Difference between revisions of "Dephosphorylation"

From ISMOC
Jump to: navigation, search
m
Line 5: Line 5:
  
 
<h2> Kinetic equation </h2>
 
<h2> Kinetic equation </h2>
−
<center><math>\frac{v_{max} \cdot [\text{phosphorylated-enzyme}] \cdot (1-\frac{[\text{unphosphorylated-enzyme}]}{[\text{phosphorylated-enzyme}] \cdot K_{eq}})}{1 + \frac{[\text{phosphorylated-enzyme}]}{Km_{\text{phosphorylated-enzyme}}} \cdot \frac{[\text{unphosphorylated-enzyme}]}{Km_{\text{unphosphorylated-enzyme}}}}</math></center>
+
<center><math>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}}})}</math></center>
 +
 
 +
<h2>General Information</h2>
 +
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<sub>max</sub> value instead or the k<sub>cat</sub> 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.
  
 
<h2>final Parameter </h2>
 
<h2>final Parameter </h2>
Line 11: Line 14:
 
<math>v_{max} =  1.13  \cdot 10^{2} \pm 3.09 \cdot 10^{2}\ \frac{1}{s}</math>
 
<math>v_{max} =  1.13  \cdot 10^{2} \pm 3.09 \cdot 10^{2}\ \frac{1}{s}</math>
  
−
<math>K_{m} = 3.83 \cdot 10^{-3} \pm 1.40 \cdot 10^{-2}\ \mu M </math>
+
<math>K_{m} = 3.83 \cdot 10^{3} \pm 1.40 \cdot 10^{2}\ \mu M </math>
  
 
<h2> Parameter</h2>
 
<h2> Parameter</h2>
Line 31: Line 34:
 
   <th>EC 3.1.3.16 - <br/>phosphoprotein phosphatase</th>
 
   <th>EC 3.1.3.16 - <br/>phosphoprotein phosphatase</th>
 
   <th>EC 3.1.3.48 - <br/>protein-tyrosine phosphatase</th>   
 
   <th>EC 3.1.3.48 - <br/>protein-tyrosine phosphatase</th>   
 +
  <th>average</th>
 
  </tr>
 
  </tr>
 
  <tr>
 
  <tr>
Line 43: Line 47:
 
   <td align="right">7.43</td>
 
   <td align="right">7.43</td>
 
   <td align="right">3.31</td>
 
   <td align="right">3.31</td>
 +
  <td align="right">3.83 mM</td>
 
  </tr>
 
  </tr>
 
  <tr>
 
  <tr>
Line 49: Line 54:
 
   <td align="right">27.74</td>
 
   <td align="right">27.74</td>
 
   <td align="right">12.90</td>
 
   <td align="right">12.90</td>
−
</tr>
+
   <td align="right">1.40 mM</td>
−
<!-- <tr>
 
−
  <td>average human</td>
 
−
  <td align="right">6.80 * 10<sup>-2</sup></td>
 
−
  <td align="right">0.45</td>
 
−
   <td align="right">3.31</td>
 
 
  </tr>
 
  </tr>
−
<tr>
 
−
  <td>std</td>
 
−
  <td align="right">0.05</td>
 
−
  <td align="right">0.92</td>
 
−
  <td align="right">14.97</td>
 
−
</tr> -->
 
 
  <tr>
 
  <tr>
 
   <td>'''turnover number [1/s]'''</td>
 
   <td>'''turnover number [1/s]'''</td>
Line 73: Line 67:
 
   <td align="right">1.09 * 10<sup>2</sup></td>
 
   <td align="right">1.09 * 10<sup>2</sup></td>
 
   <td align="right">67.8</td>
 
   <td align="right">67.8</td>
 +
  <td align="right">1.13 * 10<sup>2</sup> 1/s</td>
 
  </tr>
 
  </tr>
 
  <tr>
 
  <tr>
Line 79: Line 74:
 
   <td align="right">210.26</td>
 
   <td align="right">210.26</td>
 
   <td align="right">256.88</td>
 
   <td align="right">256.88</td>
 +
  <td align="right">3.09 * 10<sup>2</sup> 1/s</td>
 
