Difference between revisions of "Geranyl diphosphate synthase (GPPS)"

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(→‎Published Kinetic Parameter Values)
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A more detailed descriptions of the values listed above can be found [[ Geranyl diphosphate synthase: Detailed information on the kinetic values obtained from the literature | '''HERE''' ]], where I've linked and highlighted where these data came from.  
 
A more detailed descriptions of the values listed above can be found [[ Geranyl diphosphate synthase: Detailed information on the kinetic values obtained from the literature | '''HERE''' ]], where I've linked and highlighted where these data came from.  
  
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=== Substrate, Product & Enzyme Concentration Values ===
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{| class="wikitable sortable"
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|-
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! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Concentration
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! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Unit
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! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Substrate / Product
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! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Directionality
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! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 150px;" | Organism
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! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | References
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|-
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| 15
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| µM
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| IPP
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| forward
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| ''Phaedon cochleariae''
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| <ref name="Frick2013">  </ref>
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|-
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| 50
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| µM
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| DMAPP
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| forward
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| ''Phaedon cochleariae''
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| <ref name="Frick2013">  </ref>
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|-
 +
| 50
 +
| µM
 +
| DMAPP
 +
| forward
 +
| ''Phaedon cochleariae''
 +
| <ref name="Frick2013">  </ref>
 +
|-
 +
| 50
 +
| µM
 +
| IPP
 +
| forward
 +
| ''Phaedon cochleariae''
 +
| <ref name="Frick2013">  </ref>
 +
|-
 +
|}
  
 
==== Km Values ====
 
==== Km Values ====
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! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Substrate / Product  
 
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Substrate / Product  
 
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Directionality
 
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Directionality
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! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 100px;" | Organism
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! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 150px;" | Organism
 
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | References
 
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | References
 
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! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Unit
 
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Unit
 
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Directionality
 
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | Directionality
−
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 100px;" | Organism
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! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 150px;" | Organism
 
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | References
 
! style="border: 1px solid black; padding: 5px; background: #ffdead; width: 50px;" | References
 
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Revision as of 12:35, 29 March 2016

You can go back to main page of the kinetic model here.

Legend:

Have not started ·· 1 -2 data found ·· 3-4 data found ·· sufficient data found/estimated ·· data distribution generated ·· data sampled
to do DONE!

What we know

Issues

Strategies

Reaction catalysed

dimethylallyl diphosphate + isopentenyl diphosphate \rightleftharpoons geranyl diphosphate + diphosphate
DMAPP + IPP \rightleftharpoons GPP + PP

Metabolite and Enzyme 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 MetaCyc BRENDA
dimethylallyl diphosphate DMAPP
isopentenyl diphosphate IPP
geranyl diphosphate GPP C10H20O7P2 314.209 17211 41432 445995
diphosphate PP O7P2 173.94 644102
geranyl diphosphate synthase GPPS 32.16 kD (from nucleotide sequence), 36 kD (experimental) CPLX-8656 2.5.1.1

Equation Rate

Failed to parse (Cannot store math image on filesystem.): V_\mathrm{GPPS} = Vmax_\mathrm{forward} * \cfrac { \left (\cfrac{[DMAPP]}{Km_\mathrm{DMAPP}} * \cfrac{[IPP]}{Km_\mathrm{IPP}}\right )* \left ( 1 - \cfrac {[GPP]*[PP]}{[GPP]*[PP]*K_\mathrm{eq}} \right )}{\left (1 + \cfrac {[IPP]}{Km_\mathrm{IPP}} + \cfrac {[PP]}{Km_\mathrm{PP}} \right ) * \left ( 1 + \cfrac {[DMAPP]}{Km_\mathrm{DMAPP}} + \cfrac {[GPP]}{Km_\mathrm{GPP}} \right )}


Parameter Description
VGPPS Reaction rate for Geranyl diphosphate synthase
Vmaxforward Maximum reaction rate towards the production of GPP
KmGPP Michaelis-Menten constant for GPP
KmIPP Michaelis-Menten constant for IPP
KmPP Michaelis-Menten constant for PP
KmDMAPP Michaelis-Menten constant for DMAPP
Keq Equilibrium constant
[GPP] GPP concentration
[DMAPP] DMAPP concentration
[IPP] DMAPP concentration
[PP] PP concentration

Strategies for estimating the kinetic parameter values

Calculating the Equilibrium Constant

Standard Gibbs Free energy for GPPS from MetaCyc is -13.0 kcal mol-1.

The equilibrium constant can be calculated using the Van't Hoff Isotherm equation:

K_\mathrm{eq} = exp \left ( \cfrac {-∆G^{°'}}{RT} \right )


Failed to parse (Cannot store math image on filesystem.): = exp \left ( \cfrac {-(-13.0 \text { kcalmol}^{-1})}{ (1.98722 \text{ calK}^{-1} \text { mol}^{-1} * 289 K} \right )

Failed to parse (Cannot store math image on filesystem.): = exp \left ( \cfrac {13.0 \text { kcalmol}^{-1} }{ 574.30658 \text{ calK}^{-1}\text { mol}^{-1} }\right)

Failed to parse (Cannot store math image on filesystem.): = exp \left ( \cfrac{ 13000 \text {calmol}^{-1}}{574.30658 \text{ JK}^{-1}\text { mol}^{-1}} \right)

=exp \left ( XY \right )

= (INSERT RESULT)


where;

Keq Equilibrium constant
-?G° Gibbs free energy change. For GPPS it is -13.0 kcalmol-1
R Gas constant with a value of 1.98722 calK-1mol-1
T Temperature which is always expressed in kelvin, as a standard, I used 298 K

Published 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 References
15 µM IPP forward Phaedon cochleariae [1]
50 µM DMAPP forward Phaedon cochleariae [1]
50 µM DMAPP forward Phaedon cochleariae [1]
50 µM IPP forward Phaedon cochleariae [1]

Km Values

Km (mM) Unit Substrate / Product Directionality Organism References
0.84 μM IPP forward Phaedon cochleariae [1]
11.6 μM DMAPP forward Phaedon cochleariae [1]

Vmax values

Vmax Unit Directionality Organism References
0.44 µmol/min/mg (unit) forward Phaedon cochleariae [1]
0.67 µmol/min/mg (unit) forward Phaedon cochleariae [1]
2.39 µmol/min/mg (unit) forward Phaedon cochleariae [1]
0.17 µmol/min/mg (unit) forward Phaedon cochleariae [1]

Kcat values

Kcat Unit Organism Reference
value s-1 Organism ref e.g. Alonso 1992 [2]

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

Simulations

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 Cite error: Invalid <ref> tag; name "Frick2013" defined multiple times with different content
  2. ↑ 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
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