Difference between revisions of "Part:BBa K4165078"

 
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<partinfo>BBa_K4165078 short</partinfo>
 
<partinfo>BBa_K4165078 short</partinfo>
  
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a serine protease inhibitor used to inhibit the action of HTRA1
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This basic part encodes Human serine protease inhibitor known as SPINK6 which is able to inhibit serine peptidases.
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<!-- Add more about the biology of this part here
 
 
===Usage and Biology===
 
===Usage and Biology===
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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].
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<!-- Uncomment this to enable Functional Parameter display
 
 
===Functional Parameters===
 
===Functional Parameters===
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GC% Content
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54.6%
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Isoelectric point (PI)
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8.117
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Charge at pH 7
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3.635
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Molecular Weight (Protein)
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8.585 kDa
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It has both NMR structure and a predicted model (AlphaFold2).
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PDB structure:
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https://drive.google.com/drive/folders/1OhqZoqIootmRPpiVkemM_npNaA5WMO9b
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NMR structure:
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https://www.rcsb.org/structure/2N52
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Molprobity: 2.47
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Clash Score: 9.35
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Ramachandran Favoured: 94.44%
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Ramachandran Outliers: 0%
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Rotamers Outliers: 6%
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C-beta Deviations: 0%
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Q-Mean: 0.83 土 0.11
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AlphaFold2:
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https://drive.google.com/drive/folders/1o_e_vCFs-bwbqS0z-3XsDzY9ENKnag4I
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Molprobity: 1.11
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Clash Score: 0
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Ramachandran Favoured: 92.21%
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Ramachandran Outliers: 0%
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Rotamers Outliers: 1.49%
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C-beta Deviations: 0%
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Q-Mean: 0.65 土 0.1
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===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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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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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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<partinfo>BBa_K4165078 parameters</partinfo>
 
<partinfo>BBa_K4165078 parameters</partinfo>
 
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Revision as of 17:07, 5 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]


Functional Parameters

GC% Content 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: https://drive.google.com/drive/folders/1OhqZoqIootmRPpiVkemM_npNaA5WMO9b

NMR structure: 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

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.