Limonene Synthase
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Contents
What we know
Issues
Strategies
Reaction catalysed
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
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:
Failed to parse (Cannot store math image on filesystem.): = exp \left ( \cfrac {-(- 117.36396 \text { kJmol}^{-1})}{ (8.31 \text{ JK}^{-1} \text { mol}^{-1} * 289 K} \right )
Failed to parse (Cannot store math image on filesystem.): = exp \left ( \cfrac { + 117.36396 \text { kJmol}^{-1} }{ 2401.59 \text{ JK}^{-1}\text { mol}^{-1} }\right)
Failed to parse (Cannot store math image on filesystem.): = exp \left ( \cfrac{ 117.364 * 10^3 \text { Jmol}^{-1}}{2401.59 \text{ JK}^{-1}\text { mol}^{-1}} \right)
Failed to parse (Cannot store math image on filesystem.): =exp \left ( 48.8693 \right )
Failed to parse (Cannot store math image on filesystem.): = 1.6736 * 10^{21}
where;
Keq | Equilibrium constant |
-ΔG° | Gibbs free energy change. For Limonene Synthase it is -117.364 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 Limonene Synthase from MetaCyc (EC 4.2.3.16) is -28.049988 kcal/mol [1].
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 Limonene synthase in kJ mol-1 is:
- Failed to parse (Cannot store math image on filesystem.): \cfrac {1}{0.239 kcal.mol^-1} * -28.049988 kcal.mol^-1
- Failed to parse (Cannot store math image on filesystem.): = -117.36396 kJmol^-1
Extracting Information from Limonene Production Rates
Production rates would reflect the flux for this reaction in the forward direction.
Amount produced (mg/L) | Time (H) | Organism | Description | Reaction Flux (µM/s) |
---|---|---|---|---|
5 | 24 | Escherichia coli | Possible reason for the low limonene production might due to the insufficient supply of IPP and DMAPP [2]. | 0.0255 |
335 | 48 | Escherichia coli | Engineered E.coli in which heterologous MVA pathway was installed [3]. | 0.8537 |
35.8 | 48 | Escherichia coli | E.coli was engineered to express GPPS, LS, DXS, and IDI [4] . | 0.0912 |
4.87 | 48 | Escherichia coli | This was the initial titer. The study established a limonene biosynthesis pathway in E.coli using four different polycistronic operons based on 3 vectors with varied expression strength [5]. | 0.0124 |
17.4 | 48 | Escherichia coli | Using a plasmid with DXS and IDI over expressed [6]. | 0.0445 |
430 | 72 | Escherichia coli | [7] | 0.7306 |
Published Kinetic Parameter Values
Km (mM) | Vmax | Kcat (s-1) | Kcat/Km | Organism | Description |
---|---|---|---|---|---|
0.00125 | - | - | - | Ricciocarpos natans | GPP -> Limonene |
0.0018 | - | - | - | Mentha piperita | GPP -> Limonene |
0.00625 | 0.08 µmol/min/mg | 0.08 | 1.5 | Cannabis sativa L. | GPP -> Limonene |
0.00496 | 0.13 µmol/min/mg | 0.14 | 2.9 | Cannabis sativa L. | GPP -> Limonene |
0.0031 | 0.4748 µmol/min/mg | - | - | Citrus limon | GPP -> Limonene |
0.016 | - | 0.02 | - | Escherichia coli | GPP -> Limonene |
0.0068 | - | 0.082 | - | Cannabis sativa L. | GPP -> Limonene |
0.0067 | - | 0.081 | - | Cannabis sativa L. | GPP -> Limonene |
Simulations
References
- ↑ Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."
- ↑ Carter, Ora A. et. al.2013. "Monoterpene biosynthesis pathway construction in Escherichia coli",Phytochemistry, 64:425–433, 2003.
- ↑ Alonso-Gutierez et. al. 2013. "Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production", Metabolic Engineering, 19:33-41
- ↑ Du et. al. 2014. "Enhanced limonene production by optimizing the expression of limonene biosynthesis and MEP pathway genes in E.coli", Bioprocessing and Bioprocessing, 1:10
- ↑ Du et. al. 2014. "Enhanced limonene production by optimizing the expression of limonene biosynthesis and MEP pathway genes in E.coli", Bioprocessing and Bioprocessing, 1:10
- ↑ Du et. al. 2014. "Enhanced limonene production by optimizing the expression of limonene biosynthesis and MEP pathway genes in E.coli", Bioprocessing and Bioprocessing, 1:10
- ↑ Alonso-Gutierez et. al. 2013. "Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production", Metabolic Engineering, 19:33-41