Limonene-6-Hydroxylase (L6H)

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What we know

This enzyme is also known as (S)-limonene 6-monooxygenase, (-)-limonene 6-hydroxylase, (-)-limonene 6-monooxygenase, (-)-limonene,NADPH:oxygen oxidoreductase (6-hydroxylating)

Reaction catalysed

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

Metabolite and Enzyme Background Information

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

Metabolite	Abbreviation	Chemical Formula	Molar mass (g/mol)	ChEBI	ChEMBL	PubChem	MetaCyc
(-)-4S-limonene	Limonene	C10H16	136.24	15384	449062	22311 or 439250
(-)-trans-carveol	carveol	Chemical Formula	Molar mass (g/mol)	ChEBI	ChEMBL	PubChem	MetaCyc
NADPH	NADPH	Chemical Formula	Molar mass (g/mol)	ChEBI	ChEMBL	PubChem	MetaCyc
NADP	NADP	Chemical Formula	Molar mass (g/mol)	ChEBI	ChEMBL	PubChem	MetaCyc
Limonene-6-hydroxylase	L6H	Chemical Formula	Molar mass (g/mol)	ChEBI	ChEMBL	PubChem	LIMONENE-6-MONOOXYGENASE-RXN
Metabolite	Abbreviation	Chemical Formula	Molar mass (g/mol)	ChEBI	ChEMBL	PubChem	MetaCyc

Equation Rate

This reaction is modelled using the reversible Michaelis-Menten equation, with two substrates; Limonene and NADPH, and two products; Carveol and NADP.

$V_\mathrm{L6H} = Vmax_\mathrm{forward} * \cfrac {\cfrac{[Limonene]}{Km_\mathrm{Limonene}} * \left ( 1 - \cfrac {[Limonene]*[PP]}{[GPP]*K_\mathrm{eq}} \right )}{1 + \cfrac {[GPP]}{Km_\mathrm{GPP}} + \cfrac {[Limonene]}{Km_\mathrm{Limonene}} + \cfrac {[PP]}{Km_\mathrm{PP}} + \cfrac {[Limonene]*[PP]}{Km_\mathrm{Limonene}*Km_\mathrm{PP}}}$

Parameter	Description	Units
VL6H	Net reaction rate for Limonene-6-Hydroxylase	Unit
Vmaxforward	Maximum reaction rate towards the production of trans-carveol	Unit
Kmlimonene	Michaelis-Menten constant for Limonene	Unit
Kmcarveol	Michaelis-Menten constant for trans-carveol	Unit
KmNADPH	Michaelis-Menten constant for NADPH	Unit
KmNADP	Michaelis-Menten constant for NADP	Unit
Keq	Equilibrium constant	Unit
[Limonene]	Limonene concentration	Unit
[Carveol]	trans-carveol concentration	Unit
[NADPH]	NADPH concentration	Unit
[NADP]	NADP concentration	Unit

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 is -92.52051 kcal·mol^-1 according to MetaCyc [[1]].

Published Kinetic Parameter Values

Km Values

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

μ :-5.05354 , σ : 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

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

Detailed descriptions of kinetic values used in this model

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