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BIOMD0000000068 - Curien2003_MetThr_synthesis

 

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Reference Publication
Publication ID: 14622248
Curien G, Ravanel S, Dumas R.
A kinetic model of the branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana.
Eur. J. Biochem. 2003 Dec; 270(23): 4615-4627
Laboratoire de Physiologie Cellulaire Végétale DRDC/CEA-Grenoble, France. g.curien@cea.fr  [more]
Model
Original Model: JWS logo
Submitter: Nicolas Le Novère
Submission ID: MODEL6624146302
Submission Date: 01 Sep 2006 21:22:07 UTC
Last Modification Date: 16 May 2012 10:20:30 UTC
Creation Date: 30 Aug 2006 21:46:53 UTC
Encoders:  Jacky L Snoep
   Harish Dharuri
   Lukas Endler
set #1
bqbiol:hasTaxon Taxonomy Arabidopsis thaliana
bqbiol:hasPart KEGG Pathway map00271
KEGG Pathway Glycine, serine and threonine metabolism
set #2
bqbiol:hasPart Gene Ontology threonine biosynthetic process
Gene Ontology L-methionine biosynthetic process from O-phospho-L-homoserine and cystathionine
Notes

This a model from the article:
A kinetic model of the branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana.
Curien G, Ravanel S, Dumas R Eur. J. Biochem. 2003 Dec; Volume: 270 (Issue: 23 )]:4615-27 14622248 ,
Abstract:
This work proposes a model of the metabolic branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana which involves kinetic competition for phosphohomoserine between the allosteric enzyme threonine synthase and the two-substrate enzyme cystathionine gamma-synthase. Threonine synthase is activated by S-adenosylmethionine and inhibited by AMP. Cystathionine gamma-synthase condenses phosphohomoserine to cysteine via a ping-pong mechanism. Reactions are irreversible and inhibited by inorganic phosphate. The modelling procedure included an examination of the kinetic links, the determination of the operating conditions in chloroplasts and the establishment of a computer model using the enzyme rate equations. To test the model, the branch-point was reconstituted with purified enzymes. The computer model showed a partial agreement with the in vitro results. The model was subsequently improved and was then found consistent with flux partition in vitro and in vivo. Under near physiological conditions, S-adenosylmethionine, but not AMP, modulates the partition of a steady-state flux of phosphohomoserine. The computer model indicates a high sensitivity of cystathionine flux to enzyme and S-adenosylmethionine concentrations. Cystathionine flux is sensitive to modulation of threonine flux whereas the reverse is not true. The cystathionine gamma-synthase kinetic mechanism favours a low sensitivity of the fluxes to cysteine. Though sensitivity to inorganic phosphate is low, its concentration conditions the dynamics of the system. Threonine synthase and cystathionine gamma-synthase display similar kinetic efficiencies in the metabolic context considered and are first-order for the phosphohomoserine substrate. Under these conditions outflows are coordinated.


SBML level 2 code generated for the JWS Online project by Jacky Snoep using PySCeS
Run this model online at http://jjj.biochem.sun.ac.za
To cite JWS Online please refer to: Olivier, B.G. and Snoep, J.L. (2004) Web-based modelling using JWS Online , Bioinformatics, 20:2143-2144

Biomodels Curation The model simulates the flux for TS and CGS under conditions given in Table 2 and reproduces the dotted lines given in Table 3 of the paper. There is a typo in the equation for the apparent specificity constant for Phser, Kts (equation13). This was changed after communication with the authors to be: Kts = 5.9E-4+6.2E-2*pow(AdoMet,2.9)/(pow(32,2.9)+pow(AdoMet,2.9)). The model was successfully tested on Jarnac and Copasi. Due to a suggestion from Pedro Mendez the parameter AdoMet, TS and CGS where made constant species.

This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2010 The BioModels.net Team.
For more information see the terms of use .
To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

Model
Publication ID: 14622248 Submission Date: 01 Sep 2006 21:22:07 UTC Last Modification Date: 16 May 2012 10:20:30 UTC Creation Date: 30 Aug 2006 21:46:53 UTC
Mathematical expressions
Reactions
Phosphohomoserine synthesis Cystathionine gamma-synthase Threonine Synthase  
Physical entities
Compartments Species
Cell Phosphohomoserine Threonine Cystathionine
Homoserine Inorganic phosphate Cysteine
S-adenosylmethionine Cystathionine gamma-synthase Threonine synthase
Reactions (3)
 
 Phosphohomoserine synthesis [Homoserine] ↔ [Phosphohomoserine];  
 
 Cystathionine gamma-synthase [Phosphohomoserine] + [Cysteine] ↔ [Cystathionine] + [Inorganic phosphate];   {Cystathionine gamma-synthase}
 
 Threonine Synthase [Phosphohomoserine] ↔ [Threonine] + [Inorganic phosphate];   {S-adenosylmethionine} , {Threonine synthase}
 
 Cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 Phosphohomoserine
Compartment: Cell
Initial concentration: 0.0
 
 Threonine
Compartment: Cell
Initial concentration: 0.0
 
 Cystathionine
Compartment: Cell
Initial concentration: 0.0
 
 Homoserine
Compartment: Cell
Initial concentration: 0.0
 
 Inorganic phosphate
Compartment: Cell
Initial concentration: 10000.0
 
 Cysteine
Compartment: Cell
Initial concentration: 15.0
 
 S-adenosylmethionine
Compartment: Cell
Initial concentration: 20.0
Constant
 
 Cystathionine gamma-synthase
Compartment: Cell
Initial concentration: 0.7
Constant
 
 Threonine synthase
Compartment: Cell
Initial concentration: 5.0
Constant
 
Phosphohomoserine synthesis (1)
 
   V0
Value: 1.0   (Units: microM_per_second)
Constant
 
Cystathionine gamma-synthase (4)
 
   kcat2
Value: 30.0   (Units: microM)
Constant
 
   KmCYS
Value: 460.0   (Units: microM)
Constant
 
   KmPHSER
Value: 2500.0   (Units: microM)
Constant
 
   Ki2
Value: 2000.0   (Units: microM)
Constant
 
Threonine Synthase (1)
 
   Ki3
Value: 1000.0   (Units: microM)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000068

Curator's comment: (updated: 15 May 2008 11:32:30 BST)

This is a reproduction of fig 3 B,C,D and E in the original publication
The results were obtained using copasi Vers. 4.4(build 26)

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