Difference between revisions of "Part:BBa K4165083"

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<span class='h3bb'>Sequence and Features</span>
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===<span class='h3bb'>Sequence and Features</span>===
 
<partinfo>BBa_K4165083 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165083 SequenceAndFeatures</partinfo>
  
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===Functional Parameters===
 
===Functional Parameters===
  
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GC% Content
 
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52.1%
 
  
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Isoelectric point (PI)
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<html>
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6.155
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<style>
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table, th, td {
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Charge at pH 7
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  border:1px solid black; margin-left:auto;margin-right:auto;
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-0.554
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}
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</style>
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Molecular Weight (Protein)
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<body>
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10.252 kDa
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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>52.1%</td>
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    <td>6.155</td>
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    <td>-0.554</td>
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    <td>10.252 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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Only a predicted model (AlphaFold).
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===Dry Lab Characteriztion===
  
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AlphaFold:
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<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
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https://alphafold.ebi.ac.uk/entry/P49223
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Molprobity:
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Clash Score:
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Ramachandran Favoured:
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Ramachandran Outliers:
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Rotamers Outliers:
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C-beta Deviations:  
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Q-Mean:
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This inhibitor was modeled by several software and the top model was acquired from Alphafold2
  
 
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<html>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/3-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/3-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 1.: A graphical illustration showing the structure of the inhibitor (AlphaFold).
  
 
===References===
 
===References===
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1 - Frochaux, V., Hildebrand, D., Talke, A., Linscheid, M. W., & Schlüter, H. (2014). Alpha-1-antitrypsin: a novel human high temperature requirement protease A1 (HTRA1) substrate in human placental tissue. PloS one, 9(10), e109483.
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1 - Frochaux, V., Hildebrand, D., Talke, A., Linscheid, M. W., & Schlüter, H. (2014). Alpha-1-antitrypsin: a novel human high temperature requirement protease A1 (HTRA1) substrate in human placental tissue. PloS one, 9(10), e109483. <br>
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2 - 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.
+
2 - 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>
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3 - 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 - 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>
−
4 - Chen, T. J., Tian, Y. F., Chou, C. L., Chan, T. C., He, H. L., Li, W. S., ... & Lai, H. Y. (2021). High spink4 expression predicts poor outcomes among rectal cancer patients receiving CCRT. Current Oncology, 28(4), 2373-2384.
+
4 - Chen, T. J., Tian, Y. F., Chou, C. L., Chan, T. C., He, H. L., Li, W. S., ... & Lai, H. Y. (2021). High spink4 expression predicts poor outcomes among rectal cancer patients receiving CCRT. Current Oncology, 28(4), 2373-2384.<br>
 
<partinfo>BBa_K4165083 parameters</partinfo>
 
<partinfo>BBa_K4165083 parameters</partinfo>
 
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Latest revision as of 12:40, 13 October 2022


SPINT3 (Serine Peptidase Inhibitor Kunitz type 3).

This basic part encodes Human serine protease inhibitor known as SPINT3 which is able to inhibit serine peptidases, like HtrA1 (BBa_K4165004).


Usage and Biology

This type of family encodes for a type of inhibitor that is able to inhibit serine proteases and it is predicted to be located extracellularly which interferes with the TGF-β signalling pathway. The inhibitor binds to trypsin-like (serine) proteases and since the catalytic core of HtrA1 (BBa_K4165004) is considered as a tyrpsin-like catalytic domain, so this inhibitor also is considered to inhibit the function of HtrA1 [1] - [4].


Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 7
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 7
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 87
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 7
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 7
  • 1000
    COMPATIBLE WITH RFC[1000]


Functional Parameters

GC Content% Isoelectric point (PI) Charge at pH 7 Molecular Weight (Protein)
52.1% 6.155 -0.554 10.252 kDa

Dry Lab Characteriztion

Modeling

This inhibitor was modeled by several software and the top model was acquired from Alphafold2 

                 Figure 1.: A graphical illustration showing the structure of the inhibitor (AlphaFold).

References

1 - Frochaux, V., Hildebrand, D., Talke, A., Linscheid, M. W., & Schlüter, H. (2014). Alpha-1-antitrypsin: a novel human high temperature requirement protease A1 (HTRA1) substrate in human placental tissue. PloS one, 9(10), e109483.
2 - 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.
3 - 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.
4 - Chen, T. J., Tian, Y. F., Chou, C. L., Chan, T. C., He, H. L., Li, W. S., ... & Lai, H. Y. (2021). High spink4 expression predicts poor outcomes among rectal cancer patients receiving CCRT. Current Oncology, 28(4), 2373-2384.