Difference between revisions of "Part:BBa K4165088"
 
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===Usage and Biology===
 
===Usage and Biology===
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This type of family encodes for a type of inhibitor that contains a motif which consists of 8 cysteine residues capable of forming four disulfide bonds at the core of the protease, thus inhibiting its action. The main function of this inhibitor is to prevent elastase-mediated tissue proteolysis. 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].
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This type of family encodes for a type of inhibitor that contains a motif which consists of 8 cysteine residues capable of forming four disulfide bonds at the core of the protease, thus inhibiting its action. The main function of this inhibitor is to prevent elastase-mediated tissue proteolysis. 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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<span class='h3bb'>Sequence and Features</span>
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===<span class='h3bb'>Sequence and Features</span>===
 
<partinfo>BBa_K4165088 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165088 SequenceAndFeatures</partinfo>
  
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===Functional Parameters===
 
===Functional Parameters===
  
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GC Content%
 
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67.5%
 
  
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Isoelectric point (PI)
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<html>
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8.641
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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>67.5%</td>
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    <td>8.641</td>
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    <td>6.373</td>
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    <td>12.27</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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Charge at pH 7
 
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6.373
 
  
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Molecular Weight (Protein)
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===Modeling===
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12.27 kDa
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===PDB structure===
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X-ray, NMR, and the predicted structures (AlphaFold2) are all present.
 
X-ray, NMR, and the predicted structures (AlphaFold2) are all present.
  
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X-ray
 
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https://www.rcsb.org/structure/1FLE
 
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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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Rotamers outliers =
 
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Total Score =
 
  
  
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<html>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/model3.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 domains of TRIM21 (X-Ray diffraction).
  
  
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NMR:
 
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https://www.rcsb.org/structure/2REL
 
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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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Rotamers outliers =
 
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Total Score =
 
  
  
  
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AlphaFold
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<html>
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https://alphafold.ebi.ac.uk/entry/P19957
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<p><img src="https://static.igem.wiki/teams/4165/wiki/model4.jpg" style="margin-left:200px;" alt="" width="500" /></p>
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Q_Mean =  
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</html>
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Ramachandran Favoured =  
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Ramachandran Outliers =  
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                  Figure 2.: A graphical illustration showing the domains of TRIM21 (NMR).
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Clash Score =
+
 
−
C-beta Deviation =
+
−
Rotamers outliers =
+
−
Total Score =
+
  
  
  
 
<html>
 
<html>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/9-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/9-alphafold.png" style="margin-left:200px;" alt="" width="500" /></p>
 
</html>
 
</html>
  
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                   Figure 1.: A graphical illustration showing the domains of TRIM21.
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                   Figure 3.: A graphical illustration showing the domains of TRIM21 (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>
  
 
<partinfo>BBa_K4165088 parameters</partinfo>
 
<partinfo>BBa_K4165088 parameters</partinfo>
 
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Latest revision as of 12:11, 13 October 2022


WAP-four disulfide core domain 14 serine protease inhibitor.

This basic part encodes Human serine protease inhibitor WAP-four disulfide core domain 14 which is able to inhibit HtrA1 (BBa_K4165004).


Usage and Biology

This type of family encodes for a type of inhibitor that contains a motif which consists of 8 cysteine residues capable of forming four disulfide bonds at the core of the protease, thus inhibiting its action. The main function of this inhibitor is to prevent elastase-mediated tissue proteolysis. 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
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 132
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 189
  • 1000
    COMPATIBLE WITH RFC[1000]


Functional Parameters

GC Content% Isoelectric point (PI) Charge at pH 7 Molecular Weight (Protein)
67.5% 8.641 6.373 12.27


Modeling

X-ray, NMR, and the predicted structures (AlphaFold2) are all present. 


                 Figure 1.: A graphical illustration showing the domains of TRIM21 (X-Ray diffraction).




                 Figure 2.: A graphical illustration showing the domains of TRIM21 (NMR).




                 Figure 3.: A graphical illustration showing the domains of TRIM21 (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.