MODEL1004070001
type: SBMLModel
species: metaid C 6PG
reaction: 424135
species: metaid C TYR
reaction: 424122
is: http://identifiers.org/taxonomy/4932
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Holly
    family: Summersgill
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Natalie
    family: Stanford
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Kieran
    family: Smallbone
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Kieran
    family: Smallbone
rule: 424184
substance units: 178797
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Holly
    family: Summersgill
time units: 172336
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Edward
    family: Kent
units def: 178882
rule: 424186
species: metaid C PHE
name: Vaseghi1999_Pentose_PP_yeast
species: metaid C S7P
species: metaid C TRP
reaction: 424128
reaction: 424124
reaction: 424138
species: metaid C X5P
species: metaid C PRPP
species: metaid C R5P
species: metaid C NADP
created:
  W3 CDTF: Thu Apr 09 01:00:00 BST 2009
reaction: 424123
is described by: http://identifiers.org/pubmed/10935926
parameter: 424189
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Kieran
    family: Smallbone
units def: 178821
reaction: 424144
reaction: 424141
reaction: 424150
reaction: 424156
reaction: 424132
units def: 178797
species: metaid C Ru5P
units def: 178846
reaction: 424129
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Edward
    family: Kent
species: metaid C F6P
reaction: 424125
length unit: 335510
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Natalie
    family: Stanford
notes: Model as described in: In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae Vaseghi S, Baumeister A, Rizzi M, Reuss M. Metab Eng. 1999 Apr;1(2):128-40. PMID: 10935926 , doi: 10.1006/mben.1998.0110 ; Abstract: The in vivo dynamics of the pentose phosphate pathway has been studied with transient experiments in continuous culture of Saccharomyces cerevisiae. Rapid sampling was performed with a special sampling device after disturbing the steady state with a pulse of glucose. The time span of observation was 120 s after the pulse. During this short time period the dynamic effect of protein biosynthesis can be neglected. The metabolites of interest (glucose 6-phosphate, NADP, NADPH, 6-phosphogluconate, and MgATP2-) we determined with enzymatic assays and HPLC. The experimental observations were then used for the identification of kinetic rate equations and parameters under in vivo conditions. In accordance with results from in vitro studies the in vivo diagnosis supports an ordered Bi-Bi mechanism with noncompetitive inhibition by MgATP2- for the enzyme glucose-6-phosphate dehydrogenase. In the case of 6-phosphogluconate dehydrogenase an ordered Bi-Ter mechanism with a competitive inhibition by MgATP2- has been found. Because the MgATP2- concentration decreases abruptly after the pulse of glucose the inhibitory effect vanishes and the flux through the pentose phosphate pathway increases. This regulation phenomenon guarantees the balance of fluxes through glycolysis and pentose phosphate pathway during the dynamic time period. Typographical errors found and corrected from the original manuscript: rMax given for 6GPDH and 6PGDH are reversed (by solving their defining equations) Eq (52) should read C_NADPH(t) = 0.16 + ... (from Fig. 2) While the model is identical to the one described in the article, it cannot reproduce all time courses displayed in the article. The time courses for S7P and X5P differ from fig 5 and some of the reaction rates show s…
modified:
  W3 CDTF: Fri Feb 03 11:10:46 GMT 2012
modified:
  W3 CDTF: Fri Feb 03 11:10:46 GMT 2012
curated: false
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Holly
    family: Summersgill
species: metaid C E4P
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Natalie
    family: Stanford
modified:
  W3 CDTF: Fri Feb 03 11:10:46 GMT 2012
species: metaid C NADPH
creator:
  ORG:
    orgname: University of Manchester
  n:
    given: Edward
    family: Kent
reaction: 424153
species: metaid C MgATP
volume units: 950046
area units: area
rule: 424185
species: metaid C G6P
species: metaid C GAP
rule: 424187
compartment: metaid CV
reaction: 424147
modified:
  W3 CDTF: Fri Feb 03 11:10:46 GMT 2012

metaid C 6PG
type: Species
is: CHEBI:16863
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.25
initial amount: NaN
in compartment: metaid CV
name: 6-phosphogluconate

metaid CV
type: Compartment
is: GO:0005576
constant: true
size: 1.0
spatial dimensions: 3.0
name: intracellular

424135
type: Reaction
kinetic law: 179352
product: 179340
reactant: 179328
fast: false
reversible: false
name: RPPK

424176
type: LocalParameter
units: 178882
value: 0.003

178882
type: SBMLUnitsDef
unit: 178919
unit: 178907
unit: 178895
name: mM per second

178919
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exponent: -1.0
scale: 0
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kind: SECOND

