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BIOMD0000000066 - Chassagnole2001_Threonine Synthesis

 

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Reference Publication
Publication ID: 11368770
Chassagnole C, Fell DA, Raïs B, Kudla B, Mazat JP.
Control of the threonine-synthesis pathway in Escherichia coli: a theoretical and experimental approach.
Biochem. J. 2001 Jun; 356(Pt 2): 433-444
INSERM EMI 9929, University Victor Segalen Bordeaux 2, 146 rue Léo Saignat, 33076 Bordeaux, France.  [more]
Model
Original Model: JWS logo
Submitter: Nicolas Le Novère
Submission ID: MODEL6624131052
Submission Date: 31 Aug 2006 16:15:50 UTC
Last Modification Date: 16 May 2012 10:20:51 UTC
Creation Date: 29 Aug 2006 10:11:33 UTC
Encoders:  Jacky L Snoep
   Harish Dharuri
set #1
bqbiol:isVersionOf KEGG Pathway Glycine, serine and threonine metabolism
set #2
bqbiol:hasTaxon Taxonomy Escherichia coli (strain K12)
set #3
bqbiol:hasPart Gene Ontology aspartate metabolic process
Gene Ontology threonine biosynthetic process
Notes

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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

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Biomodels Curation: The model reproduces Fig 2f of the paper. The Vmax values for different reactions are obtained by multiplying the specific activites given in Table 3 of the paper with the protein concentration and an assay correction factor that was provided by the authors. The protein concentration is 202 mg/litre. The specific activities that need to be taken into consideration are those given for "variable threonine" in Table 3. The following are the assay correction factors provided by the authors: vak1=1.49; vak3=1.12; vasd=1.14; vhsd=1.42; vts=1.15; vhk=1.13. The model was successfully tested on MathSBML and Jarnac

Model
Publication ID: 11368770 Submission Date: 31 Aug 2006 16:15:50 UTC Last Modification Date: 16 May 2012 10:20:51 UTC Creation Date: 29 Aug 2006 10:11:33 UTC
Mathematical expressions
Reactions
Aspartate Kinase Aspartate semialdehyde dehydrogenase Homoserine dehydrogenase Threonine synthase
Homoserine kinase Endogenous consumption of NADPH ATPase  
Physical entities
Compartments Species
compartment Aspartyl phosphate Aspartate beta-semialdehyde Homoserine
O-Phospho-homoserine Phos Threonine
Aspartate NADP NADPH
ADP ATP  
Reactions (7)
 
 Aspartate Kinase [ATP] + [Aspartate] ↔ [Aspartyl phosphate] + [ADP];   {Threonine}
 
 Aspartate semialdehyde dehydrogenase [NADPH] + [Aspartyl phosphate] ↔ [NADP] + [Phos] + [Aspartate beta-semialdehyde];  
 
 Homoserine dehydrogenase [NADPH] + [Aspartate beta-semialdehyde] ↔ [Homoserine] + [NADP];   {Aspartate} , {Threonine}
 
 Threonine synthase [O-Phospho-homoserine] ↔ [Threonine] + [Phos];  
 
 Homoserine kinase [Homoserine] + [ATP] ↔ [O-Phospho-homoserine] + [ADP];   {Threonine}
 
 Endogenous consumption of NADPH [NADPH] ↔ [NADP];  
 
 ATPase [ATP] ↔ [ADP] + [Phos];  
 
  Spatial dimensions: 3.0  Compartment size: 1.0
 
 Aspartyl phosphate
Compartment: compartment
Initial concentration: 0.0
 
 Aspartate beta-semialdehyde
Compartment: compartment
Initial concentration: 0.0
 
 Homoserine
Compartment: compartment
Initial concentration: 0.0
 
 O-Phospho-homoserine
Compartment: compartment
Initial concentration: 0.0
 
 Phos
Compartment: compartment
Initial concentration: 0.0
 
 Threonine
Compartment: compartment
Initial concentration: 2.0
 
 Aspartate
Compartment: compartment
Initial concentration: 2.0
 
 NADP
Compartment: compartment
Initial concentration: 0.0
 
 NADPH
Compartment: compartment
Initial concentration: 2.0
 
 ADP
Compartment: compartment
Initial concentration: 0.0
 
 ATP
Compartment: compartment
Initial concentration: 10.0
 
Aspartate Kinase (17)
 
