Limonene-3-hydroxylase (L3H)

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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	BRENDA	PlantCyc
limonene-3-hydroxylase	L3H		56.1 kD				1.14.13.47	MONOMER-6761
(-)-4S-limonene	Limonene	C10H16	136.24	15384	449062	22311 or 439250
(-)-trans-isopiperitenol		C10H16O	152.23344	15406		439410
NADPH		C21H30N7O17P3	745.42116	16474
NADP+		C21H29N7O17P3	744.41322	18009
Dioxygen	O2	O2	31.99880	15379
water	H2O	H2O	18.01530	15377

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:

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

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

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

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

$=exp \left ( XY \right )$

$= (INSERT RESULT)$

where;

Keq	Equilibrium constant
-ΔG°	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:

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

$= (INSERT RESULT) kJmol^-1$

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

Published Kinetic Parameter Values

Km (mM)	Vmax	Kcat (s-1)	Kcat/Km	Organism	Description
0.00125	-	-	-	Z	A -> B
0.0018	-	-	-	Z	A -> B
Y	Y	Y	Y	Z	A -> B
Y	Y	Y	Y	Z	A -> B
Y	Y	-	-	Z	A -> B
Y	-	Y	-	Z	GPP -> B
Y	-	Y	-	Z	GPP -> B
x	-	y	-	Z.	A -> B