Double-bond reductase (DBR)
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Contents
Reaction catalysed
Enzyme and Metabolite Background Information
Long metabolite names are abbreviated in the model for clarity and standard identification purposes.
Compound | Abbreviation | Chemical Formula | Molar mass (g/mol) | ChEBI | ChEMBL | PubChem | BRENDA | PlantCyc |
---|---|---|---|---|---|---|---|---|
Double-bond reductase | DBR | 37914 Da | 1.3.1.81 | |||||
pulegone | C10H16O | 136.24 | ||||||
menthone | ||||||||
NADPH | C21H30N7O17P3 | 745.42116 | 16474 | |||||
NADP+ | C21H29N7O17P3 | 744.41322 | 18009 | |||||
isomenthone |
Equation Rate
DBR is modelled using two equations that describes: 1) Pulegone to Menthone and 2) Pulegone to Isomenthone. The predominant product for DBR is menthone where the ratio of menthone to isomenthone production have been reported as 40:33 [1], 55:45 [2] and 70:30 [3]. To model the variability of the product yield for DBR, variability factors which are calculated from the average ratio is included in the equations.
Reaction 1: Conversion of pulegone to menthone
- Failed to parse (Cannot store math image on filesystem.): V_\mathrm{DBR} = Kcat_\mathrm{forward} * X1*[DBR] * \cfrac {\left ( \cfrac{[pulegone]}{Km_\mathrm{pulegone}} * \cfrac {[NADPH]}{Km_\mathrm{NADPH}} \right ) * \left ( 1 - \cfrac {[menthone]*[NADP]}{[pulegone]*[NADPH]*K_\mathrm{eq}} \right )} { \left (1 + \cfrac {[NADPH]}{Km_\mathrm{NADPH}} + \cfrac {[NADP]}{Km_\mathrm{NADP}} \right ) + \left ( 1+ \cfrac {[pulegone]}{Km_\mathrm{pulegone}} + \cfrac {[menthone]}{Km_\mathrm{menthone}} \right ) }
Reaction 2: Conversion of pulegone to isomenthone
- Failed to parse (Cannot store math image on filesystem.): V_\mathrm{DBR} = Kcat_\mathrm{forward} *X2* [DBR] * \cfrac {\left ( \cfrac{[pulegone]}{Km_\mathrm{pulegone}} * \cfrac {[NADPH]}{Km_\mathrm{NADPH}} \right ) * \left ( 1 - \cfrac {[isomenthone]*[NADP]}{[pulegone]*[NADPH]*K_\mathrm{eq}} \right )} { \left (1 + \cfrac {[NADPH]}{Km_\mathrm{NADPH}} + \cfrac {[NADP]}{Km_\mathrm{NADP}} \right ) + \left ( 1+ \cfrac {[pulegone]}{Km_\mathrm{pulegone}} + \cfrac {[isomenthone]}{Km_\mathrm{isomenthone}} \right ) }
Parameter | Description | Units |
---|---|---|
VPGR | Reaction rate for Limonene-3-hydroxylase | μM/min |
Kcatforward | Catalytic constant in the forward direction | s-1 |
Kmpulegone | Michaelis-Menten constant for pulegone | μM |
Kmmenthone | Michaelis-Menten constant for menthone | μM |
Kmisomenthone | Michaelis-Menten constant for isomenthone | μM |
KmNADPH | Michaelis-Menten constant for NADPH | μM |
KmNADP | Michaelis-Menten constant for NADP+ | μM |
Keq | Equilibrium constant | |
X1 , X2 | Variability factors | |
[PGR] | enzyme concentration | μM |
[pulegone] | Pulegone concentration | μM |
[menthone] | Menthone concentration | μM |
[isomenthone] | Isomenthone concentration | μM |
[NADPH] | NADPH concentration | μM |
[NADP] | NADP+ concentration | μM |
Strategies for estimating the kinetic parameter values
Standard Gibbs Free energy
The Gibbs free energy for PGR is -3.9565125 kcal.mol^-1. This value is estimated from the 'Contribution group' method by Latendresse, M. and is available from MetaCyc (EC 1.3.1.81) [4].
Calculating the Equilibrium Constant
The equilibrium constant can be calculated using the Van't Hoff Isotherm equation:
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 |
Extracting Information from menthone Production Rates
A table will go here
Published Kinetic Parameter Values
Km Values
Parameter | Directionality | Substrate / Product | Value | unit | Method notes | References |
---|---|---|---|---|---|---|
Km | Forward | pulegone | 2.3 | µM | Gene from peppermint oil gland secretory cell cDNA, expressed in E. coli, optimal pH 5.0, menthone:isomenthone ratio of 55:45 | Ringer2003 |
Km | Forward | pulegone | 2.9 | µM | Gene from peppermint oil gland secretory cell cDNA, expressed in E. coli, optimal pH 5.0, menthone:isomenthone ratio of 55:45, Km 2.3 +/- 0.6 | Ringer2003 |
Km | Forward | NADPH | 6.9 | µM | Gene from peppermint oil gland secretory cell cDNA, expressed in E. coli, optimal pH 5.0, menthone:isomenthone ratio of 55:45 | Ringer2003 |
Detailed description of kinetic values obtained from literature
A more detailed description of the values listed above can be found here .
Simulations
References
- ↑ 1.0 1.1 Toogood, H. et. al.2015. "Enzymatic menthol production: One-pot approach using engioneered Escherichia coli ", ACS Synthetic Biology, 4:1112-1123 Cite error: Invalid
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- ↑ Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."