geranylgeranyl diphosphate (YMDB00631)

Identification
YMDB IDYMDB00631
Namegeranylgeranyl diphosphate
SpeciesSaccharomyces cerevisiae
StrainBaker's yeast
DescriptionGeranylgeranyl-PP, also known as GGDP or GGPP diphosphate, belongs to the class of organic compounds known as acyclic diterpenoids. These are diterpenoids (compounds made of four consecutive isoprene units) that do not contain a cycle. Thus, geranylgeranyl-PP is considered to be an isoprenoid lipid molecule. Geranylgeranyl-PP is a very hydrophobic molecule, practically insoluble (in water), and relatively neutral.
Structure
Thumb
MOLSDF3D-SDFPDBSMILESInChI View 3D Structure
Synonyms
  • all-trans-geranylgeranyl diphosphate
  • all-trans-geranylgeranyl pyrophosphate
  • geranylgeranyl pyrophosphate
  • ggpp
  • Geranylgeranyl diphosphate
  • GGDP
  • (2E,6E,10E)-3,7,11,15-Tetramethylhexadeca-2,6,10,14-tetraen-1-yl diphosphate
  • all-trans-Geranylgeranyl diphosphoric acid
  • all-trans-Geranylgeranyl pyrophosphoric acid
  • Geranylgeranyl diphosphoric acid
  • Geranylgeranyl pyrophosphoric acid
  • (2E,6E,10E)-3,7,11,15-Tetramethylhexadeca-2,6,10,14-tetraen-1-yl diphosphoric acid
  • 2-trans,6-trans,10-trans-Geranylgeranyl diphosphate
  • 3,7,11,15-Tetramethyl-2,6,10,14-hexadecatetraenyl diphosphate
  • all-trans-Geranyl-geranyl-PP
  • Geranylgeranyl-diphosphate
  • Geranylgeraniol diphosphate
  • Geranylgeranyl pyrophosphate, (Z,e,e)-isomer
  • Nerylneryl diphosphate
  • GGPP Diphosphate
  • Geranylgeranyl pyrophosphate, 14C-labeled, (e,e,e)-isomer
  • GGPP CPD
CAS number6699-20-3
WeightAverage: 450.4432
Monoisotopic: 450.19362653
InChI KeyOINNEUNVOZHBOX-QIRCYJPOSA-N
InChIInChI=1S/C20H36O7P2/c1-17(2)9-6-10-18(3)11-7-12-19(4)13-8-14-20(5)15-16-26-29(24,25)27-28(21,22)23/h9,11,13,15H,6-8,10,12,14,16H2,1-5H3,(H,24,25)(H2,21,22,23)/b18-11+,19-13+,20-15+
IUPAC Name{[hydroxy({[(2E,6E,10E)-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-yl]oxy})phosphoryl]oxy}phosphonic acid
Traditional IUPAC Namegeranylgeranyl diphosphate
Chemical FormulaC20H36O7P2
SMILESCC(C)=CCCC(C)=CCCC(C)=CCCC(C)=CCOP(O)(=O)OP(O)(O)=O
Chemical Taxonomy
Description belongs to the class of organic compounds known as acyclic diterpenoids. These are diterpenoids (compounds made of four consecutive isoprene units) that do not contain a cycle.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassDiterpenoids
Direct ParentAcyclic diterpenoids
Alternative Parents
Substituents
  • Acyclic diterpenoid
  • Organic pyrophosphate
  • Isoprenoid phosphate
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External Descriptors
Physical Properties
StateNot Available
Charge0
Melting pointNot Available
Experimental Properties
PropertyValueReference
Water SolubilityNot AvailablePhysProp
LogPNot AvailablePhysProp
Predicted Properties
PropertyValueSource
Water Solubility0.0046 g/LALOGPS
logP3.57ALOGPS
logP5.28ChemAxon
logS-5ALOGPS
pKa (Strongest Acidic)1.77ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count5ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area113.29 ŲChemAxon
Rotatable Bond Count14ChemAxon
Refractivity120.53 m³·mol⁻¹ChemAxon
Polarizability47.82 ųChemAxon
Number of Rings0ChemAxon
Bioavailability0ChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleYesChemAxon
MDDR-like RuleYesChemAxon
Biological Properties
Cellular Locations
  • lipid particle
Organoleptic PropertiesNot Available
SMPDB Pathways
Terpenoid backbone biosynthesisPW002485 ThumbThumb?image type=greyscaleThumb?image type=simple
KEGG Pathways
Terpenoid backbone biosynthesisec00900 Map00900
SMPDB ReactionsNot Available
KEGG Reactions
Farnesyl pyrophosphate + Isopentenyl pyrophosphate ↔ Pyrophosphate + geranylgeranyl diphosphate
Isopentenyl pyrophosphate + geranylgeranyl diphosphate ↔ Pyrophosphate + pentaprenyl diphosphate + hydron
Concentrations
Intracellular ConcentrationsNot Available
Extracellular ConcentrationsNot Available
Spectra
Spectra
Spectrum TypeDescriptionSplash KeyView
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positivesplash10-00p1-8966200000-998d239f267a150b43edJSpectraViewer
Predicted GC-MSPredicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, PositiveNot AvailableJSpectraViewer
