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Metabolic Modeling Tutorial
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MetaCyc Compound: geranyl diphosphate

Synonyms: geranyl-diphosphate, geranyl-pyrophosphate, GPP, geranyl-PP, geranyl pyrophosphate, ω,E-geranyl diphosphate

Superclasses: a lipid an isoprenoid a terpenoid a terpenoid derivative a monoterpenoid derivative a monoterpenyl phosphate a monoterpenyl diphosphate
a lipid an isoprenoid an isoprenoid phosphate an isoprenoid diphosphate
a secondary metabolite a terpenoid a terpenoid derivative a monoterpenoid derivative a monoterpenyl phosphate a monoterpenyl diphosphate

Chemical Formula: C10H17O7P2

Molecular Weight: 311.19 Daltons

Monoisotopic Molecular Weight: 314.0684260167 Daltons

SMILES: CC(=CCCC(=CCOP([O-])(OP(=O)([O-])[O-])=O)C)C

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)/p-3/b10-7+

InChIKey: InChIKey=GVVPGTZRZFNKDS-JXMROGBWSA-K

Unification Links: ChEBI:58057 , ChemSpider:14211068 , HMDB:HMDB01285 , IAF1260:34675 , KEGG:C00341 , KNApSAcK:C00000846 , MetaboLights:MTBLC58057 , PubChem:19379894

Standard Gibbs Free Energy of Change Formation (ΔfG in kcal/mol): -239.2895 Inferred by computational analysis [Latendresse13]

Reactions known to consume the compound:

(+)-camphor biosynthesis , bornyl diphosphate biosynthesis :
geranyl diphosphate → (+)-bornyl-diphosphate

(-)-camphor biosynthesis :
geranyl diphosphate → (-)-bornyl-diphosphate

(4R)-carvone biosynthesis , menthol biosynthesis , perillyl aldehyde biosynthesis :
geranyl diphosphate → (4S)-limonene + diphosphate

(4S)-carvone biosynthesis :
geranyl diphosphate → (4R)-limonene + diphosphate

2-methylisoborneol biosynthesis :
S-adenosyl-L-methionine + geranyl diphosphateS-adenosyl-L-homocysteine + (E)-2-methylgeranyl diphosphate + H+

3-carene biosynthesis :
geranyl diphosphate → (+)-3-carene + diphosphate

cannabinoid biosynthesis :
geranyl diphosphate + olivetolate → cannabigerolate + diphosphate

fenchol biosynthesis I , fenchone biosynthesis :
geranyl diphosphate + H2O → (-)-endo-fenchol + diphosphate

fenchol biosynthesis II :
geranyl diphosphate → (-)-α-pinene + diphosphate
geranyl diphosphate → (4S)-limonene + diphosphate
geranyl diphosphate + H2O → (-)-endo-fenchol + diphosphate

geraniol and geranial biosynthesis , secologanin and strictosidine biosynthesis :
geranyl diphosphate + H2O → geraniol + diphosphate

hyperforin and adhyperforin biosynthesis :
diprenylphlorisobutyrophenone + dimethylallyl diphosphate + geranyl diphosphate → hyperforin + 2 diphosphate

ipsdienol biosynthesis :
geranyl diphosphate → β-myrcene + diphosphate

linalool biosynthesis I :
geranyl diphosphate + H2O → (3R)-linalool + diphosphate

linalool biosynthesis II :
geranyl diphosphate + H2O → (3S)-linalool + diphosphate

mono-trans, poly-cis decaprenyl phosphate biosynthesis :
geranyl diphosphate + isopentenyl diphosphate → (2Z,6E)-farnesyl diphosphate + diphosphate

monoterpene biosynthesis :
geranyl diphosphate → (-)-β-pinene + diphosphate
geranyl diphosphate → (-)-α-pinene + diphosphate
geranyl diphosphate → terpinolene + diphosphate
geranyl diphosphate + H2O → 1,8-cineole + diphosphate
geranyl diphosphate → (E)-β-ocimene + diphosphate
geranyl diphosphate → β-myrcene + diphosphate
geranyl diphosphate → sabinene + diphosphate
geranyl diphosphate → (4S)-limonene + diphosphate

nonaprenyl diphosphate biosynthesis I :
geranyl diphosphate + 7 isopentenyl diphosphate → all-trans-nonaprenyl diphosphate + 7 diphosphate