  </tr>
 
  </tr>
−
<!-- <tr>
 
−
  <td>average human</td>
 
−
  <td></td> 
 
−
  <td align="right">47.1</td>
 
−
  <td align="right">24.5</td>
 
−
</tr>
 
−
<tr>
 
−
  <td>std</td>
 
−
  <td></td>
 
−
  <td align="right">82.15</td>
 
−
  <td align="right">40.89</td>
 
−
</tr> -->
 
 
</table>
 
</table>
 
</td>
 
</td>
 
</tr>
 
</tr>
 
</table>
 
</table>
 +
 +
<h2>Screenshots of the BRENDA database </h2>
 +
 +
 +
'''<u>[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.3 3.1.3.3-phosphoserine phosphatase]</u>'''
 +
 +
<gallery mode="nolines">
 +
File:L 3.1.3.3-phosphoserine phosphatase.png|3.1.3.3-phosphoserine phosphatase
 +
</gallery>
 +
 +
'''<u>[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.16 3.1.3.16-phosphoprotein phosphatase] </u>'''
 +
 +
<gallery mode="nolines">
 +
File:L 3.1.3.16-phosphoprotein phosphatase Km.png|3.1.3.16-phosphoprotein phosphatase Km
 +
File:L 3.1.3.16-phosphoprotein phosphatase vmax.png|3.1.3.16-phosphoprotein phosphatase vmax
 +
</gallery>
 +
 +
'''<u>[http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.1.3.48 3.1.3.48 protein-tyrosine-phosphatase] </u>'''
 +
 +
'''K<sub>m</sub>'''
 +
<gallery mode="nolines">
 +
File:L 3.1.3.48 protein-tyrosine-phosphatase 1.png|3.1.3.48 protein-tyrosine-phosphatase Km1
 +
File:L 3.1.3.48 protein-tyrosine-phosphatase 2.png|3.1.3.48 protein-tyrosine-phosphatase Km2
 +
File:L 3.1.3.48 protein-tyrosine-phosphatase 3.png|3.1.3.48 protein-tyrosine-phosphatase Km3
 +
File:3.1.3.48 protein-tyrosine-phosphatase 4.png|3.1.3.48 protein-tyrosine-phosphatase Km4
 +
File:L 3.1.3.48 protein-tyrosine-phosphatase 5.png|3.1.3.48 protein-tyrosine-phosphatase Km5
 +
</gallery>
 +
 +
'''v<sub>max</sub>'''
 +
<gallery mode="nolines">
 +
File:L 3.1.3.48 protein-tyrosine-phosphatase vmax 1.png|3.1.3.48 protein-tyrosine-phosphatase vmax1
 +
File:L 3.1.3.48 protein-tyrosine-phosphatase vmax 2.png|3.1.3.48 protein-tyrosine-phosphatase vmax2
 +
File:L 3.1.3.48 protein-tyrosine-phosphatase vmax 3.png|3.1.3.48 protein-tyrosine-phosphatase vmax3
 +
File:L 3.1.3.48 protein-tyrosine-phosphatase vmax 4.png|3.1.3.48 protein-tyrosine-phosphatase vmax4
 +
File:L 3.1.3.48 protein-tyrosine-phosphatase vmax 5.png|3.1.3.48 protein-tyrosine-phosphatase vmax5
 +
</gallery>

Revision as of 09:57, 31 March 2014

L MAPK SignallingNetwork.png

-> back to the overview

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

  • 3.1.3.3-phosphoserine phosphatase

3.1.3.16-phosphoprotein phosphatase

  • 3.1.3.16-phosphoprotein phosphatase Km

  • 3.1.3.16-phosphoprotein phosphatase vmax

3.1.3.48 protein-tyrosine-phosphatase

Km

  • 3.1.3.48 protein-tyrosine-phosphatase Km1

  • 3.1.3.48 protein-tyrosine-phosphatase Km2

  • 3.1.3.48 protein-tyrosine-phosphatase Km3

  • 3.1.3.48 protein-tyrosine-phosphatase Km4

  • 3.1.3.48 protein-tyrosine-phosphatase Km5

vmax

  • 3.1.3.48 protein-tyrosine-phosphatase vmax1

  • 3.1.3.48 protein-tyrosine-phosphatase vmax2

  • 3.1.3.48 protein-tyrosine-phosphatase vmax3

  • 3.1.3.48 protein-tyrosine-phosphatase vmax4

  • 3.1.3.48 protein-tyrosine-phosphatase vmax5

Retrieved from ‘http://www.systemsbiology.ls.manchester.ac.uk/wiki/index.php?title=Dephosphorylation&oldid=1055’