Limonene Synthase
You can go back to main page of the kinetic model here.
Model construction progress :
Enzyme | Pathway | Keq | Kcat | VmaxF | KmGPP | KmSub2 | [GPP] | [Sub2] | VmaxR | KmLim | KmPP | [Limonene] | [PP] |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
02_LimSynth | Limonene Biosynthesis | 1 | 5 | 3 | >6 | no Sub2 | 4 | no Sub2 | estimated | estimated | estimated | estimated | estimated |
Legend:
Have not started ·· | 1 -2 data found ·· | 3-4 data found ·· | sufficient data found/estimated ·· | data distribution generated ·· | data sampled |
to do | DONE! |
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 | ||
limonene synthase | LimSynth | 70.03 kDa [1], 72.4 kDa [2] ; 60kDa [3]; 56 kDa [4] |
Equation Rate
The reversible Michaelis-Menten equation to model the dynamic changes of LimSynth is:
where :
Parameter | Description | Units |
---|---|---|
VLimSynth | Reaction rate for Limonene Synthase | |
Vmaxforward | Maximum reaction rate towards the production of limonene | ref |
KmGPP | Michaelis-Menten constant for GPP | mM |
KmLimonene | Michaelis-Menten constant for Limonene | mM |
KmPP | Michaelis-Menten constant for PP | mM |
Keq | Equilibrium constant | |
[GPP] | GPP concentration | mM |
[Limonene] | Limonene concentration | mM |
[PP] | PP concentration | mM |
Strategies for estimating the kinetic parameter values
Calculating the Equilibrium Constant
Standard Gibbs Free energy
Standard Gibbs Free energy for Limonene Synthase from MetaCyc (EC 4.2.3.16) is -28.049988 kcal/mol [5].
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
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 |
Kinetic Parameter Values
Values for the kinetic parameter required to simulate this model can be obtained from published and unpublished literature.
A more detailed descriptions of the values listed above can be found HERE , where I've linked and highlighted where these data came from.
Substrate, Product & Enzyme Concentration Values
Concentration | Unit | Substrate / Product | Directionality | Organism | Method notes | References |
---|---|---|---|---|---|---|
10 | µM | GPP | forward | Citrus sinensis | enzyme activity assay, pH 7, 37°C, with 0.3µM enzyme | [6] |
40 | µM | GPP | forward | Citrus sinensis | enzyme activity assay, pH 7, 37°C, with 0.3µM enzyme | [6] |
0.3 | µM | Limonene synthase | - | Citrus sinensis | enzyme activity assay, pH 7, 37°C, with 10-40µM GPP | [6] |
25 | µM | GPP | forward | E. coli | [7] | |
10 | µM | GPP | forward | Cannabis sativa L. | [8] | |
10 | µM | GPP | forward | Mentha sp. | [4] | |
2 | µM | GPP | forward | Citrus limon | [9] | |
150 | µg | Limonene synthase | - | E. coli | [7] | |
0.07 | µM | Limonene synthase | - | Citrus sinensis | with 200µM GPP as substrate, at 20°C, pH7.5 | [10] |
0.26 | µM | Limonene synthase | - | Citrus sinensis | with 200µM GPP, at 37°C, pH7.5 | [10] |
200 | µM | GPP | forward | Citrus sinensis | used for Limonene synthase activity assay at 20°C and 37°C, pH 7.5 | [10] |
100 | µM | GPP | - | Citrus limon | [9] | |
0.1 | µM | GPP | - | Citrus limon | [9] |
Km Values
Km (μM) | Unit | Substrate / Product | Directionality | Organism | Method notes | References |
---|---|---|---|---|---|---|
130 | μM | GPP | forward | Citrus sinensis | Enzyme assay, pH 7.5, 20°C | [10] |
1.25 | μM | GPP | forward | Ricciocarpos natans | [11] | |
1.8 | μM | GPP | forward | Mentha piperita | [4] | |
11.76 ± 2.45 | μM | GPP | forward | Cannabis sativa L. | [1] | |
3.1 | μM | GPP | forward | Citrus limon | [9] | |
