pyrophosphate 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 Kavanagh KL, Guo K, Dunford JE, Wu X, Knapp S, Ebetino FH, Rogers MJ, Russell RG, Oppermann U: The molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs. 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Biochemical and biophysical research communications (1992), 186(1), 157-65. http://hmdb.ca/system/metabolites/msds/000/001/150/original/HMDB01285.pdf?1358461907 Geranyltranstransferase P22939 ISPA_ECOLI ispA http://ecmdb.ca/proteins/P22939.xml 1,4-dihydroxy-2-naphthoate octaprenyltransferase P32166 MENA_ECOLI menA http://ecmdb.ca/proteins/P32166.xml 4-hydroxybenzoate octaprenyltransferase P0AGK1 UBIA_ECOLI ubiA http://ecmdb.ca/proteins/P0AGK1.xml Dimethylallylpyrophosphate + Isopentenyl pyrophosphate > Geranyl-PP + Pyrophosphate R01658 GPPSYN-RXN Geranyl-PP + Isopentenyl pyrophosphate + Geranyl diphosphate <> Farnesyl pyrophosphate + Pyrophosphate R02003 FPPSYN-RXN Dimethylallylpyrophosphate + Isopentenyl pyrophosphate <> Pyrophosphate + Geranyl-PP R01658 GPPSYN-RXN Geranyl-PP + Isopentenyl pyrophosphate <> Pyrophosphate + Farnesyl pyrophosphate R02003 FPPSYN-RXN Geranyl-PP + Isopentenyl pyrophosphate > Farnesyl pyrophosphate + Pyrophosphate FPPSYN-RXN all-trans-Polyprenyl diphosphate + 4-Hydroxybenzoic acid + Geranyl-PP <> 4-Hydroxy-3-polyprenylbenzoate + Pyrophosphate + 4-Hydroxy-3-polyprenylbenzoate R05000 Geranyl-PP + 1,4-Dihydroxy-2-naphthoic acid <> Demethylmenaquinol + Pyrophosphate + Carbon dioxide R10757 Dimethylallylpyrophosphate + Isopentenyl pyrophosphate + Dimethylallylpyrophosphate + Isopentenyl pyrophosphate > Pyrophosphate + Geranyl-PP + Geranyl-PP PW_R003696 Geranyl-PP + Isopentenyl pyrophosphate + Geranyl-PP + Isopentenyl pyrophosphate > Pyrophosphate + Farnesyl pyrophosphate + Farnesyl pyrophosphate PW_R003697 Dimethylallylpyrophosphate + Isopentenyl pyrophosphate > Geranyl-PP + Pyrophosphate Dimethylallylpyrophosphate + Isopentenyl pyrophosphate > Geranyl-PP + Pyrophosphate