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 11V, negativesplash10-0002-0000900000-e7c9a733fcef12117c3dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 15V, negativesplash10-0002-1000900000-51a8d5ce498d65e79691JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 19V, negativesplash10-004j-9000800000-4beea4fd2eb20ffa4ad9JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 26V, negativesplash10-004i-9000000000-4db0a53ff36e5e4b9935JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 31V, negativesplash10-004i-9000000000-cf199ce4e78be9534fb7JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 37V, negativesplash10-004i-9000000000-7867ab9db012f87e43c8JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 44V, negativesplash10-004i-9000000000-be17e3662a7647d871aaJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 52V, negativesplash10-004i-9000000000-1f4ff46767d08f6c4824JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 60V, negativesplash10-004i-9000000000-d99bb72e9136380d8698JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - Orbitrap 72V, negativesplash10-004i-9000000000-d99bb72e9136380d8698JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 31V, negativesplash10-001i-0300900000-fecb2380f7e0ec863abcJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 31V, negativesplash10-004i-9000000000-5ef060d5ec4b80c35c1aJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 31V, negativesplash10-0a4i-0900000000-dc954ce23ecf1a263189JSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 31V, negativesplash10-0a4i-0900000000-8ab5606bd668c2535e4dJSpectraViewer | MoNA
LC-MS/MSLC-MS/MS Spectrum - n/a 31V, negativesplash10-004i-9000000000-5ef060d5ec4b80c35c1aJSpectraViewer | MoNA
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0fk9-1394600000-c6d91e9bfb5eeb46563eJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00di-3592000000-c8aa1820057f6139aad8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-00xs-5690000000-5fa48d769648b6310c2dJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-0400900000-86700e111b6b2b0215c0JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Negativesplash10-057i-7900100000-c5c0d2a89df8d138cebbJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Negativesplash10-004i-9000000000-0ec0eed3d4d479d9c002JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Positivesplash10-0udi-1214900000-f698165f4dfead7c9d55JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 20V, Positivesplash10-00di-1189100000-6a265357a808fdf96bf8JSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 40V, Positivesplash10-05s1-3910000000-59003e6f3766239ee38aJSpectraViewer
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - 10V, Negativesplash10-0002-0000900000-582b037b919c4a7e747fJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
1D NMR13C NMR SpectrumNot AvailableJSpectraViewer
1D NMR1H NMR SpectrumNot AvailableJSpectraViewer
References
References:
  • Scheer, M., Grote, A., Chang, A., Schomburg, I., Munaretto, C., Rother, M., Sohngen, C., Stelzer, M., Thiele, J., Schomburg, D. (2011). "BRENDA, the enzyme information system in 2011." Nucleic Acids Res 39:D670-D676.21062828
  • Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
  • Jiang, Y., Proteau, P., Poulter, D., Ferro-Novick, S. (1995). "BTS1 encodes a geranylgeranyl diphosphate synthase in Saccharomyces cerevisiae." J Biol Chem 270:21793-21799.7665600
  • Sato, M., Sato, K., Nishikawa, S., Hirata, A., Kato, J., Nakano, A. (1999). "The yeast RER2 gene, identified by endoplasmic reticulum protein localization mutations, encodes cis-prenyltransferase, a key enzyme in dolichol synthesis." Mol Cell Biol 19:471-483.9858571
  • Grabinska, K., Palamarczyk, G. (2002). "Dolichol biosynthesis in the yeast Saccharomyces cerevisiae: an insight into the regulatory role of farnesyl diphosphate synthase." FEMS Yeast Res 2:259-265.12702274
Synthesis Reference:Not Available
External Links:
ResourceLink
CHEBI ID15831
HMDB IDHMDB0004486
Pubchem Compound ID6420192
Kegg IDC00353
ChemSpider ID23092869
FOODB IDFDB023377
Wikipediageranylgeranyl_diphosphate
BioCyc IDNot Available

Enzymes

Protein Details
1. Geranylgeranyl pyrophosphate synthase
General function:
Involved in isoprenoid biosynthetic process
Specific function:
Catalyzes the trans-addition of the 3 molecules of IPP onto DMAPP to form geranylgeranyl pyrophosphate. Required for the membrane attachment of YPT1 and SEC4. May be involved in vesicle trafficking and protein sorting
Gene Name:
BTS1
Uniprot ID:
Q12051
Molecular weight:
38651.0
Reactions
Dimethylallyl diphosphate + isopentenyl diphosphate → diphosphate + geranyl diphosphate.
