Difference between revisions of "Menthol:neomenthol reductase (MNMR)"

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(→‎Published Kinetic Parameter Values)
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=== Published Kinetic Parameter Values ===
 
=== Published Kinetic Parameter Values ===
  
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==== Km Values ====
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==== Km Values for menthone, isomenthone, neomenthol, neoisomenthol and NADPH ====
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! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Parameter
 
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! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 100px;" | Directionality
 
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! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 10px;" | References
 
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 10px;" | References
 
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|-
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| Km || Forward || menthone || 96 || µM || Km: 96.0 +/- 5.2. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING || Toogood2016
 +
|-
 +
| Km || Forward || menthone || 101.2 || µM || Km: 96.0 +/- 5.2. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING || Toogood2016
 +
|-
 +
| Km || Forward || menthone || 90.8 || µM || Km: 96.0 +/- 5.2. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING || Toogood2016
 +
|-
 +
| Kcat || Forward || menthone || 0.91 || 1/s || Kcat: 0.89 +/- 0.02. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING || Toogood2016
 +
|-
 +
| Kcat || Forward || menthone || 0.87 || 1/s || Kcat: 0.89 +/- 0.02. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING || Toogood2016
 +
|-
 +
| Kcat || Forward || isomenthone || 0.44 || 1/s || Kcat: 0.44 +/- 0.02. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING || Toogood2016
 +
|-
 +
| Kcat || Forward || isomenthone || 0.46 || 1/s || Kcat: 0.44 +/- 0.02. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING || Toogood2016
 +
|-
 +
| Kcat || Forward || isomenthone || 0.42 || 1/s || Kcat: 0.44 +/- 0.02. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING || Toogood2016
 +
|-
 +
| Km || Forward || isomenthone || 186.5 || µM || Km: 186.5 +/- 16.8. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING || Toogood2016
 +
|-
 +
| Km || Forward || isomenthone || 203.3 || µM || Km: 186.5 +/- 16.8. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING || Toogood2016
 +
|-
 +
| Km || Forward || isomenthone || 169.7 || µM || Km: 186.5 +/- 16.8. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING || Toogood2016
 +
|-
 +
| Km || Forward || menthone || 7.1 || µM || producing neomenthol. KM: 7.1 +/- 1.4. from Artemisia annua, pH 7.0, Temp 30C, || Ryden2010
 +
|-
 +
| Km || Forward || menthone || 8.5 || µM || producing neomenthol. KM: 7.1 +/- 1.4. from Artemisia annua, pH 7.0, Temp 30C, || Ryden2010
 +
|-
 +
| Km || Forward || menthone || 5.7 || µM || producing neomenthol. KM: 7.1 +/- 1.4. from Artemisia annua, pH 7.0, Temp 30C, || Ryden2010
 +
|-
 +
| Km || Reverse || neomenthol || 305 || µM || producing menthone from neomenthol (reverse). KM: 305 +/- 100. from Artemisia annua, pH 7.0, Temp 30C, || Ryden2010
 +
|-
 +
| Km || Reverse || neomenthol || 405 || µM || producing menthone from neomenthol (reverse). KM: 305 +/- 100. from Artemisia annua, pH 7.0, Temp 30C, || Ryden2010
 +
|-
 +
| Km || Reverse || neomenthol || 205 || µM || producing menthone from neomenthol (reverse). KM: 305 +/- 100. from Artemisia annua, pH 7.0, Temp 30C, || Ryden2010
 +
|-
 +
| Kcat || Forward || menthone || 0.6 || 1/s || producing neomenthol (reverse). Kcat: 0.60. from Artemisia annua, pH 7.0, Temp 30C, || Ryden2010
 +
|-
 +
| Kcat || Reverse || neomenthol || 0.91 || 1/s || producing neomenthol (reverse). Kcat: 0.91. from Artemisia annua, pH 7.0, Temp 30C, || Ryden2010
 +
|-
 +
| Km || Forward || menthone || 674 || µM || menthone -> neomenthone, Km: 674 +/- 78, pH 9.3, temp 30 c, from Mentha piperita, expressed in E.coli.  || Davis2005
 +
|-
 +
| Km || Forward || menthone || 752 || µM || menthone -> neomenthone, Km: 674 +/- 78, pH 9.3, temp 30 c, from Mentha piperita, expressed in E.coli.  || Davis2005
 +
|-
 +
| Km || Forward || menthone || 596 || µM || menthone -> neomenthone, Km: 674 +/- 78, pH 9.3, temp 30 c, from Mentha piperita, expressed in E.coli.  || Davis2005
 +
|-
 +
| Km || Forward || isomenthone || 1000 || µM || isomenthone -> neomenthone, Km: >1000, pH 9.3, temp 30 c, from Mentha piperita, expressed in E.coli.  || Davis2005
 +
|-
 +
| Km || Forward || NADPH || 10 || µM || isomenthone/menthone + nadph -> neomenthone, Km: >1000, pH 9.3, temp 30 c, from Mentha piperita, expressed in E.coli.  || Davis2005
 +
|-
 +
| Km || Forward || NADPH || 11 || µM || isomenthone/menthone + nadph -> neomenthone, Km: >1000, pH 9.3, temp 30 c, from Mentha piperita, expressed in E.coli.  || Davis2005
 +
|-
 +
| Km || Forward || NADPH || 9 || µM || isomenthone/menthone + nadph -> neomenthone, Km: >1000, pH 9.3, temp 30 c, from Mentha piperita, expressed in E.coli.  || Davis2005
 +
|-
 +
| Km || Forward || menthone || 22 || µM || menthone -> neomenthol, pH 7.5, 30C, from Mentha piperita, expressed in E. coli || Kjonaas1982
 +
|-
 +
| Km || Forward || NADPH || 20 || µM || menthone -> neomenthol, pH 7.5, 30C, from Mentha piperita, expressed in E. coli || Kjonaas1982
 