178907
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kind: LITRE

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kind: MOLE

424175
type: LocalParameter
units: 178846
value: 0.009

178846
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unit: 178870
unit: 178858
name: mM

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kind: MOLE

179340
type: SpeciesReference
stoichiometry: 1.0
species: metaid C PRPP

metaid C PRPP
type: Species
is: CHEBI:17111
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid CV
name: phosphoribosylpyrophosphate

179328
type: SpeciesReference
stoichiometry: 1.0
species: metaid C R5P

metaid C R5P
type: Species
is: CHEBI:17797
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.118
initial amount: NaN
in compartment: metaid CV
name: ribose 5-phosphate

metaid C TYR
type: Species
is: CHEBI:18186
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid CV
name: tyrosine

424122
type: Reaction
product: 178967
fast: false
kinetic law: 178991
reactant: 178931
reversible: false
product: 178955
modifier: 178979
name: G6PDH
reactant: 178943

178967
type: SpeciesReference
stoichiometry: 1.0
species: metaid C NADPH

metaid C NADPH
type: Species
is: CHEBI:16474
constant: false
boundary condition: true
has only substance units: false
initial concentration: 0.16
initial amount: NaN
in compartment: metaid CV
name: NADPH

424160
type: LocalParameter
units: 178846
value: 1.702

424159
type: LocalParameter
units: 178846
value: 0.33

424158
type: LocalParameter
units: 178846
value: 0.116

424157
type: LocalParameter
units: 178882
value: 0.654

178931
type: SpeciesReference
stoichiometry: 1.0
species: metaid C G6P

metaid C G6P
type: Species
is: CHEBI:14314
constant: false
boundary condition: true
has only substance units: false
initial concentration: 0.9
initial amount: NaN
in compartment: metaid CV
name: glucose 6-phosphate

178955
type: SpeciesReference
stoichiometry: 1.0
species: metaid C 6PG

metaid C MgATP
type: Species
is: CHEBI:30617
constant: false
boundary condition: true
has only substance units: false
initial concentration: 2.3
initial amount: NaN
in compartment: metaid CV
name: MgATP

178943
type: SpeciesReference
stoichiometry: 1.0
species: metaid C NADP

metaid C NADP
type: Species
is: CHEBI:18009
constant: false
boundary condition: true
has only substance units: false
initial concentration: 0.17
initial amount: NaN
in compartment: metaid CV
name: NADP+

178797
type: SBMLUnitsDef
unit: 178809
name: millimole

178809
type: SBMLUnit
exponent: 1.0
scale: -3
multipler: 1.0
kind: MOLE

metaid C PHE
type: Species
is: CHEBI:28044
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid CV
name: phenylalanine

metaid C S7P
type: Species
is: CHEBI:15721
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.082
initial amount: NaN
in compartment: metaid CV
name: sedoheptulose 7-phosphate

metaid C TRP
type: Species
is: CHEBI:27897
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.0
initial amount: NaN
in compartment: metaid CV
name: tryptophan

424128
type: Reaction
kinetic law: 179196
product: 179184
reactant: 179172
fast: false
reversible: false
name: Ru5PE

424170
type: LocalParameter
units: 178882
value: 0.85

179184
type: SpeciesReference
stoichiometry: 1.0
species: metaid C X5P

metaid C X5P
type: Species
is: CHEBI:16332
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.041
initial amount: NaN
in compartment: metaid CV
name: xylulose 5-phosphate

179172
type: SpeciesReference
stoichiometry: 1.0
species: metaid C Ru5P

metaid C Ru5P
type: Species
is: CHEBI:17363
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.033
initial amount: NaN
in compartment: metaid CV
name: ribulose 5-phosphate

424124
type: Reaction
kinetic law: 179100
product: 179088
reactant: 179076
fast: false
reversible: false
name: R5PI

424167
type: LocalParameter
units: 178882
value: 0.57

179088
type: SpeciesReference
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species: metaid C R5P

179076
type: SpeciesReference
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species: metaid C Ru5P

424138
type: Reaction
kinetic law: 179412
product: 179400
product: 179388
reactant: 179376
reactant: 179364
fast: false
reversible: false
name: TAL

424178
type: LocalParameter
units: 178882
value: 3.0

179400
type: SpeciesReference
stoichiometry: 1.0
species: metaid C F6P

metaid C F6P
type: Species
is: CHEBI:15946
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.17
initial amount: NaN
in compartment: metaid CV
name: fructose 6-phosphate

179388
type: SpeciesReference
stoichiometry: 1.0
species: metaid C E4P

metaid C E4P
type: Species
is: CHEBI:48153
constant: false
boundary condition: false
has only substance units: false
initial concentration: 0.029
initial amount: NaN
in compartment: metaid CV
name: erythrose 4-phosphate

