2.02012-05-31 13:49:08 -06002015-09-13 12:56:10 -0600ECMDB01285M2MDB000324Geranyl-PPGeranyl 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 diphosphateω,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 acidGeranyl diphosphateGeranyl diphosphoric acidGeranyl pyrophosphateGeranyl pyrophosphoric acidGeranyl-diphosphateGeranyl-diphosphoric acidGeranyl-PPGeranyl-pyrophosphateGeranyl-pyrophosphoric acidGPPMonoterpenyl diphosphateMonoterpenyl diphosphoric acidNeryl diphosphateNeryl diphosphoric acidOmega,E-geranyl diphosphateOmega,e-geranyl diphosphoric acidTrans-Geranyl pyrophosphatetrans-Geranyl pyrophosphoric acidC10H20O7P2314.2091314.068426018[({[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acidgeranyl diphosphate763-10-0CC(C)=CCC\C(C)=C\CO[P@@](=O)(O)OP(=O)(O)OInChI=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-NSolidCytosollogp1.63logs-2.54solubility9.02e-01 g/llogp1.96pka_strongest_acidic1.77iupac[({[(2E)-3,7-dimethylocta-2,6-dien-1-yl]oxy}(hydroxy)phosphoryl)oxy]phosphonic acidaverage_mass314.2091mono_mass314.068426018smilesCC(C)=CCC\C(C)=C\CO[P@@](=O)(O)OP(=O)(O)OformulaC10H20O7P2inchiInChI=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+inchikeyGVVPGTZRZFNKDS-JXMROGBWSA-Npolar_surface_area113.29refractivity72.93polarizability28.52rotatable_bond_count8acceptor_count5donor_count3physiological_charge-2formal_charge0Ubiquinone and other terpenoid-quinone biosynthesisec00130Terpenoid backbone biosynthesisec00900Metabolic pathwayseco01100Secondary 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 diphosphatePW000958Metabolic<i>trans, trans</i>-farnesyl diphosphate biosynthesisPWY-5123Specdb::CMs3098Specdb::CMs132354Specdb::CMs140088Specdb::NmrOneD279698Specdb::NmrOneD279699Specdb::NmrOneD279700Specdb::NmrOneD279701Specdb::NmrOneD279702Specdb::NmrOneD279703Specdb::NmrOneD279704Specdb::NmrOneD279705Specdb::NmrOneD279706Specdb::NmrOneD279707Specdb::NmrOneD279708Specdb::NmrOneD279709Specdb::NmrOneD279710Specdb::NmrOneD279711Specdb::NmrOneD279712Specdb::NmrOneD279713Specdb::NmrOneD279714Specdb::NmrOneD279715Specdb::NmrOneD279716Specdb::NmrOneD279717Specdb::MsMs23015Specdb::MsMs23016Specdb::MsMs23017Specdb::MsMs29813Specdb::MsMs29814Specdb::MsMs29815Specdb::MsMs1471813Specdb::MsMs1471814Specdb::MsMs1471815Specdb::MsMs1471816Specdb::MsMs1471817Specdb::MsMs1471818Specdb::MsMs1471819Specdb::MsMs1471820Specdb::MsMs1471821Specdb::MsMs1471822Specdb::MsMs1471823Specdb::MsMs1471824Specdb::MsMs1471825Specdb::MsMs1471826Specdb::MsMs1471827Specdb::MsMs1471828Specdb::MsMs1471829Specdb::MsMs1471830Specdb::MsMs1471831HMDB01285445995393471C0584717211GERANYL-PPGPPGeranyl pyrophosphateKeseler, 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-D114.22080510van 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 370:17-25.17765195Kavanagh 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. Proc Natl Acad Sci U S A. 2006 May 16;103(20):7829-34. Epub 2006 May 9.16684881Micali E, Chehade KA, Isaacs RJ, Andres DA, Spielmann HP: Protein farnesyltransferase isoprenoid substrate discrimination is dependent on isoprene double bonds and branched methyl groups. Biochemistry. 