Difference between revisions of "Part:BBa K4165086"
 
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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 is predicted to be able to inhibit serine proteases and it is predicted also to be located extracellularly . 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].
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This type of family encodes for a type of inhibitor that is predicted to be able to inhibit serine proteases and it is predicted also to be located extracellularly. 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 <sup>[1-4]</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_K4165086 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165086 SequenceAndFeatures</partinfo>
  
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===Functional Parameters===
  
  
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===Functional Parameters===
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<html>
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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>58.2%</td>
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    <td>9.448</td>
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    <td>8.538</td>
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    <td>11.421 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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===Dry Lab Characterization===
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<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
  
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GC% Content
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This inhibitor was modeled by several software and the top model was acquired by Alphafold.
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58.2%
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Isoelectric point (PI)
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<html>
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9.448
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/switches/6-alphafold.png" style="margin-left:200px;" alt="" width="500" /></p>
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</html>
  
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Charge at pH 7
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                      Figure 1.: A graphical illustration showing the structure of the inhibitor.
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8.538
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Molecular Weight (Protein)
 
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11.421 kDa
 
  
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===PDB Structure===
 
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Only a predicted model (AlphaFold).
 
  
  
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AlphaFold:
 
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https://alphafold.ebi.ac.uk/entry/Q6UDR6
 
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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:
 
  
 
===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.
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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.<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.
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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.<br>
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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.
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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_K4165086 parameters</partinfo>
 
<partinfo>BBa_K4165086 parameters</partinfo>
 
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Latest revision as of 12:15, 13 October 2022


SPINT4 (Serine Peptidase Inhibitor Kunitz type 4).

This basic part encodes Human serine protease inhibitor known as SPINT4 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 predicted to be able to inhibit serine proteases and it is predicted also to be located extracellularly. 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
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

Functional Parameters

GC Content% Isoelectric point (PI) Charge at pH 7 Molecular Weight (Protein)
58.2% 9.448 8.538 11.421 kDa


Dry Lab Characterization

Modeling

This inhibitor was modeled by several software and the top model was acquired by Alphafold. 

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



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.