179376
type: SpeciesReference
stoichiometry: 1.0
species: metaid C S7P

179364
type: SpeciesReference
stoichiometry: 1.0
species: metaid C GAP

metaid C GAP
type: Species
is: CHEBI:17138
constant: true
boundary condition: true
has only substance units: false
initial concentration: 0.064
initial amount: NaN
in compartment: metaid CV
name: glyceraldehyde 3-phosphate

424123
type: Reaction
name: 6PGDH
reactant: 179015
fast: false
product: 179040
modifier: 179052
kinetic law: 179064
reversible: false
product: 179027
reactant: 179003

179015
type: SpeciesReference
stoichiometry: 1.0
species: metaid C NADP

179040
type: SpeciesReference
stoichiometry: 1.0
species: metaid C Ru5P

424166
type: LocalParameter
units: 178846
value: 0.055

424163
type: LocalParameter
units: 178846
value: 0.109

424162
type: LocalParameter
units: 178846
value: 1.848

424161
type: LocalParameter
units: 178882
value: 44.19

179027
type: SpeciesReference
stoichiometry: 1.0
species: metaid C NADPH

179003
type: SpeciesReference
stoichiometry: 1.0
species: metaid C 6PG

424189
type: Parameter
constant: true
units: 178821
value: 2.77778E-5
name: specific growth rate

178821
type: SBMLUnitsDef
unit: 178833
name: per second

178833
type: SBMLUnit
exponent: -1.0
scale: 0
multipler: 1.0
kind: SECOND

424144
type: Reaction
kinetic law: 179460
reactant: 179448
fast: false
reversible: false
name: uRu5P

179448
type: SpeciesReference
stoichiometry: 1.0
species: metaid C Ru5P

424141
type: Reaction
kinetic law: 179436
reactant: 179424
fast: false
reversible: false
name: u6PG

179424
type: SpeciesReference
stoichiometry: 1.0
species: metaid C 6PG

424150
type: Reaction
kinetic law: 179508
reactant: 179496
fast: false
reversible: false
name: uX5P

179496
type: SpeciesReference
stoichiometry: 1.0
species: metaid C X5P

424156
type: Reaction
kinetic law: 179556
reactant: 179544
fast: false
reversible: false
name: uE4P

179544
type: SpeciesReference
stoichiometry: 1.0
species: metaid C E4P

424132
type: Reaction
kinetic law: 179316
product: 179304
product: 179292
product: 179280
reactant: 179268
fast: false
reversible: false
name: PKDHA

424174
type: LocalParameter
units: 178882
value: 0.004

424173
type: LocalParameter
units: 178846
value: 0.009

179304
type: SpeciesReference
stoichiometry: 1.0
species: metaid C TYR

179292
type: SpeciesReference
stoichiometry: 1.0
species: metaid C TRP

179280
type: SpeciesReference
stoichiometry: 1.0
species: metaid C PHE

179268
type: SpeciesReference
stoichiometry: 1.0
species: metaid C E4P

424129
type: Reaction
kinetic law: 179256
product: 179244
product: 179232
reactant: 179220
reactant: 179208
fast: false
reversible: false
name: TKL2

424172
type: LocalParameter
units: 178882
value: 10.5

179244
type: SpeciesReference
stoichiometry: 1.0
species: metaid C GAP

179232
type: SpeciesReference
stoichiometry: 1.0
species: metaid C F6P

179220
type: SpeciesReference
stoichiometry: 1.0
species: metaid C X5P

179208
type: SpeciesReference
stoichiometry: 1.0
species: metaid C E4P

424125
type: Reaction
kinetic law: 179160
product: 179148
product: 179136
reactant: 179124
reactant: 179112
fast: false
reversible: false
name: TKL1

424169
type: LocalParameter
units: 178882
value: 3.24

179148
type: SpeciesReference
stoichiometry: 1.0
species: metaid C S7P

179136
type: SpeciesReference
stoichiometry: 1.0
species: metaid C GAP

179124
type: SpeciesReference
stoichiometry: 1.0
species: metaid C X5P

179112
type: SpeciesReference
stoichiometry: 1.0
species: metaid C R5P

424153
type: Reaction
kinetic law: 179532
reactant: 179520
fast: false
reversible: false
name: uS7P

179520
type: SpeciesReference
stoichiometry: 1.0
species: metaid C S7P

424147
type: Reaction
kinetic law: 179484
reactant: 179472
fast: false
reversible: false
name: uR5P

179472
type: SpeciesReference
stoichiometry: 1.0
species: metaid C R5P