Difference between revisions of "Part:BBa K4165200"
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This parts code for the trim21 E3 ligase having his PRYSPRY domain truncated (BBa_K3396007), fused to type 1 Cohesin module derived from Clostridium thermocellum cellulosome scaffoldin using Glycine serine flexible linker repeated three times to maintain part flexibility needed during target ubiquitination | This parts code for the trim21 E3 ligase having his PRYSPRY domain truncated (BBa_K3396007), fused to type 1 Cohesin module derived from Clostridium thermocellum cellulosome scaffoldin using Glycine serine flexible linker repeated three times to maintain part flexibility needed during target ubiquitination | ||
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===Usage and Biology=== | ===Usage and Biology=== | ||
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| − | + | this part is the main part in our Snitch system, it is supposed to bind to the protac which in turn will bind to tau protein. The hypothesis is when the binding occurs between the three parts, Trim21 will recruit E2 conjugating enzyme that carries ubiquitin and move the ubiquitin from the E2 to tau. After ubiquitination, tau protein is supposed to be degraded by 26S proteasome | |
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===<span class='h3bb'>Sequence and Features</span>=== | ===<span class='h3bb'>Sequence and Features</span>=== | ||
the sequence was optimized for <i>E.coli</i> expression | the sequence was optimized for <i>E.coli</i> expression | ||
<partinfo>BBa_K4165200 SequenceAndFeatures</partinfo> | <partinfo>BBa_K4165200 SequenceAndFeatures</partinfo> | ||
| − | === | + | ===Modeling=== |
| − | + | Trim21-(G<sub>4</sub>S) <sub>3</sub>-Coh2 is modeled by AlphaFold2, ITASSER, MODELLER and TrRosetta, best model obtained from TrRosetta. | |
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<html> | <html> | ||
| − | <p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/switches/trim-g4s3-coh.png" style="margin-left: | + | <p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/switches/trim-g4s3-coh.png" style="margin-left:200px;" alt="" width="500" /></p> |
</html> | </html> | ||
| − | + | Figure 1.: Predicted 3D structure of our fusion protein tTrim21-(G<sub>4</sub>S)<sub>3</sub>-Coh2. | |
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| − | <p style=" font-weight: bold; font-size:13px;"> Table 1: Quality assessment parameters of | + | <p style=" font-weight: bold; font-size:13px;"> Table 1: Quality assessment parameters of Trim21-(G<sub>4</sub>S)<sub>3</sub>-Coh2. model. </p> |
<html> | <html> | ||
Latest revision as of 14:08, 13 October 2022
Trim21-(GGGGS)3-Coh2
This parts code for the trim21 E3 ligase having his PRYSPRY domain truncated (BBa_K3396007), fused to type 1 Cohesin module derived from Clostridium thermocellum cellulosome scaffoldin using Glycine serine flexible linker repeated three times to maintain part flexibility needed during target ubiquitination
Usage and Biology
this part is the main part in our Snitch system, it is supposed to bind to the protac which in turn will bind to tau protein. The hypothesis is when the binding occurs between the three parts, Trim21 will recruit E2 conjugating enzyme that carries ubiquitin and move the ubiquitin from the E2 to tau. After ubiquitination, tau protein is supposed to be degraded by 26S proteasome
Sequence and Features
the sequence was optimized for E.coli expression
- 10COMPATIBLE WITH RFC[10]
- 12INCOMPATIBLE WITH RFC[12]Illegal NheI site found at 225
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal NgoMIV site found at 182
- 1000COMPATIBLE WITH RFC[1000]
Modeling
Trim21-(G4S) 3-Coh2 is modeled by AlphaFold2, ITASSER, MODELLER and TrRosetta, best model obtained from TrRosetta.
Figure 1.: Predicted 3D structure of our fusion protein tTrim21-(G4S)3-Coh2.
Table 1: Quality assessment parameters of Trim21-(G4S)3-Coh2. model.
References
1- Carvalho AL, Dias FM, Nagy T, Prates JA, Proctor MR, Smith N, Bayer EA, Davies GJ, Ferreira LM, Romão MJ, Fontes CM, Gilbert HJ. Evidence for a dual binding mode of dockerin modules to cohesins. Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3089-94. doi: 10.1073/pnas.0611173104. Epub 2007 Feb 20. PMID: 17360613; PMCID: PMC1805526.