|}
 
|}
  

Latest revision as of 11:48, 3 June 2016

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What we know

Menthone: neomenthol reductase(s) (MNMR) catalyses the NADPH-dependent convertion of menthone to neomenthol and the conversion of isomenthone to neoisomenthol.

Issues

Strategies

Reaction catalysed

menthone + NADPH \rightleftharpoons menthol + NADP^+
isomenthone + NADPH \rightleftharpoons isomenthol + NADP^+

Enzyme and 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
menthone:menthol reductase MMR 34070 Da [1], 35000 Da [2] 1.1.1.207
menthone
isomenthone
NADPH C21H30N7O17P3 745.42116 16474
NADP+ C21H29N7O17P3 744.41322 18009

Equation Rate

Two MMR reactions are included in the kinetic model with one converting menthone to neomenthol, and one converting isomenthone to neoisomenthol. Both reactions are parameterised using random Bi-Bi reversible Michaelis-Menten equation.

Reaction 1: Conversion of menthone to neomenthol

V_\mathrm{MNMR} = Kcat_\mathrm{forward} * [MNMR] * \cfrac {\left ( \cfrac{[menthone]}{Km_\mathrm{menthone}} * \cfrac {[NADPH]}{Km_\mathrm{NADPH}} \right ) * \left ( 1 - \cfrac {[neomenthol]*[NADP]}{[menthone]*[NADPH]*K_\mathrm{eq}} \right )} { \left (1 + \cfrac {[NADPH]}{Km_\mathrm{NADPH}} + \cfrac {[NADP]}{Km_\mathrm{NADP}} \right ) + \left ( 1+ \cfrac {[menthone]}{Km_\mathrm{menthone}} + \cfrac {[neomenthol]}{Km_\mathrm{neomenthol}} \right ) }

Reaction 2: Conversion of isomenthone to neoisomenthol

V_\mathrm{MNMR} = Kcat_\mathrm{forward} * [MNMR] * \cfrac {\left ( \cfrac{[isomenthone]}{Km_\mathrm{isomenthone}} * \cfrac {[NADPH]}{Km_\mathrm{NADPH}} \right ) * \left ( 1 - \cfrac {[neoisomenthol]*[NADP]}{[isomenthone]*[NADPH]*K_\mathrm{eq}} \right )} { \left (1 + \cfrac {[NADPH]}{Km_\mathrm{NADPH}} + \cfrac {[NADP]}{Km_\mathrm{NADP}} \right ) + \left ( 1+ \cfrac {[isomenthone]}{Km_\mathrm{isomenthone}} + \cfrac {[neoisomenthol]}{Km_\mathrm{neoisomenthol}} \right ) }
Parameter Description Units
VMMR Reaction rate for MNMR μM/min
Kcatforward Catalytic constant in the forward direction s-1
Kmmenthone Michaelis-Menten constant for menthone μM
Kmneomenthol Michaelis-Menten constant for neomenthol μM
Kmisomenthone Michaelis-Menten constant for isomenthone μM
Kmneoisomenthol Michaelis-Menten constant for neoisomenthol μM
KmNADPH Michaelis-Menten constant for NADPH μM
KmNADP Michaelis-Menten constant for NADP+ μM
Keq Equilibrium constant
[MMR] enzyme concentration μM
[neomenthol] neomenthol concentration μM
[menthone] Menthone concentration μM
[isomenthone] Isomenthone concentration μM
[neoisomenthol] neoisomenthol concentration μM
[NADPH] NADPH concentration μM
[NADP] NADP+ concentration μM

