Geranyl diphosphate synthase (GPPS)

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Reaction catalysed

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

$DMAPP + IPP \rightleftharpoons GPP + PP$

Metabolite 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
dimethylallyl diphosphate	DMAPP
isopentenyl diphosphate	IPP
geranyl diphosphate	GPP	C10H20O7P2	314.209	17211	41432	445995
diphosphate	PP	O7P2	173.94			644102

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 )}{1 + \cfrac {[GPP]}{Km_\mathrm{GPP}} + \cfrac {[Limonene]}{Km_\mathrm{Limonene}} + \cfrac {[PP]}{Km_\mathrm{PP}} + \cfrac {[Limonene]*[PP]}{Km_\mathrm{Limonene}*Km_\mathrm{PP}}}

Parameter	Description
VLimSynth	Reaction rate for Limonene Synthase
Vmaxforward	Maximum reaction rate towards the production of limonene
KmGPP	Michaelis-Menten constant for GPP
KmLimonene	Michaelis-Menten constant for Limonene
KmPP	Michaelis-Menten constant for PP
Keq	Equilibrium constant
[GPP]	GPP concentration
[Limonene]	Limonene concentration
[PP]	PP concentration

Strategies for estimating the kinetic parameter values

Calculating the Equilibrium Constant

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

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

$= exp \left ( \cfrac {-(XY \text { kJmol}^{-1})}{ (8.31 \text{ JK}^{-1} \text { mol}^{-1} * 289 K} \right )$

$= exp \left ( \cfrac { XY \text { kJmol}^{-1} }{ 2401.59 \text{ JK}^{-1}\text { mol}^{-1} }\right)$

$= exp \left ( \cfrac{ XY \text { Jmol}^{-1}}{2401.59 \text{ JK}^{-1}\text { mol}^{-1}} \right)$

$=exp \left ( XY \right )$

$= (INSERT RESULT)$

where;

Keq	Equilibrium constant
-?G°	Gibbs free energy change. For (INSERT ENZYME) it is (INSERT VALUE) kJmol-1
R	Gas constant with a value of 8.31 JK-1mol-1
T	Temperature which is always expressed in kelvin

Standard Gibbs Free energy

Standard Gibbs Free energy for (INSERT ENZYME) from MetaCyc (EC 4.2.3.16) is (INSERT VALUE) kcal/mol .

SI derived unit for Gibbs free energy is Joules per mol (J mol^-1). 1 kJ·mol^-1 is equal to 0.239 kcal·mol^-1.

Therefore, the Gibbs free energy for (INSERT ENZYME) in kJ mol^-1 is:

$\cfrac {1}{0.239 kcal.mol^-1} * (INSERT VALUE) kcal.mol^-1$

$= (INSERT RESULT) kJmol^-1$

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