Difference between revisions of "Part:BBa K4165011"

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===<span class='h3bb'>Sequence and Features</span>===
 
===<span class='h3bb'>Sequence and Features</span>===
 
<partinfo>BBa_K4165011 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4165011 SequenceAndFeatures</partinfo>
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===Dry Lab===
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<p style=" font-weight: bold; font-size:14px;"> Mathematical modeling </p>
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<p style=" font-weight: bold; font-size:14px;">Transcription rate and translation rate under T7 promotor </p>
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the mathematical modeling was based on our code for the calculation of transcription and translation (you can find it in the code section) beside with the estimated results from the wet lab.
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<html>
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<p><img src="https://static.igem.wiki/teams/4165/wiki/dry-lab/mathematical-modeling/ube2n2.png" style="margin-left:200px;" alt="" width="500" /></p>
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</html>
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                  Figure 1. this figure shows the results from the transcription and translation code showing the
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                      variation of mRNA and protein concentrations with time compared with the wet lab results.
  
 
===Wet-Lab Results===
 
===Wet-Lab Results===
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<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/wetlab-results/ube2n-pgs.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/wetlab-results/ube2n-pgs.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 
</html>
 
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                                   Figure 1. Transformed plate of His UBE2N + pGS-21a
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                                   Figure 2. Transformed plate of His UBE2N + pGS-21a
 
<p style=" font-weight: bold; font-size:14px;"> Transformation of His UBE2N in DH-5 alpha using pJET vector </p>
 
<p style=" font-weight: bold; font-size:14px;"> Transformation of His UBE2N in DH-5 alpha using pJET vector </p>
 
<html>
 
<html>
 
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/wetlab-results/ube2n-pjet.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 
<p><img src="https://static.igem.wiki/teams/4165/wiki/parts-registry/wetlab-results/ube2n-pjet.jpg" style="margin-left:200px;" alt="" width="500" /></p>
 
</html>
 
</html>
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                                Figure 2. Transformed plate of His UBE2N + pJET
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                                    Figure 3. Transformed plate of His UBE2N + pJET
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  
 
===Functional Parameters===
 
===Functional Parameters===

Revision as of 21:55, 11 October 2022


UBE2N

Ubiquitin-conjugating E2 ligase that has a role in the ubiquitination cascade for protein degradation.

Usage and Biology

This part encodes for the UBE2N enzyme which is a member of the E2 ubiquitin-conjugating enzyme family. It acts as the second enzyme in the ubiquitination cascade to receive the thio-esterified ubiquitin from the E1 active site. The cascade starts with UBE2W being one of the few E2 types which binds to Trim21 (E3 ligase) and this specificity for trim21 is due to the presence of RING domain. The next step is the formation of UBE2N/UBE2V2 complex which function in the chain building and extending poly-ubiquitin chains from the mono-ubiquitinated proteins by UBE2W. This protein may also be involved in DNA post replication repair according to studies that have been done on mice.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 221
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

Dry Lab

Mathematical modeling

Transcription rate and translation rate under T7 promotor

the mathematical modeling was based on our code for the calculation of transcription and translation (you can find it in the code section) beside with the estimated results from the wet lab. 

                 Figure 1. this figure shows the results from the transcription and translation code showing the 
                     variation of mRNA and protein concentrations with time compared with the wet lab results.

Wet-Lab Results

Transformation of His UBE2N in BL-21 using pGS-21a vector 

                                 Figure 2. Transformed plate of His UBE2N + pGS-21a

Transformation of His UBE2N in DH-5 alpha using pJET vector 

                                   Figure 3. Transformed plate of His UBE2N + pJET

Refrences

1. UBE2N ubiquitin conjugating enzyme E2 N [Homo sapiens (human)] - Gene - NCBI. (2022). 2. Pharos: Ubiquitin-conjugating enzyme E2 N (Tchem). (2022). 3. Kleiger, G., & Mayor, T. (2014). Perilous journey: a tour of the ubiquitin-proteasome system. Trends in cell biology, 24(6), 352-359. 3. Vittal, V., Wenzel, D. M., Brzovic, P. S., & Klevit, R. E. (2013). Biochemical and structural characterization of the ubiquitin-conjugating enzyme UBE2W reveals the formation of a noncovalent homodimer. Cell biochemistry and biophysics, 67(1), 103-110.