Difference between revisions of "Part:BBa K4165078"
(→‎Functional Parameters)
 
(4 intermediate revisions by 2 users not shown)
Line 7: Line 7:
  
 
===Usage and Biology===
 
===Usage and Biology===
−
This type of family encodes for a type of inhibitor that is able to inhibit serine peptidases, especially kallkreins. The inhibitor’s main function is to inhibit kallikrein-related peptidases in the skin. The inhibitor binds to serine peptidases and since the catalytic core of HtrA1 (BBa_K4165004) is considered as a serine catalytic domain, so this inhibitor also is considered to inhibit the function of HtrA1 [1] - [3].
+
This type of family encodes for a type of inhibitor that is able to inhibit serine peptidases, especially kallkreins. The inhibitor’s main function is to inhibit kallikrein-related peptidases in the skin. The inhibitor binds to serine peptidases and since the catalytic core of HtrA1 (BBa_K4165004) is considered as a serine catalytic domain, so this inhibitor also is considered to inhibit the function of HtrA1 <sup>[1-3]</sup>.
  
  
 
<!-- -->
 
<!-- -->
−
<span class='h3bb'>Sequence and Features</span>
+
===<span class='h3bb'>Sequence and Features</span>===
 
<partinfo>BBa_K4165078 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165078 SequenceAndFeatures</partinfo>
  
  
−
===Functional Parameters===
+
===Dry-Lab Characterization===
−
GC% Content
+
===Modelling===
−
54.6%
+
−
Isoelectric point (PI)
+
−
8.117
+
−
Charge at pH 7
+
−
3.635
+
−
Molecular Weight (Protein)
+
−
8.585 kDa
+
  
−
It has both NMR structure and a predicted model (AlphaFold2).
 
  
−
PDB structure:
+
<html>
−
https://drive.google.com/drive/folders/1OhqZoqIootmRPpiVkemM_npNaA5WMO9b
+
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/switches/q6uwn8-nmr.png" style="margin-left:200px;" alt="" width="500" /></p>
 +
</html>
  
−
NMR structure:
+
                  Figure 1.: A graphical illustration showing the structure of the inhibitor (NMR).
−
https://www.rcsb.org/structure/2N52
+
−
Molprobity: 2.47
+
−
Clash Score: 9.35
+
−
Ramachandran Favoured: 94.44%
+
−
Ramachandran Outliers: 0%
+
−
Rotamers Outliers: 6%
+
−
C-beta Deviations: 0%
+
−
Q-Mean: 0.83 土 0.11
+
−
 
+
−
AlphaFold2:
+
−
https://drive.google.com/drive/folders/1o_e_vCFs-bwbqS0z-3XsDzY9ENKnag4I
+
−
Molprobity: 1.11
+
−
Clash Score: 0
+
−
Ramachandran Favoured: 92.21%
+
−
Ramachandran Outliers: 0%
+
−
Rotamers Outliers: 1.49%
+
−
C-beta Deviations: 0%
+
−
Q-Mean: 0.65 土 0.1
+
  
 
===References===
 
===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.
+
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>
−
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.
  

Latest revision as of 00:11, 12 October 2022


SPINK6 (Serine Peptidase Inhibitor Kazal type 6).

This basic part encodes Human serine protease inhibitor known as SPINK6 which is able to inhibit serine peptidases.


Usage and Biology

This type of family encodes for a type of inhibitor that is able to inhibit serine peptidases, especially kallkreins. The inhibitor’s main function is to inhibit kallikrein-related peptidases in the skin. The inhibitor binds to serine peptidases and since the catalytic core of HtrA1 (BBa_K4165004) is considered as a serine catalytic domain, so this inhibitor also is considered to inhibit the function of 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 102
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Dry-Lab Characterization

Modelling

                 Figure 1.: 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.