Difference between revisions of "Part:BBa K4165094"
 
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===Usage and Biology===
 
===Usage and Biology===
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ATP, opioids, and phosphatidylethanolamine are all bound. Phosphatidylinositol and phosphatidylcholine have a lesser affinity for it. Inhibits thrombin, neuropsin, and chymotrypsin but not trypsin, tissue type plasminogen activator, and elastase (By similarity). RAF1 kinase activity is inhibited by preventing its activation, dissociating the RAF1/MEK complex, and serving as a competitive inhibitor of MEK phosphorylation. HCNP may be implicated in the function of central nervous system presynaptic cholinergic neurons. HCNP enhances choline acetyltransferase synthesis but not acetylcholinesterase.This type of inhibitor is very effective and has high affinity for trypsin-like proteases (serine proteases), and in our case it would act as an inhibitor for the trypsin-like catalytic domain of serine protease HtrA1[1]-[3].
+
ATP, opioids, and phosphatidylethanolamine are all bound. Phosphatidylinositol and phosphatidylcholine have a lesser affinity for it. Inhibits thrombin, neuropsin, and chymotrypsin but not trypsin, tissue type plasminogen activator, and elastase (By similarity). RAF1 kinase activity is inhibited by preventing its activation, dissociating the RAF1/MEK complex, and serving as a competitive inhibitor of MEK phosphorylation. HCNP may be implicated in the function of central nervous system presynaptic cholinergic neurons. HCNP enhances choline acetyltransferase synthesis but not acetylcholinesterase.This type of inhibitor is very effective and has high affinity for trypsin-like proteases (serine proteases), and in our case it would act as an inhibitor for the trypsin-like catalytic domain of serine protease HtrA1<sup>[1-3]</sup>.
  
  
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===Functional Parameters===
 
===Functional Parameters===
  
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GC Content%
 
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66.8%
 
  
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Isoelectric point (PI)
 
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7.225
 
  
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Charge at pH 7
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<html>
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0.376
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<style>
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table, th, td {
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  border:1px solid black; margin-left:auto;margin-right:auto;
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}
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</style>
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<body>
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<table style="width:65%">
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<table>
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  <tr>
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    <th>GC Content%</th>
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    <th>Isoelectric point (PI)</th>
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    <th>Charge at pH 7</th>
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    <th>Molecular Weight (Protein)</th>
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  </tr>
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  <tr>
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    <td>66.8</td>
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    <td>7.225</td>
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    <td>0.376</td>
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    <td>21.057 kDa</td>
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  </tr>
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</table>
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</body>
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</html>
  
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Molecular Weight (Protein)
 
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21.057 kDa
 
  
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===PDB Sturcture===
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===Modeling===
 
The available structures are the predicted one (AlphaFold) and the x-ray structures.
 
The available structures are the predicted one (AlphaFold) and the x-ray structures.
  
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X-ray
 
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https://www.rcsb.org/structure/1BD9
 
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Q_Mean =
 
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Ramachandran Favoured =
 
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Ramachandran Outliers =
 
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Clash Score =
 
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C-beta Deviation =
 
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Total Score =
 
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AlphaFold
 
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https://alphafold.ebi.ac.uk/entry/P30086
 
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Q_Mean =
 
−
Ramachandran Favoured =
 
−
Ramachandran Outliers =
 
−
Clash Score =
 
−
C-beta Deviation =
 
−
Total Score =
 
  
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<html>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/model.jpg" style="margin-left:200px;" alt="" width="500" /></p>
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</html>
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                  Figure 1.: A graphical illustration showing the structure of the inhibitor (X-Ray diffraction).
  
  
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<html>
 
<html>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/15-alphafold.png" style="margin-left:200px;" alt="" width="500" /></p>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/switches/15-alphafold.png" style="margin-left:200px;" alt="" width="500" /></p>
 
</html>
 
</html>
  
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                   Figure 1.: A graphical illustration showing the structure of the inhibitor (AlphaFold).
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                   Figure 2.: A graphical illustration showing the structure of the inhibitor (AlphaFold).
  