Strategies for estimating the kinetic parameter values

Estimating parameters for MMR

Standard Gibbs Free energy

The Gibbs free energy for MMR is -1.6264343 kcal.mol-1. This value is estimated from the 'Contribution group' method by Latendresse, M. and is available from MetaCyc (EC 1.1.1.207) [3].

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

Extracting Information from menthone Production Rates

A table will go here

Published Kinetic Parameter Values

Km Values for menthone, isomenthone, neomenthol, neoisomenthol and NADPH

Parameter Directionality Substrate / Product Value unit Method notes References
Km Forward menthone 96 µM Km: 96.0 +/- 5.2. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING Toogood2016
Km Forward menthone 101.2 µM Km: 96.0 +/- 5.2. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING Toogood2016
Km Forward menthone 90.8 µM Km: 96.0 +/- 5.2. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING Toogood2016
Kcat Forward menthone 0.91 1/s Kcat: 0.89 +/- 0.02. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING Toogood2016
Kcat Forward menthone 0.87 1/s Kcat: 0.89 +/- 0.02. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING Toogood2016
Kcat Forward isomenthone 0.44 1/s Kcat: 0.44 +/- 0.02. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING Toogood2016
Kcat Forward isomenthone 0.46 1/s Kcat: 0.44 +/- 0.02. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING Toogood2016
Kcat Forward isomenthone 0.42 1/s Kcat: 0.44 +/- 0.02. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING Toogood2016
Km Forward isomenthone 186.5 µM Km: 186.5 +/- 16.8. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING Toogood2016
Km Forward isomenthone 203.3 µM Km: 186.5 +/- 16.8. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING Toogood2016
Km Forward isomenthone 169.7 µM Km: 186.5 +/- 16.8. From Helen's data, would need to ask for experimental conditions, unpublished. Assume optimal conditions. NEEDS CONFIRMING Toogood2016
Km Forward menthone 7.1 µM producing neomenthol. KM: 7.1 +/- 1.4. from Artemisia annua, pH 7.0, Temp 30C, Ryden2010
Km Forward menthone 8.5 µM producing neomenthol. KM: 7.1 +/- 1.4. from Artemisia annua, pH 7.0, Temp 30C, Ryden2010
Km Forward menthone 5.7 µM producing neomenthol. KM: 7.1 +/- 1.4. from Artemisia annua, pH 7.0, Temp 30C, Ryden2010
Km Reverse neomenthol 305 µM producing menthone from neomenthol (reverse). KM: 305 +/- 100. from Artemisia annua, pH 7.0, Temp 30C, Ryden2010
Km Reverse neomenthol 405 µM producing menthone from neomenthol (reverse). KM: 305 +/- 100. from Artemisia annua, pH 7.0, Temp 30C, Ryden2010
Km Reverse neomenthol 205 µM producing menthone from neomenthol (reverse). KM: 305 +/- 100. from Artemisia annua, pH 7.0, Temp 30C, Ryden2010
Kcat Forward menthone 0.6 1/s producing neomenthol (reverse). Kcat: 0.60. from Artemisia annua, pH 7.0, Temp 30C, Ryden2010
Kcat Reverse neomenthol 0.91 1/s producing neomenthol (reverse). Kcat: 0.91. from Artemisia annua, pH 7.0, Temp 30C, Ryden2010
Km Forward menthone 674 µM menthone -> neomenthone, Km: 674 +/- 78, pH 9.3, temp 30 c, from Mentha piperita, expressed in E.coli. Davis2005
Km Forward menthone 752 µM menthone -> neomenthone, Km: 674 +/- 78, pH 9.3, temp 30 c, from Mentha piperita, expressed in E.coli. Davis2005
Km Forward menthone 596 µM menthone -> neomenthone, Km: 674 +/- 78, pH 9.3, temp 30 c, from Mentha piperita, expressed in E.coli. Davis2005
Km Forward isomenthone 1000 µM isomenthone -> neomenthone, Km: >1000, pH 9.3, temp 30 c, from Mentha piperita, expressed in E.coli. Davis2005
Km Forward NADPH 10 µM isomenthone/menthone + nadph -> neomenthone, Km: >1000, pH 9.3, temp 30 c, from Mentha piperita, expressed in E.coli. Davis2005
Km Forward NADPH 11 µM isomenthone/menthone + nadph -> neomenthone, Km: >1000, pH 9.3, temp 30 c, from Mentha piperita, expressed in E.coli. Davis2005
Km Forward NADPH 9 µM isomenthone/menthone + nadph -> neomenthone, Km: >1000, pH 9.3, temp 30 c, from Mentha piperita, expressed in E.coli. Davis2005
Km Forward menthone 22 µM menthone -> neomenthol, pH 7.5, 30C, from Mentha piperita, expressed in E. coli Kjonaas1982
Km Forward NADPH 20 µM menthone -> neomenthol, pH 7.5, 30C, from Mentha piperita, expressed in E. coli Kjonaas1982

