Dephosphorylation

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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 v_max value instead or the k_cat 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.

Km_P value and equilibrium constant

The K_m value for the product is assumed to be similar to but slightly smaller than the the K_m value of the substrate because of the similarity of the both species. Therefore the K_m 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_substrate by 50%.

For information about the equilibrium constant please see here.