Difference between revisions of "Dephosphorylation"

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<h2>Km<sub>P</sub> value and equilibrium constant </h2>
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The K<sub>m</sub> value for the product is assumed to be similar to but slightly smaller than the the K<sub>m</sub> value of the substrate because of the similarity of the both species. Therefore the K<sub>m</sub> value of the substrate is multiplied by 0.95 to gain the one of the product and the uncertainty is increased by increasing the error on Km<sub>substrate</sub> b< 50%.
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For information about the equilibrium constant please see [[Equilibrium_constants|here]].

Revision as of 10:44, 31 March 2014

Binding Reaction

 \text{phosphorylated-enzyme} \rightleftharpoons \text{unphosphorylated-enzyme}

Kinetic equation

Failed to parse (Cannot store math image on filesystem.): v_{dephosphorylation} = \frac{v_{max} \cdot [\text{phosphorylated-enzyme}] \cdot (1-\frac{[\text{unphosphorylated-enzyme}]}{[\text{phosphorylated-enzyme}] \cdot K_{eq}})}{Km_{\text{phosphorylated-enzyme}} \cdot (1 + \frac{[\text{phosphorylated-enzyme}]}{Km_{\text{phosphorylated-enzyme}}} \cdot \frac{[\text{unphosphorylated-enzyme}]}{Km_{\text{unphosphorylated-enzyme}}})}

General Information

The most enzymes in the MAP-Kinase signaling pathway are activated by phosphorylation. The inactivation is therefore due to a dephosphorylation step. The amino acids that are phosphorylated are tyrosine, serine, threonine, so the three main dephosphatases address phosphate residues at these side chains. In BRENDA there are several values measured, for the Km and vmax value. In contrast to the reactions in which the enyzme that catalyses the reaction appears also as substrate in the model the concentration of the dephosphatases is assumed to be constant and therefore the vmax value instead or the kcat value is used. Because of the reason that it is not clear which dephoshpatase is mainly responsible for the inactivation an average of all measured dephosphatase values is used in our model.

final Parameter

v_{max} =  1.13  \cdot 10^{2} \pm 3.09 \cdot 10^{2}\ \frac{1}{s}

K_{m} = 3.83 \cdot 10^{3} \pm 1.40 \cdot 10^{2}\ \mu M

Parameter

Notes Data
There are three main deophosphatases, phosphoserine phosphatase (EC 3.1.3.3), phosphoprotein phosphatase (EC 3.1.3.16), protein-tyrosine phosphatase (3.1.3.48). The data available in BRENDA is used to calculate the average and standard deviation.
EC 3.1.3.3 -
phosphoserine phosphatase
EC 3.1.3.16 -
phosphoprotein phosphatase
EC 3.1.3.48 -
protein-tyrosine phosphatase
average
Km [mM]
average all 0.75 7.43 3.31 3.83 mM
std 1.29 27.74 12.90 1.40 mM
turnover number [1/s]
average all 1.62*102 1.09 * 102 67.8 1.13 * 102 1/s
std 359.51 210.26 256.88 3.09 * 102 1/s

Screenshots of the BRENDA database


3.1.3.3-phosphoserine phosphatase

3.1.3.16-phosphoprotein phosphatase

3.1.3.48 protein-tyrosine-phosphatase

Km

vmax

KmP value and equilibrium constant

The Km value for the product is assumed to be similar to but slightly smaller than the the Km value of the substrate because of the similarity of the both species. Therefore the Km value of the substrate is multiplied by 0.95 to gain the one of the product and the uncertainty is increased by increasing the error on Kmsubstrate b< 50%.

For information about the equilibrium constant please see here.