   vm11
Value: 0.15   (Units: mM_per_min)
Constant
 
   keqak
Value: 6.4E-4   (Units: dimensionless)
Constant
 
   k11
Value: 0.97   (Units: mM)
Constant
 
   k1thr
Value: 0.167   (Units: mM)
Constant
 
   nak1
Value: 4.09   (Units: dimensionless)
Constant
 
   alpha
Value: 2.47   (Units: dimensionless)
Constant
 
   k1aspp
Value: 0.017   (Units: mM)
Constant
 
   k1atp
Value: 0.98   (Units: mM)
Constant
 
   k1adp
Value: 0.25   (Units: mM)
Constant
 
   vm13
Value: 0.0722   (Units: mM_per_min)
Constant
 
   lys
Value: 0.46   (Units: mM)
Constant
 
   k1lys
Value: 0.391   (Units: mM)
Constant
 
   nak3
Value: 2.8   (Units: dimensionless)
Constant
 
   k13
Value: 0.32   (Units: mM)
Constant
 
   k13aspp
Value: 0.017   (Units: mM)
Constant
 
   k13atp
Value: 0.22   (Units: mM)
Constant
 
   k13adp
Value: 0.25   (Units: mM)
Constant
 
Aspartate semialdehyde dehydrogenase (7)
 
   vm2f
Value: 0.1812   (Units: mM_per_min)
Constant
 
   k2eq
Value: 56.4150334574039   (Units: dimensionless)
Constant
 
   k2aspp
Value: 0.022   (Units: mM)
Constant
 
   k2asa
Value: 0.11   (Units: mM)
Constant
 
   k2p
Value: 10.0   (Units: mM)
Constant
 
   k2nadph
Value: 0.029   (Units: mM)
Constant
 
   k2nadp
Value: 0.144   (Units: mM)
Constant
 
Homoserine dehydrogenase (9)
 
   vm3f
Value: 1.001   (Units: mM_per_min)
Constant
 
   k3eq
Value: 3162.27766016838   (Units: dimensionless)
Constant
 
   k3thr
Value: 0.097   (Units: mM)
Constant
 
   nhdh1
Value: 1.41   (Units: dimensionless)
Constant
 
   alpha3
Value: 3.93   (Units: dimensionless)
Constant
 
   k3asa
Value: 0.24   (Units: mM)
Constant
 
   k3hs
Value: 3.39   (Units: mM)
Constant
 
   k3nadph
Value: 0.037   (Units: mM)
Constant
 
   k3nadp
Value: 0.067   (Units: mM)
Constant
 
Threonine synthase (2)
 
   vm5
Value: 0.0434   (Units: mM_per_min)
Constant
 
   k5hsp
Value: 0.31   (Units: mM)
Constant
 
Homoserine kinase (8)
 
   vm4f
Value: 0.1   (Units: mM_per_min)
Constant
 
   lys
Value: 0.46   (Units: mM)
Constant
 
   k4lys
Value: 9.45   (Units: mM)
Constant
 
   k4atp
Value: 0.072   (Units: mM)
Constant
 
   k4ihs
Value: 4.7   (Units: mM)
Constant
 
   k4hs
Value: 0.11   (Units: mM)
Constant
 
   k4thr
Value: 1.09   (Units: mM)
Constant
 
   k4iatp
Value: 4.35   (Units: mM)
Constant
 
Endogenous consumption of NADPH (2)
 
   knadph
Value: 5.4E-6   (Units: litre_per_mg_per_min)
Constant
 
   Protein
Value: 202.0   (Units: mg_per_litre)
Constant
 
ATPase (2)
 
   katpase
Value: 4.1E-5   (Units: millimole_per_mg_per_min)
Constant
 
   Protein
Value: 202.0   (Units: mg_per_litre)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000066

Curator's comment: (updated: 19 Dec 2006 00:06:37 GMT)

The plots above correspond to Fig 2f of the paper. Simulation results obtained with MathSBML.

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