Difference between revisions of "3-phosphoglycerate mutase"

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|0.94 <ref name="Hernandez_2006"> Marín-Hernández A , Rodríguez-Enríquez S, Vital-González P A, ''et al.'' (2006). ''Determining and understanding the control of glycolysis in fast-growth tumor cells. Flux control by an over-expressed but strongly product-inhibited hexokinase''. FEBS J., 273 , pp. 1975–1988([http://dx.doi.org/doi:10.1111/j.1742-4658.2006.05214.x doi]) </ref>
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* As the value of the <math>K_{eq}</math> does not depend on the organism, the mean and std. dev. of the distribution can be calculated from the various values reported in the literature. <ref name="Achcar_2012">Achcar, F., Kerkhoven, E. J., Bakker, B. M., Barrett, M. P., Breitling, R. (2012), ''Dynamic modelling under uncertainty: the case of Trypanosoma brucei energy metabolism'', PLoS Comput. Biol. 8, e1002352.</ref>
 
* As the value of the <math>K_{eq}</math> does not depend on the organism, the mean and std. dev. of the distribution can be calculated from the various values reported in the literature. <ref name="Achcar_2012">Achcar, F., Kerkhoven, E. J., Bakker, B. M., Barrett, M. P., Breitling, R. (2012), ''Dynamic modelling under uncertainty: the case of Trypanosoma brucei energy metabolism'', PLoS Comput. Biol. 8, e1002352.</ref>
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*<math>V_{mr}</math> can be sampled based on Haldane equation <br> <math>K_{eq} = \frac{V_{forward}*K_{product}}{V_{reverse}*K_{substrate}}</math> or '''Alternatively''',  
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*<math>V_{mr}</math> can be sampled based on Haldane equation <br> <math>K_{eq} = \frac{V_{forward}*K_{product}}{V_{reverse}*K_{substrate}}</math> or '''Alternatively''', same percentage of error mentioned for <math>V_{mf}</math> considering the value for <math>V_{mf}</math> reported in the model file of Hernandez (2011)<ref name="Hernandez2011"></ref>. This gives the value of <math>V_{mr} = 0.36 \pm 0.25</math>
  
 
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Revision as of 16:18, 23 May 2014

Phosphoglycerate mutase (PGAM) is an enzyme that catalyzes the internal transfer of a phosphate group from C-3 to C-2 which results in the conversion of 3-phosphoglycerate (3PG) to 2-phosphoglycerate (2PG).

Chemical equation

3PG \rightleftharpoons 2PG

Rate equation

Mono-substrate reversible Michaelis-Menten equation is used. [1]

\frac{V_{mf}\frac{[3PG]}{Km_{3PG}}-V_{mr}\frac{[2PG]}{Km_{2PG}}}{1 + \frac{[3PG]}{Km_{3PG}} + \frac{[2PG]}{Km_{2PG}}}

Parameter values

Parameter Value Units Organism Remarks
V_{mf} 0.94 [1] \text{mM min}^{-1} HeLa cell line
V_{mr} 0.36 [1] \text{mM min}^{-1}
Km_{3PG} 0.19[1] mM
Km_{2PG} 0.12[1] mM

Parameters with uncertainty

  • Three reported values of Km_{3PG} are considered. 0.19 [1], 0.5[2] and 0.4[3].
  • Two values of Km_{3PG} are found for Human cells. They are reported as 0.28[2] and 0.12[1]. Averaging them gives mean value of 0.2 and 0.08
  • As the value of the K_{eq} does not depend on the organism, the mean and std. dev. of the distribution can be calculated from the various values reported in the literature. [4]
  • V_{mr} can be sampled based on Haldane equation
    K_{eq} = \frac{V_{forward}*K_{product}}{V_{reverse}*K_{substrate}} or Alternatively, same percentage of error mentioned for V_{mf} considering the value for V_{mf} reported in the model file of Hernandez (2011)[1]. This gives the value of V_{mr} = 0.36 \pm 0.25
Parameter Value Units Organism Remarks
V_{mf} 1.4 \pm 1 [5] \text{mM min}^{-1} HeLa cell line
V_{mr} Sampled based on Haldane equation
K_{eq} = \frac{V_{forward}*K_{product}}{V_{reverse}*K_{substrate}} 		\text{mM min}^{-1}
Km_{3PG} 0.36 \pm 0.12 mM Multiple tissue of Human cell
Km_{2PG} 0.2 \pm 0.08 mM Multiple tissue of Human cell


Equilibrium constant

Equilibrium constant Conditions Source
0.15 pH=7, T=25°C Voet et al.[6] from Newshole et al. (1973) [7]p 97:

\Delta G' = 4.7\ kJ.mol^{-1}, Keq = exp(-\frac{\Delta G'}{RT}) = exp(\frac{-4700}{8.31*298.15}) \approx 0.15

0.17 pH=7, T=25°C Lehninger, (1975)[8] p 412:

\Delta G' = 4.4\ kJ.mol^{-1}, Keq = exp(-\frac{\Delta G'}{RT}) = exp(\frac{-4400}{8.31*298.15}) \approx 0.17

0.167 pH=7, T=297.15 K From Meyerhof et al. 1949 (NIST database[9] [49MEY/OES_1388])
0.19 pH=7.2, T=25°C From Chiba et al. 1959 (NIST database[9] [59CHI/SUG_1391])
0.20 pH=6, T=25°C From Grisolia et al. 1975 (NIST database[9] [75GRI/CAR_1396])

Averaging all those values gives K_{eq} = 0.17 \pm 0.019

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 Marín-Hernández A, Gallardo-Pérez JC, Rodríguez-Enríquez S et al (2011) Modeling cancer glycolysis. Biochim Biophys Acta 1807:755–767 (doi)
  2. ↑ 2.0 2.1 Marin-Hernandez, A., Gallardo-Perez, J. C., Ralph, S. J., Rodriguez-Enriquez, S. & Moreno-Sanchez, R. (2009), HIF-1α modulates energy metabolism in cancer cells by inducing over-expression of specific glycolytic isoforms. Mini-Rev. Med. Chem. 9, 1084–1101
  3. ↑ de Atauri, P.; Repiso, A.; Oliva, B.; Vives-Corrons, J.L.; Climent, F.; Carreras, J. (2005), Characterization of the first described mutation of human red blood cell phosphoglycerate mutase, Biochim. Biophys. Acta 1740, 403-410
  4. ↑ Achcar, F., Kerkhoven, E. J., Bakker, B. M., Barrett, M. P., Breitling, R. (2012), Dynamic modelling under uncertainty: the case of Trypanosoma brucei energy metabolism, PLoS Comput. Biol. 8, e1002352.
  5. ↑ Marín-Hernández A , Rodríguez-Enríquez S, Vital-González P A, et al. (2006). Determining and understanding the control of glycolysis in fast-growth tumor cells. Flux control by an over-expressed but strongly product-inhibited hexokinase. FEBS J., 273 , pp. 1975–1988(doi)
  6. ↑ Voet, D., Voet., J.G. and Pratt, C. W. (1999) Fundamentals of biochemistry, Wiley
  7. ↑ Newshole, E.A. and Stuart, C. (1973) Regulation in Metabolism, Wiley
  8. ↑ Lehninger, A.L. (1975) Biochemistry (2nd edn), Worth
  9. ↑ 9.0 9.1 9.2 Goldberg R.N., Tewari Y.B. and Bhat T.N. (2004) Bioinformatics 20(16):2874-2877 [pmid: 15145806]
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