Difference between revisions of "Part:BBa K4165079"

Latest revision as of 00:37, 12 October 2022

SPINK2 (Serine Peptidase Inhibitor Kazal type 2).

This basic part encodes Human serine protease inhibitor known as SPINK2 which is able to inhibit trypsin-like proteases, like HtrA1 (BBa_K4165004).

Usage and Biology

This type of family encodes for a type of inhibitor that is able to inhibit trypsins. The main function of the inhibitor is hindering the premature activation of proacrosin and many other proteases, thus preventing defects in the spermiogenesis process. The inhibitor binds to trypsin proteases and since the catalytic core of HtrA1 (BBa_K4165004) is considered as a trypsin-like catalytic domain, so this inhibitor also is considered to inhibit the function of HtrA1 [1] - [3].

Sequence and Features

Assembly Compatibility:

10
INCOMPATIBLE WITH RFC[10]
Illegal PstI site found at 105
12
INCOMPATIBLE WITH RFC[12]
Illegal PstI site found at 105
21
COMPATIBLE WITH RFC[21]
23
INCOMPATIBLE WITH RFC[23]
Illegal PstI site found at 105
25
INCOMPATIBLE WITH RFC[25]
Illegal PstI site found at 105
1000
COMPATIBLE WITH RFC[1000]

Dry-Lab Characterization

Modelling

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

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

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.

@@ Line 9: / Line 9: @@
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-<span class='h3bb'>Sequence and Features</span>
+===<span class='h3bb'>Sequence and Features</span>===
 <partinfo>BBa_K4165079 SequenceAndFeatures</partinfo>
-===Functional Parameters===
+===Dry-Lab Characterization===
-GC% Content
-.1%
-Isoelectric point (PI)
-.811
-Charge at pH 7
-.702
-Molecular Weight (Protein)
-.291 kDa
-It has x-ray structure, NMR, and a predicted model (AlphaFold2).
+===Modelling===
-PDB structure
-X-ray structure: https://www.rcsb.org/structure/2JXD
-Molprobity:
-Clash Score:
-Ramachandran Favoured:
-Ramachandran Outliers:
-Rotamers Outliers:
-C-beta Deviations:
-Q-Mean:
 <html>
-<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/p20155-xray.png" style="margin-left:200px;" alt="" width="500" /></p>
+<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/switches/p20155-xray.png" style="margin-left:200px;" alt="" width="500" /></p>
 </html>
@@ Line 42: / Line 25: @@
-NMR:
-https://www.rcsb.org/structure/2JXD
-Molprobity:
-Clash Score:
-Ramachandran Favoured:
-Ramachandran Outliers:
-Rotamers Outliers:
-C-beta Deviations:
-Q-Mean:
 <html>
-<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/p20155-nmr.png" style="margin-left:200px;" alt="" width="500" /></p>
+<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/switches/p20155-nmr.png" style="margin-left:200px;" alt="" width="500" /></p>
 </html>
                    Figure 2.: A graphical illustration showing the structure of the inhibitor (NMR).
-AlphaFold:
-https://alphafold.ebi.ac.uk/entry/P20155
-Molprobity:
-Clash Score:
-Ramachandran Favoured:
-Ramachandran Outliers:
-Rotamers Outliers:
-C-beta Deviations:
-Q-Mean:
-<html>
-<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/p20155-alphafold.png" style="margin-left:200px;" alt="" width="500" /></p>
-</html>
-                  Figure 3.: A graphical illustration showing the structure of the inhibitor (AlphaFold).
 ===References===
-- 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.
+- 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>
-- 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.
+- 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>
-- 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.
+- 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>
 <partinfo>BBa_K4165079 parameters</partinfo>
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