2001 Oct 16;40(41):12254-65.11591144Holstein SA, Hohl RJ: Isoprenoids: remarkable diversity of form and function. Lipids. 2004 Apr;39(4):293-309.15357017Gan X, Kaplan R, Menke JG, MacNaul K, Chen Y, Sparrow CP, Zhou G, Wright SD, Cai TQ: Dual mechanisms of ABCA1 regulation by geranylgeranyl pyrophosphate. J Biol Chem. 2001 Dec 28;276(52):48702-8. Epub 2001 Oct 18.11641412Sagami H, Ogura K: [A new development in isoprenoid biochemistry brought by the discovery of prenylated proteins] Seikagaku. 1994 Dec;66(12):1488-501.7884273Loza-Tavera H: Monoterpenes in essential oils. Biosynthesis and properties. Adv Exp Med Biol. 1999;464:49-62.10335385Barnard GF, Popjak G: Human liver prenyltransferase and its characterization. Biochim Biophys Acta. 1981 Sep 15;661(1):87-99.7295734Pont F, Luciani B, Belmant C, Fournie JJ: Characterization of phosphoantigens by high-performance anion-exchange chromatography-electrospray ionization ion trap mass spectrometry and nanoelectrospray ionization ion trap mass spectrometry. Anal Chem. 2001 Aug 1;73(15):3562-9.11510819Smit A, Mushegian A: Biosynthesis of isoprenoids via mevalonate in Archaea: the lost pathway. Genome Res. 2000 Oct;10(10):1468-84.11042147Runquist M; Ericsson J; Thelin A; Chojnacki T; Dallner G Biosynthesis of trans,trans,trans-geranylgeranyl diphosphate by the cytosolic fraction from rat tissues. Biochemical and biophysical research communications (1992), 186(1), 157-65.http://hmdb.ca/system/metabolites/msds/000/001/150/original/HMDB01285.pdf?1358461907GeranyltranstransferaseP22939ISPA_ECOLIispAhttp://ecmdb.ca/proteins/P22939.xml1,4-dihydroxy-2-naphthoate octaprenyltransferaseP32166MENA_ECOLImenAhttp://ecmdb.ca/proteins/P32166.xml4-hydroxybenzoate octaprenyltransferaseP0AGK1UBIA_ECOLIubiAhttp://ecmdb.ca/proteins/P0AGK1.xmlDimethylallylpyrophosphate + Isopentenyl pyrophosphate > Geranyl-PP + PyrophosphateR01658GPPSYN-RXNGeranyl-PP + Isopentenyl pyrophosphate + Geranyl diphosphate <> Farnesyl pyrophosphate + PyrophosphateR02003FPPSYN-RXNDimethylallylpyrophosphate + Isopentenyl pyrophosphate <> Pyrophosphate + Geranyl-PPR01658GPPSYN-RXNGeranyl-PP + Isopentenyl pyrophosphate <> Pyrophosphate + Farnesyl pyrophosphateR02003FPPSYN-RXNGeranyl-PP + Isopentenyl pyrophosphate > Farnesyl pyrophosphate + PyrophosphateFPPSYN-RXNall-trans-Polyprenyl diphosphate + 4-Hydroxybenzoic acid + Geranyl-PP <> 4-Hydroxy-3-polyprenylbenzoate + Pyrophosphate + 4-Hydroxy-3-polyprenylbenzoateR05000Geranyl-PP + 1,4-Dihydroxy-2-naphthoic acid <> Demethylmenaquinol + Pyrophosphate + Carbon dioxideR10757 Dimethylallylpyrophosphate + Isopentenyl pyrophosphate + Dimethylallylpyrophosphate + Isopentenyl pyrophosphate > Pyrophosphate + Geranyl-PP + Geranyl-PPPW_R003696Geranyl-PP + Isopentenyl pyrophosphate + Geranyl-PP + Isopentenyl pyrophosphate > Pyrophosphate + Farnesyl pyrophosphate + Farnesyl pyrophosphatePW_R003697Dimethylallylpyrophosphate + Isopentenyl pyrophosphate > Geranyl-PP + PyrophosphateDimethylallylpyrophosphate + Isopentenyl pyrophosphate > Geranyl-PP + Pyrophosphate