 
===References===
 
===References===
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1. Clauss, A., Lilja, H., & Lundwall, Å. (2005). The evolution of a genetic locus encoding small serine proteinase inhibitors. Biochemical and biophysical research communications, 333(2), 383-389.
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1. Clauss, A., Lilja, H., & Lundwall, Å. (2005). The evolution of a genetic locus encoding small serine proteinase inhibitors. Biochemical and biophysical research communications, 333(2), 383-389. <br>
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2. Eigenbrot, C., Ultsch, M., Lipari, M. T., Moran, P., Lin, S. J., Ganesan, R., ... & Kirchhofer, D. (2012). Structural and functional analysis of HtrA1 and its subdomains. Structure, 20(6), 1040-1050.
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2. Eigenbrot, C., Ultsch, M., Lipari, M. T., Moran, P., Lin, S. J., Ganesan, R., ... & Kirchhofer, D. (2012). Structural and functional analysis of HtrA1 and its subdomains. Structure, 20(6), 1040-1050.<br>
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3. Grau, S., Baldi, A., Bussani, R., Tian, X., Stefanescu, R., Przybylski, M., ... & Ehrmann, M. (2005). Implications of the serine protease HtrA1 in amyloid precursor protein processing. Proceedings of the National Academy of Sciences, 102(17), 6021-6026.
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3. Grau, S., Baldi, A., Bussani, R., Tian, X., Stefanescu, R., Przybylski, M., ... & Ehrmann, M. (2005). Implications of the serine protease HtrA1 in amyloid precursor protein processing. Proceedings of the National Academy of Sciences, 102(17), 6021-6026.<br>
  
  

Latest revision as of 11:13, 13 October 2022


Phosphatidylethanolamine-binding protein 1(PEBP1).

This basic part encodes Human serine protease inhibitor phosphotidylethanolamine-binding protein 1 which is able to inhibit HtrA1 (BBa_K4165004).


Usage and Biology

ATP, opioids, and phosphatidylethanolamine are all bound. Phosphatidylinositol and phosphatidylcholine have a lesser affinity for it. Inhibits thrombin, neuropsin, and chymotrypsin but not trypsin, tissue type plasminogen activator, and elastase (By similarity). RAF1 kinase activity is inhibited by preventing its activation, dissociating the RAF1/MEK complex, and serving as a competitive inhibitor of MEK phosphorylation. HCNP may be implicated in the function of central nervous system presynaptic cholinergic neurons. HCNP enhances choline acetyltransferase synthesis but not acetylcholinesterase.This type of inhibitor is very effective and has high affinity for trypsin-like proteases (serine proteases), and in our case it would act as an inhibitor for the trypsin-like catalytic domain of serine protease HtrA1[1-3].


Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 40
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 40
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 40
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 40
  • 1000
    COMPATIBLE WITH RFC[1000]


Functional Parameters

GC Content% Isoelectric point (PI) Charge at pH 7 Molecular Weight (Protein)
66.8 7.225 0.376 21.057 kDa


Modeling

The available structures are the predicted one (AlphaFold) and the x-ray structures. 


                 Figure 1.: A graphical illustration showing the structure of the inhibitor (X-Ray diffraction).




                 Figure 2.: A graphical illustration showing the structure of the inhibitor (AlphaFold).

References

1. Clauss, A., Lilja, H., & Lundwall, Å. (2005). The evolution of a genetic locus encoding small serine proteinase inhibitors. Biochemical and biophysical research communications, 333(2), 383-389.
2. Eigenbrot, C., Ultsch, M., Lipari, M. T., Moran, P., Lin, S. J., Ganesan, R., ... & Kirchhofer, D. (2012). Structural and functional analysis of HtrA1 and its subdomains. Structure, 20(6), 1040-1050.
3. Grau, S., Baldi, A., Bussani, R., Tian, X., Stefanescu, R., Przybylski, M., ... & Ehrmann, M. (2005). Implications of the serine protease HtrA1 in amyloid precursor protein processing. Proceedings of the National Academy of Sciences, 102(17), 6021-6026.