Difference between revisions of "Part:BBa K4165084"

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<span class='h3bb'>Sequence and Features</span>
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===<span class='h3bb'>Sequence and Features</span>===
 
<partinfo>BBa_K4165084 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165084 SequenceAndFeatures</partinfo>
  
  
  
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===Functional Parameters===
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===Dry-Lab characterization===
  
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GC% Content
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<p style=" font-weight: bold; font-size:14px;"> Modeling </p>
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60.3%
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Isoelectric point (PI)
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This peptide was modeled by several software and the top model was acquired by RosettaFold.
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7.904
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Charge at pH 7
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2.835
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Molecular Weight (Protein)
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11.051 kDa
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It has a predicted model (AlphaFold).
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AlphaFold:
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https://alphafold.ebi.ac.uk/entry/Q1W4C9
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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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<p style=" font-weight: bold; font-size:14px;"> Quality Assessment </p>
  
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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>cbeta_deviations</th>
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    <th>clashscore</th>
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    <th>ramachandran_favored</th>
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    <th>ramachandran_outliers</th>
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    <th>Qmean_4</th>
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    <th>Qmean_6</th>
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  </tr>
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  <tr>
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    <td>0</td>
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    <td>160.16</td>
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    <td>98.91</td>
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    <td>0</td>
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    <td>-0.31071</td>
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    <td>-1.23442</td>
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  </tr>
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</table>
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</body>
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</html>
  
 
<html>
 
<html>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/4-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-inhibitors/6.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.
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                Figure 1.: A graphical illustration showing the structure of the inhibitor (Model 4-RosettaFold).
  
 
===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>
−
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 - Cai, S., Zhang, P., Dong, S., Li, L., Cai, J., & Xu, M. (2018). Downregulation of SPINK13 promotes metastasis by regulating uPA in ovarian cancer cells. Cellular Physiology and Biochemistry, 45(3), 1061-1071.
 
4 - Cai, S., Zhang, P., Dong, S., Li, L., Cai, J., & Xu, M. (2018). Downregulation of SPINK13 promotes metastasis by regulating uPA in ovarian cancer cells. Cellular Physiology and Biochemistry, 45(3), 1061-1071.
  

Latest revision as of 12:38, 13 October 2022


SPINK13 (Serine Peptidase Inhibitor Kazal type 13).

This basic part encodes Human serine protease inhibitor known as SPINK13 which is able to inhibit trypsin-like proteases, like HtrA1 (BBa_K4165004).


Usage and Biology

This part encodes for a type of inhibitor that is predicted to be able to inhibit serine peptidases. The inhibitor is present extracellularly and is predicted to be involved in the feedback inhibition of acivation of premature acrosomal reaction sperms. The inhibitor binds to trypsin 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
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 135
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Dry-Lab characterization

Modeling

This peptide was modeled by several software and the top model was acquired by RosettaFold.

Quality Assessment

cbeta_deviations clashscore ramachandran_favored ramachandran_outliers Qmean_4 Qmean_6
0 160.16 98.91 0 -0.31071 -1.23442 

               Figure 1.: A graphical illustration showing the structure of the inhibitor (Model 4-RosettaFold).

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 - Cai, S., Zhang, P., Dong, S., Li, L., Cai, J., & Xu, M. (2018). Downregulation of SPINK13 promotes metastasis by regulating uPA in ovarian cancer cells. Cellular Physiology and Biochemistry, 45(3), 1061-1071.