Parameter uncertainty

Probability distribution has been generated for each of the parameter in this reaction.

Values and weights of Km for isomenthone
Parameter Direction Substrate Value Unit Weight weight counter Probability distribution Parameter details
Km Forward isomenthone 35 µM 512 512 07 MMR Km isomenthone v1.png Mode: 63.5
Km Forward isomenthone 41 µM 512 1024 Value Range: 41 - 91.8 μM
Km Forward isomenthone 46 µM 512 1536 CI factor: 1.497
Km Forward isomenthone 81 µM 512 2048 μ:4.1902
Km Forward isomenthone 86.4 µM 512 2560 σ: 0.19798
Km Forward isomenthone 91.8 µM 512 3072
Values and weights of Km for menthone
Parameter Direction Substrate Value Unit Weight weight counter Probability distribution Parameter details
Km Forward menthone 2.4 µM 512 512 08 MMR Km menthone v1.png Mode: 34.8
Km Forward menthone 3 µM 512 1024 Value Range: 3.7 - 326.84 μM
Km Forward menthone 3.6 µM 512 1536 CI factor: 9.39
Km Forward menthone 66 µM 512 2048 μ:4.31152
Km Forward menthone 69.9 µM 512 2560 σ:0.87287
Km Forward menthone 73.8 µM 512 3072
Km Forward menthone 250 µM 256 3328
Values and weights of Km for NADPH
Parameter Direction Substrate Value Unit Weight weight counter Probability distribution Parameter details
Km Forward NADPH 0.12 µM 512 512 09 MMR Km nadph v1.png Mode: 0.14
Km Forward NADPH 0.16 µM 512 1024 Value Range: 0.0019 - 10.1225 μM
Km Forward NADPH 0.08 µM 512 1536 CI factor: 72.304
Km Forward NADPH 20 µM 256 1792 μ:-0.0343, σ:1.3898
Values and weights of Kcat for Menthone
Parameter Direction Substrate Value Unit Weight weight counter Probability distribution Parameter details
Kcat Forward menthone 0.6 s-1 512 512 10 MMR Kcat menthone v1.png Mode: 2.35
Kcat Forward menthone 2.29 s-1 512 1024 Value Range: 0.9468 - 5.6602 μM
Kcat Forward menthone 2.34 s-1 512 1536 CI factor: 2.445
Kcat Forward menthone 2.39 s-1 512 2048 μ:1.0108, σ:0.414
Values and weights of Kcat for isomenthone
Parameter Direction Substrate Value Unit Weight weight counter Probability distribution Parameter details
Kcat Forward isomenthone 0.6 1/s 512 512 11 MMR Kcat isomenthone v1.png Mode: 2.25
Kcat Forward isomenthone 2.22 1/s 512 1024 Value Range: 0.9395 - 5.3887 μM
Kcat Forward isomenthone 2.28 1/s 512 1536 CI factor: 2.395
Kcat Forward isomenthone 2.34 1/s 512 2048 μ:0.9754, σ:0.4055

Detailed description of kinetic values obtained from literature

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

Simulations

References

  1. ↑ Davis, E.M. et. al. (2005). "Monoterpene metabolism. Cloning, Expression, and Characterization of Menthone Reductases from Peppermint.", Vol 137, pp. 873-881
  2. ↑ Kjonaas, R. et. al. (1982). Metabolism of monoterpenes: Conversion of l-Menthone to l-Menthol and d-Neomenthol by stereospecific dehydrogenases from peppermint (Mentha piperita) leaves, vol 69, pp.1013-1017.
  3. ↑ Latendresse M. (2013). "Computing Gibbs Free Energy of Compounds and Reactions in MetaCyc."
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