16.0 | μM | GPP | forward | Escherichia coli | [7] | |
6.7 | μM | GPP | forward | Escherichia coli (wt) | [12] | |
6.8 | μM | GPP | forward | Cannabis sativa L. | CsTPS1, pH6.5, 40°C, 1.25 μg [LimSynth] per 500μl assay mixture, 10μM [GPP] | [8] |
8.6 | μM | GPP | forward | Escherichia coli (Q53). | [7] | |
6.0 | μM | GPP | forward | Escherichia coli (E57). | [7] | |
12.6 | μM | GPP | forward | Escherichia coli (R58). | [7] | |
29.9 | μM | GPP | forward | Escherichia coli (R59). | [7] | |
32.4 | μM | GPP | forward | Escherichia coli (R58P59) | [7] | |
27.5 | μM | GPP | forward | Escherichia coli (R58A59) | [7] | |
18.8 | μM | GPP | forward | Escherichia coli (S60) | [7] | |
0.7 | μM | GPP | forward | Citrus limon | [9] | |
6.25 ± 0.41 | μM | GPP | forward | Cannabis sativa L | [1] |
Vmax values
Vmax | Unit | Directionality | Organism | Organism | References |
---|---|---|---|---|---|
0.08 | µmol/min/mg | forward | Cannabis sativa L. | [1] | |
0.12 ± 0.01 | µmol/min/mg | forward | Cannabis sativa | [1] | |
0.4748 | µmol/min/mg | forward | Citrus limon | References | |
0.53 | µM/min | forward | Citrus sinensis | 200µM GPP, 20°C, [E]: 0.07µM, pH7.5 | [10] |
0.64 | µM/min | forward | Citrus sinensis | 200µM GPP, 37°C, [E]: 0.26µM, pH7.5 | [10] |
19 | µmol/h/mg | forward | Mentha x piperita & Mentha spicata | Maximum specific activity, 1-10µg protein per mixture, pH &.0, 30°C | References |
Kcat values
Kcat | Unit | Directionality | Organism | Method notes | Reference |
---|---|---|---|---|---|
0.13 | s-1 | forward | Citrus sinensis | 200mM GPP, 20°C, [E]: 0.07 mM, pH7.5 | [10] |
0.04 | s-1 | forward | Citrus sinensis | 200mM GPP, 37°C, [E]: 0.26mM, pH7.5 | [10] |
0.3 | s-1 | forward | Mentha piperita & Mentha spicata | pH7.0, 30°C, Limonene synthase assay, 10 μM [GPP], 1-10 μg protein per mixture | [4] |
0.09 | s-1 | forward | Cannabis sativa L. | [1] | |
0.13 | s-1 | forward | Cannabis sativa L. | [1] | |
0.02 | s-1 | forward | E. coli | [7] | |
0.082 | s-1 | forward | Cannabis sativa L. | CsTPS1, pH6.5, 40°C, 1.25 mg [LimSynth] per 500ml assay mixture, 10mM [GPP] | [8] |
0.000039 | s-1 | forward | Citrus sinenesis | Limonene synthase assay, with 40 μM GPP, 37°C | [6] |
0.0024 | s-1 | forward | E. coli (wt) | [12] | |
0.0020 | s-1 | forward | E. coli (preprotein) | [7] | |
0.0036 | s-1 | forward | E. coli (Q54) | [12] [7] | |
0.0034 | s-1 | forward | E. coli (E57) | [12] [7] | |
0.0037 | s-1 | forward | E. coli (R58) | [12] [7] | |
<0.0004 | s-1 | forward | E. coli (R59) | [12] [7] | |
<0.0004 | s-1 | forward | E. coli (R58P59) | [12] [7] | |
<0.0004 | s-1 | forward | E. coli (R58A59) | [12] [7] | |
<0.0004 | s-1 | forward | E. coli (S60) | [12] [7] |
Extracting Information from Limonene Production Rates
The production rates would reflect on the flux for this enzyme, and this would provide provide the insights on the Vmax of this enzyme.
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 [13]. | 0.0255 |
335 | 48 | Escherichia coli | Engineered E.coli in which heterologous MVA pathway was installed [14]. | 0.8537 |
35.8 | 48 | Escherichia coli | E.coli was engineered to express GPPS, LS, DXS, and IDI [15] . | 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 [15]. | 0.0124 |
17.4 | 48 | Escherichia coli | Using a plasmid with DXS and IDI over expressed [15]. | 0.0445 |
430 | 72 | Escherichia coli | [14] | 0.7306 |
Parameter estimation
This section can be found HERE
Simulations
Simulations performed can be found HERE.
