Isopiperitenol Dehydrogenase (IPDH)

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Reaction catalysed

$Limonene + NADPH + O_2 \rightleftharpoons (-)-trans-isopiperitenol + NADP^+ + H_2O$

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
geranyl diphosphate	GPP	C10H20O7P2	314.209	17211	41432	445995
(-)-4S-limonene	Limonene	C10H16	136.24	15384	449062	22311 or 439250
diphosphate	PP	O7P2	173.94			644102

Equation Rate

$V_\mathrm{LimSynth} = Vmax_\mathrm{forward} * \cfrac {\cfrac{[GPP]}{Km_\mathrm{GPP}} * \left ( 1 - \cfrac {[Limonene]*[PP]}{[GPP]*K_\mathrm{eq}} \right )}{1 + \cfrac {[GPP]}{Km_\mathrm{GPP}} + \cfrac {[Limonene]}{Km_\mathrm{Limonene}} + \cfrac {[PP]}{Km_\mathrm{PP}} + \cfrac {[Limonene]*[PP]}{Km_\mathrm{Limonene}*Km_\mathrm{PP}}}$

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

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

µ :-5.05354 , s : 0.49474

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

Detailed description of kinetic values obtained from the literature

A more detailed description of the values listed above can be found here.