Geranyl diphosphate synthase (GPPS)

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Reaction catalysed

$dimethylallyl diphosphate + isopentenyl diphosphate \rightleftharpoons geranyl diphosphate + diphosphate$

$DMAPP + IPP \rightleftharpoons GPP + PP$

Metabolite and Enzyme Background Information

Long metabolite names are abbreviated in the model for clarity and standard identification purposes.

Metabolite	Abbreviation	Chemical Formula	Molar mass (g/mol)	ChEBI	ChEMBL	PubChem	MetaCyc
dimethylallyl diphosphate	DMAPP
isopentenyl diphosphate	IPP
geranyl diphosphate	GPP	C10H20O7P2	314.209	17211	41432	445995
diphosphate	PP	O7P2	173.94			644102
geranyl diphosphate synthase	GPPS		32.16 kD (from nucleotide sequence), 36 kD (experimental)				CPLX-8656

Equation Rate

Failed to parse (Cannot store math image on filesystem.): V_\mathrm{GPPS} = Vmax_\mathrm{forward} * \cfrac { \left (\cfrac{[DMAPP]}{Km_\mathrm{DMAPP}} * \cfrac{[IPP]}{Km_\mathrm{IPP}}\right )* \left ( 1 - \cfrac {[GPP]*[PP]}{[GPP]*[PP]*K_\mathrm{eq}} \right )}{\left (1 + \cfrac {[IPP]}{Km_\mathrm{IPP}} + \cfrac {[PP]}{Km_\mathrm{PP}} \right ) * \left ( 1 + \cfrac {[DMAPP]}{Km_\mathrm{DMAPP}} + \cfrac {[GPP]}{Km_\mathrm{GPP}} \right )}

Parameter	Description
VGPPS	Reaction rate for Geranyl diphosphate synthase
Vmaxforward	Maximum reaction rate towards the production of GPP
KmGPP	Michaelis-Menten constant for GPP
KmIPP	Michaelis-Menten constant for IPP
KmPP	Michaelis-Menten constant for PP
KmDMAPP	Michaelis-Menten constant for DMAPP
Keq	Equilibrium constant
[GPP]	GPP concentration
[DMAPP]	DMAPP concentration
[IPP]	DMAPP concentration
[PP]	PP concentration

Strategies for estimating the kinetic parameter values

Calculating the Equilibrium Constant

Standard Gibbs Free energy for GPPS from MetaCyc is -13.0 kcal mol^-1.

The equilibrium constant can be calculated using the Van't Hoff Isotherm equation:

$K_\mathrm{eq} = exp \left ( \cfrac {-∆G^{°'}}{RT} \right )$

Failed to parse (Cannot store math image on filesystem.): = exp \left ( \cfrac {-(-13.0 \text { kcalmol}^{-1})}{ (1.98722 \text{ calK}^{-1} \text { mol}^{-1} * 289 K} \right )

Failed to parse (Cannot store math image on filesystem.): = exp \left ( \cfrac {13.0 \text { kcalmol}^{-1} }{ 574.30658 \text{ calK}^{-1}\text { mol}^{-1} }\right)

Failed to parse (Cannot store math image on filesystem.): = exp \left ( \cfrac{ 13000 \text {calmol}^{-1}}{574.30658 \text{ JK}^{-1}\text { mol}^{-1}} \right)

$=exp \left ( XY \right )$

$= (INSERT RESULT)$

where;

Keq	Equilibrium constant
-?G°	Gibbs free energy change. For GPPS it is -13.0 kcalmol-1
R	Gas constant with a value of 1.98722 calK-1mol-1
T	Temperature which is always expressed in kelvin, as a standard, I used 298 K

Published Kinetic Parameter Values

Km Values

Km (mM)	Unit	Substrate / Product	Directionality	Organism	References
Value	unit	substrate	directionality	organism	Ref

Vmax values

Vmax	Unit	Directionality	Organism	References
Value	µmol/min/mg (unit)	directionality	Organism	References

Kcat values

Kcat	Unit	Organism	Reference
value	s-1	Organism	ref e.g. Alonso 1992

Extracting Information from (INSERT SUBSTRATE/PRODUCT) Production Rates

Amount produced (mg/L)	Time (H)	Organism	Description	Reaction Flux (µM/s)
X	X	Y	Z	Z
X	X	Y	Z	Z
X	X	Y	Z	Z
X	X	Y	Z	Z
X	X	Y	Z	Z
X	X	Y	Z	Z