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BIOMD0000000458 - Smallbone2013 - Serine biosynthesis

 

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Reference Publication
Publication ID: 23417802
Smallbone K, Stanford NJ.
Kinetic modeling of metabolic pathways: application to serine biosynthesis.
Methods Mol. Biol. 2013; 985: 113-121
Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, UK. kieran.smallbone@manchester.ac.uk  [more]
Model
Original Model: BIOMD0000000458.xml.origin
Submitter: Kieran Smallbone
Submission ID: MODEL1203210000
Submission Date: 21 Mar 2012 11:03:14 UTC
Last Modification Date: 10 Jun 2013 13:56:22 UTC
Creation Date: 20 Mar 2012 00:00:00 UTC
Encoders:  Vijayalakshmi Chelliah
   Kieran Smallbone
set #1
bqbiol:occursIn Taxonomy Escherichia coli
set #2
bqbiol:isVersionOf Gene Ontology L-serine biosynthetic process
Notes
Smallbone2013 - Serine biosynthesis

Kinetic modelling of metabolic pathways in application to Serine biosynthesis.

This model is described in the article:

Kieran Smallbone, Natalie J. Stanford
Methods in Molecular Biology. 2013; 985:113-121

Abstract:

In this chapter, we describe the steps needed to create a kinetic model of a metabolic pathway using kinetic data from both experimental measurements and literature review. Our methodology is presented by using the example of serine biosynthesis in E. coli.

As there are no plots to be reproduced as curation figure, table 6 and 7 that corresponds to steady state concentration of metabolite and steady state fluxes of reactions has been reproduced.

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Model
Publication ID: 23417802 Submission Date: 21 Mar 2012 11:03:14 UTC Last Modification Date: 10 Jun 2013 13:56:22 UTC Creation Date: 20 Mar 2012 00:00:00 UTC
Mathematical expressions
Reactions
phosphoglycerate dehydrogenase phosphoserine aminotransferase phosphoserine phosphatase  
Physical entities
Compartments Species
cell 3-phosphoglycerate phosphohydroxypyruvate phosphoserine
serine serA serC
serB    
Reactions (3)
 
 phosphoglycerate dehydrogenase [3-phosphoglycerate] ↔ [phosphohydroxypyruvate];   {serA} , {serine} , {serA} , {3-phosphoglycerate} , {phosphohydroxypyruvate} , {serine}
 
 phosphoserine aminotransferase [phosphohydroxypyruvate] ↔ [phosphoserine];   {serC} , {serC} , {phosphohydroxypyruvate} , {phosphoserine}
 
 phosphoserine phosphatase [phosphoserine] ↔ [serine];   {serB} , {serB} , {phosphoserine} , {serine}
 
 cell Spatial dimensions: 3.0  Compartment size: 1.0
 
 3-phosphoglycerate
Compartment: cell
Initial concentration: 2.36
Constant
 
 phosphohydroxypyruvate
Compartment: cell
Initial concentration: 0.6
 
 phosphoserine
Compartment: cell
Initial concentration: 0.09
 
 serine
Compartment: cell
Initial concentration: 4.9
Constant
 
 serA
Compartment: cell
Initial concentration: 1.15
Constant
 
 serC
Compartment: cell
Initial concentration: 0.1
Constant
 
 serB
Compartment: cell
Initial concentration: 0.25
Constant
 
phosphoglycerate dehydrogenase (4)
 
   kcatA
Value: 0.55   (Units: per s)
Constant
 
   KAp3g
Value: 1.2   (Units: mM)
Constant
 
   KAphp
Value: 0.0032   (Units: mM)
Constant
 
   KiAser
Value: 0.0038   (Units: mM)
Constant
 
phosphoserine aminotransferase (3)
 
   kcatC
Value: 1.75   (Units: per s)
Constant
 
   KCphp
Value: 0.0015   (Units: mM)
Constant
 
   KCpser
Value: 0.0017   (Units: mM)
Constant
 
phosphoserine phosphatase (3)
 
   kcatB
Value: 1.43   (Units: per s)
Constant
 
   KBpser
Value: 0.0015   (Units: mM)
Constant
 
   KBser
Value: 0.15   (Units: mM)
Constant
 
Representative curation result(s)
Representative curation result(s) of BIOMD0000000458

Curator's comment: (updated: 27 Feb 2013 14:14:44 GMT)

Table 6 and 7 that corresponds to the steady state concentrations of metabolites and steady state fluxes of reactions are reproduced as curation figure.
The model was simulated using Copasi v4.8 (Build 35).

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