oleoresin monoterpene volatiles biosynthesis :
geranyl diphosphate → (-)-β-pinene + diphosphate
geranyl diphosphate → (-)-α-pinene + diphosphate
geranyl diphosphate → (-)-camphene + diphosphate
geranyl diphosphate → (+)-3-carene + diphosphate
geranyl diphosphate → tricyclene + diphosphate
geranyl diphosphate → (-)-β-phellandrene + diphosphate
geranyl diphosphate → β-myrcene + diphosphate
geranyl diphosphate → (4S)-limonene + diphosphate

shikonin biosynthesis :
geranyl diphosphate + 4-hydroxybenzoate → 3-geranyl-4-hydroxybenzoate + diphosphate

superpathway of linalool biosynthesis :
geranyl diphosphate + H2O → (3S)-linalool + diphosphate
geranyl diphosphate + H2O → (3R)-linalool + diphosphate

Not in pathways:
a monoterpenyl diphosphate + H2O → a monoterpenol + diphosphate + H+

linoleate biosynthesis I (plants) :
oleoyl-CoA + a lipid + H+ → a lipid oleoyl-group + coenzyme A

Reactions known to produce the compound:

glutathione redox reactions I :
a lipid hydroperoxide + 2 glutathione + H+a lipid + glutathione disulfide + 2 H2O

Reactions known to both consume and produce the compound:

all-trans-farnesol biosynthesis :
dimethylallyl diphosphate + isopentenyl diphosphate ↔ geranyl diphosphate + diphosphate
geranyl diphosphate + isopentenyl diphosphate ↔ (2E,6E)-farnesyl diphosphate + diphosphate

bisabolene biosynthesis :
dimethylallyl diphosphate + isopentenyl diphosphate ↔ geranyl diphosphate + diphosphate
geranyl diphosphate + isopentenyl diphosphate ↔ (2E,6E)-farnesyl diphosphate + diphosphate

geranyl diphosphate biosynthesis , ipsdienol biosynthesis , linalool biosynthesis I , linalool biosynthesis II , mono-trans, poly-cis decaprenyl phosphate biosynthesis , superpathway of linalool biosynthesis :
dimethylallyl diphosphate + isopentenyl diphosphate ↔ geranyl diphosphate + diphosphate

trans, trans-farnesyl diphosphate biosynthesis :
dimethylallyl diphosphate + isopentenyl diphosphate ↔ geranyl diphosphate + diphosphate
geranyl diphosphate + isopentenyl diphosphate ↔ (2E,6E)-farnesyl diphosphate + diphosphate

In Reactions of unknown directionality:

monoterpene biosynthesis :
geranyl diphosphate = (+)-camphene + diphosphate
geranyl diphosphate = (Z)-β-ocimene + diphosphate

Not in pathways:
geranyl diphosphate + 2-O,3-dimethylflaviolin = 7-O-geranyl-2-O,3-dimethylflaviolin + diphosphate
geranyl diphosphate + 2-O,3-dimethylflaviolin = 6-linalyl-2-O,3-dimethylflaviolin + diphosphate
geranyl diphosphate + flaviolin + H+ = 3-linalylflaviolin + diphosphate
geranyl diphosphate = (-)-sabinene + diphosphate
geranyl diphosphate = γ-terpinene + diphosphate
geranyl diphosphate = (+)-α-pinene + diphosphate
geranyl diphosphate = (+)-β-pinene + diphosphate
geranyl diphosphate = α-terpinene + diphosphate
geranyl diphosphate + H2O = (+)-α-terpineol + diphosphate
geranyl diphosphate + H2O = (-)-(4S)-α-terpineol + diphosphate
geranyl diphosphate = (1R,5R)-sabinene + diphosphate
geranyl diphosphate = (-)-2-carene + diphosphate
geranyl diphosphate = (-)-3-carene + diphosphate
geranyl diphosphate = (+)-2-carene + diphosphate
geranyl diphosphate = α-thujene + diphosphate
geranyl diphosphate + H2O = sabinene hydrate + diphosphate


an isoprenoid diphosphate + 4-hydroxybenzoate = a 4-hydroxy-3-polyprenylbenzoate + diphosphate

Enzymes inhibited by geranyl diphosphate, sorted by the type of inhibition, are:

Inhibitor (Other types) of: mevalonate kinase [Dorsey68]

Credits:
Revised 14-Feb-2012 by Caspi R , SRI International


References

Dorsey68: Dorsey JK, Porter JW (1968). "The inhibition of mevalonic kinase by geranyl and farnesyl pyrophosphates." J Biol Chem 243(18);4667-70. PMID: 4300840

Latendresse13: Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Mon Dec 22, 2014, BIOCYC13A.