References
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 Gunnewich, N. 2008. "Expression and characterization of terpene synthases from Cannabis sativa L. and Salvia sclarea L. Doctoral thesis. Cite error: Invalid
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tag; name "Gunnewich2008" defined multiple times with different content - ↑ Turner,G. et. al.1999. "Limonene synthase, the enzyme responsible for monoterpene biosynthesis in peppermint, is localized to leucoplasts of oil gland secretory cells", Plant Physiology 120(3): 879-886
- ↑ Maruyama, T. et. al. 2002. "Molecular cloning, functional expression and characterization of d-Limonene synthase from Agastache rugosa" Biol. Pharm. Bull. 25(5): 661-665
- ↑ 4.0 4.1 4.2 4.3 Alonso et. al. 1992. "Purification of 4S-Limonene Synthase, a Monoterpene Cyclase from the Glandular Trichomes of Peppermint (Mentha x piperita) and Spearmint (Mentha spicata)", The Journal of Biological Chemistry, 267(11):7582-7587
- ↑ Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."
- ↑ 6.0 6.1 6.2 6.3 Olsen, S.N. 2011. "Isolation, Purification, and Characterization of (+)-4R-limonene synthase: The first step in exploring enzyme stereospecificity in terpenoid biosynthesis",Masters thesis, Brandeis university Cite error: Invalid
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tag; name "Olsen2011" defined multiple times with different content Cite error: Invalid<ref>
tag; name "Olsen2011" defined multiple times with different content Cite error: Invalid<ref>
tag; name "Olsen2011" defined multiple times with different content - ↑ 7.00 7.01 7.02 7.03 7.04 7.05 7.06 7.07 7.08 7.09 7.10 7.11 7.12 7.13 7.14 7.15 7.16 7.17 7.18 Williams, D.C. et. al. 1998. "Truncation of Limonene Synthase preprotein provides a fully active 'pseudomature' form of this monoterpene cyclase and reveals the function of the amino-terminal arginine pair ",Biochemistry, 37:12213-12220 Cite error: Invalid
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tag; name "Williams1998" defined multiple times with different content - ↑ 8.0 8.1 8.2 Gunnewich, N., et al. 2006."Functional expression and characterization of trichome-specific (-)-limonene synthase and (+)-α-pinene synthase from Cannabis sativa", Natural Product Communications, 0(0): pp1-10 Cite error: Invalid
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tag; name "Gunnewich2006" defined multiple times with different content - ↑ 9.0 9.1 9.2 9.3 9.4 Lücker, J. et. al. 2002."Monoterpene biosynthesis in lemon (Citrus limon). cDNA isolation and functional analysis of four monoterpene synthases", Eur. J. Biochem. 269: pp3160-3171
- ↑ 10.0 10.1 10.2 10.3 10.4 10.5 10.6 10.7 Entova, S. 2013. "Kinetic characterization, crystallization, and photosynthetic expression of (+)-4R-limonene synthase from C. sinensis", Masters Thesis, Brandeis Univeristy Cite error: Invalid
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tag; name "Entova2013" defined multiple times with different content - ↑ Adam, K. et. al. 1996. "Partial purification and characterization of a monoterpene cyclase, limonene synthase, from the liverwort Ricciocarpos natans. 332(2):pp 352-356.
- ↑ 12.0 12.1 12.2 12.3 12.4 12.5 12.6 12.7 12.8 Ogura, K. & Koyama, T. 1997, "Dynamic aspects of Natural Products Chemistry". pp 1-23.
- ↑ Carter, Ora A. et. al.2013. "Monoterpene biosynthesis pathway construction in Escherichia coli",Phytochemistry, 64:425–433, 2003.
- ↑ 14.0 14.1 Alonso-Gutierez et. al. 2013. "Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production", Metabolic Engineering, 19:33-41 Cite error: Invalid
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tag; name "AlonsoGutierez2013" defined multiple times with different content - ↑ 15.0 15.1 15.2 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