Geranyl diphosphate + isopentenyl diphosphate → diphosphate + (2E,6E)-farnesyl diphosphate.
Trans,trans-farnesyl diphosphate + isopentenyl diphosphate → diphosphate + geranylgeranyl diphosphate.
Protein Details
2. Putative dehydrodolichyl diphosphate synthase
General function:
Involved in transferase activity, transferring alkyl or aryl (other than methyl) groups
Specific function:
Could be a cis-prenyl transferase that adds multiple copies of isopentenyl pyrophosphate (ipp) to farnesyl pyrophosphate (FPP) to produce dehydrodolichyl diphosphate (DeDol- PP)
Gene Name:
SRT1
Uniprot ID:
Q03175
Molecular weight:
40199.69922
Reactions
Protein Details
3. Dehydrodolichyl diphosphate synthase
General function:
Involved in transferase activity, transferring alkyl or aryl (other than methyl) groups
Specific function:
Cis-prenyl transferase that adds multiple copies of isopentenyl pyrophosphate (IPP) to farnesyl pyrophosphate (FPP) to produce dehydrodolichyl diphosphate (Dedol-PP)
Gene Name:
RER2
Uniprot ID:
P35196
Molecular weight:
32693.30078
Reactions
Protein Details
4. Geranylgeranyl transferase type-1 subunit beta
General function:
Involved in catalytic activity
Specific function:
Catalyzes the transfer of a geranyl-geranyl moiety from geranyl-geranyl pyrophosphate to proteins having the C-terminal sequence Cys-Ile-Ile-Leu or Cys-Val-Leu-Leu. Acts, among other substrates, on Rho1 and Rho2 and CDC42 proteins. Participates in a RAS-like C-terminal modification of proteins involved in nuclear division and bud growth. It is involved in bud positioning and cell polarity
Gene Name:
CDC43
Uniprot ID:
P18898
Molecular weight:
42689.10156
Reactions
Geranylgeranyl diphosphate + protein-cysteine → S-geranylgeranyl-protein + diphosphate.
Protein Details
5. Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha
General function:
Involved in protein prenyltransferase activity
Specific function:
Catalyzes the transfer of a farnesyl or geranyl-geranyl moiety from farnesyl or geranyl-geranyl pyrophosphate to a cysteine at the fourth position from the C-terminus of several proteins having the C-terminal sequence Cys-aliphatic-aliphatic-X. The alpha subunit is thought to participate in a stable complex with the substrate. The beta subunit binds the peptide substrate
Gene Name:
RAM2
Uniprot ID:
P29703
Molecular weight:
37507.30078
Reactions
Farnesyl diphosphate + protein-cysteine → S-farnesyl protein + diphosphate.
Geranylgeranyl diphosphate + protein-cysteine → S-geranylgeranyl-protein + diphosphate.
Protein Details
6. Geranylgeranyl transferase type-2 subunit beta
General function:
Involved in catalytic activity
Specific function:
Catalyzes the transfer of a geranyl-geranyl moiety from geranyl-geranyl pyrophosphate to proteins having the C-terminal -XCC or -XCXC, where both cysteines may become modified. Acts on YPT1 and SEC4
Gene Name:
BET2
Uniprot ID:
P20133
Molecular weight:
36665.60156
Reactions
Geranylgeranyl diphosphate + protein-cysteine → S-geranylgeranyl-protein + diphosphate.
Protein Details
7. Geranylgeranyl transferase type-2 subunit alpha
General function:
Involved in protein prenyltransferase activity
Specific function:
Catalyzes the transfer of a geranyl-geranyl moiety from geranyl-geranyl pyrophosphate to proteins having the C-terminal -XCC or -XCXC, where both cysteines may become modified. Acts on YPT1 and SEC4
Gene Name:
BET4
Uniprot ID:
Q00618
Molecular weight:
39674.30078
Reactions
Geranylgeranyl diphosphate + protein-cysteine → S-geranylgeranyl-protein + diphosphate.