Difference between revisions of "Part:BBa K4165079"
(→‎Functional Parameters)
 
Line 13: Line 13:
  
  
−
===Functional Parameters===
+
===Dry-Lab Characterization===
−
GC% Content
+
−
59.1%
+
−
Isoelectric point (PI)
+
−
8.811
+
−
Charge at pH 7
+
−
5.702
+
−
Molecular Weight (Protein)
+
−
9.291 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>
 
<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:
 
  
  
Line 59: Line 32:
  
 
                   Figure 2.: A graphical illustration showing the structure of the inhibitor (NMR).
 
                   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/switches/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===
 
===References===

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.