Difference between revisions of "3-phosphoglycerate kinase"

Revision as of 13:19, 22 September 2014

3-Phosphoglycerate kinase (PGK) is an enzyme that catalyzes the reversible transfer of a phosphate group from 1,3-bisphosphoglycerate (1,3-BPG) to ADP producing 3-phosphoglycerate (3-PG) and ATP. Like all kinases it is a transferase.

1,3BPG + ADP \rightleftharpoons 3PG + ATP

Random Bi-Bi reversible Michaelis-Menten euation for non-interacting substrates are used. ^[1]

\frac{V_{mf}\frac{[1,3BPG][ADP]}{K_{1,3BPG} K_{ADP}} - V_{mr}\frac{[3PG][ATP]}{K_{3PG} K_{ATP}}}{1 + \frac{[1,3BPG]}{K_{1,3BPG}} + \frac{[ADP]}{K_{ADP}} + \frac{[1,3BPG][ADP]}{K_{1,3BPG} K_{ADP}} + \frac{[3PG][ATP]}{K_{3PG} K_{ATP}} + \frac{[3PG]}{K_{3PG}} + \frac{[ADP]}{K_{ADP}} }

Modified rate law to consider thermodynamic constraint

\frac{V_{mf}\frac{[1,3BPG][ADP]}{K_{1,3BPG} K_{ADP}} \left( 1 - \frac{[3PG][ATP]}{K_{eq} [1,3BPG][ADP]} \right)}{1 + \frac{[1,3BPG]}{K_{1,3BPG}} + \frac{[ADP]}{K_{ADP}} + \frac{[1,3BPG][ADP]}{K_{1,3BPG} K_{ADP}} + \frac{[3PG][ATP]}{K_{3PG} K_{ATP}} + \frac{[3PG]}{K_{3PG}} + \frac{[ADP]}{K_{ADP}} }

Parameter	Value	Units	Organism
$V_{mf}$	8.7 ^[2]	$mM \times min^{-1}$	HeLa cell line
$V_{mr}$	2.5^[1]	$mM \times min^{-1}$
$Km_{1,3BPG}$	0.079^[1]	mM
$Km_{3PG}$	0.13^[1]	mM
$Km_{ADP}$	0.04^[1]	mM
$Km_{ATP}$	0.27^[1]	mM

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. ^[3]
Alternative: Same percent of error reported for $V_{mf}$ can be considered for $V_{mr}$ while the mean value as reported in ^[2] can be considered. In that case the value would be $2.5 \pm 1.15$

Parameter	Value	Units	Organism
$V_{mf}$	$13 ± 6$ ^[2] Failed to parse (Cannot store math image on filesystem.): 8.7 ± 4.1 ^[2]	$U\cdot(\text{mg protein})^{-1}$ $mM \times min^{-1}$	Human
$V_{mr}$	Sampled based on Haldane relation or Alternative value	$mM \times min^{-1}$
$Km_{1,3BPG}$	$0.0005 \pm 0.0002$ ^[4]	mM
$Km_{3PG}$ ^[4]	$0.05 \pm 0.02$	mM
$Km_{ADP}$	$0.12 \pm 0.02$ ^[4]	mM
$Km_{ATP}$	$0.11 \pm 0.02$ ^[4]	mM

Equilibrium constant	Conditions	Source
1974.16	pH=7, T=25°C	Lehninger, (2008)^[5] p 553: $\Delta G' = -18.8\ kJ.mol^{-1}$ , $Keq = exp(-\frac{\Delta G'}{RT}) = exp(\frac{18800}{8.31*298.15}) \approx 1974.16$
3333	pH=6.9, T=298.15 K	From Krietsch et al. (1970) ^[6]
3571	pH=6.9, T=298.15 K	From Krietsch et al. (1970) ^[6]

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 Marín-Hernández A, Gallardo-Pérez JC, Rodríguez-Enríquez S et al (2011) Modeling cancer glycolysis. Biochim Biophys Acta 1807:755–767 (doi)
↑ ^2.0 ^2.1 ^2.2 ^2.3 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)
↑ 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.
↑ ^4.0 ^4.1 ^4.2 ^4.3 Szabo, J.; Varga, A.; Flachner, B.; Konarev, P.V.; Svergun, D.I.; Zavodszky, P.; Vas, M. (2008), Role of side-chains in the operation of the main molecular hinge of 3-phosphoglycerate kinase, FEBS Lett. 582, 1335-1340
↑ David L. Nelson, Michael M. Cox (2008), Lehninger Principles of Biochemistry (5th edn), W. H. Freeman and Company
↑ ^6.0 ^6.1 Krietsch WZ and Bücher T. (1970) Eur J Biochem. 17(3):568-80. [pmid: 5493986]

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 |<math>V_{mf}</math>
-|<math>13 ± 6</math><ref name="Hernandez_2006"></ref>
+|<math>13 ± 6</math><ref name="Hernandez_2006"></ref> <br> <math>8.7 ± 4.1</math><ref name="Hernandez_2006"></ref>
-|<math>mM \times min^{-1}</math>
+|<math>U\cdot(\text{mg protein})^{-1}</math> <br> <math>mM \times min^{-1}</math>
 |rowspan="6"|Human
 |rowspan="6"|