Part:BBa_K4165014

UBC (Ubiquitin C)

This basic part encodes ubiquitin C which is essential in the degradation of misfolded proteins through the ubiquitin-proteasome cascade.

Usage and Biology

Ubiquitin c involved in the proteasomal degradation pathway of proteins. Ubiquitination of a misfolded protein starts with ubiquitin molecule being transferred by E1 ligase to E2 then to E3 ligase with both steps being in an ATP-dependent manner. Finally, The E3 ubiquitin ligase then promotes the transfer of ubiquitin onto the substrate by binding to both the protein substrate and the E2-bound ubiquitin. This results in recognition of polyubiquitinated protein by the 26S proteasomes to initiate its degradation.

Covalently attached ubiquitin can be a monomer (monoubiquitin), a polymer (polyubiquitin chains), or a linear polymer (polyubiquitin chains with a Met as the initiator) (linear polyubiquitin chains). When polyubiquitin chains bind to a protein, the Lys residue of the ubiquitin determines the chain's function.

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 5
  
• 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.

References

1. Komander D. (2009). The emerging complexity of protein ubiquitination. Biochemical Society transactions, 37(Pt 5), 937–953. https://doi.org/10.1042/BST0370937.

2. David, Y., Ziv, T., Admon, A., & Navon, A. (2010). The E2 ubiquitin-conjugating enzymes direct polyubiquitination to preferred lysines. The Journal of biological chemistry, 285(12), 8595–8604. https://doi.org/10.1074/jbc.M109.089003.

3. Metzger, M. B., Pruneda, J. N., Klevit, R. E., & Weissman, A. M. (2014). RING-type E3 ligases: master manipulators of E2 ubiquitin-conjugating enzymes and ubiquitination. Biochimica et Biophysica Acta (BBA)-Molecular Cell Research, 1843(1), 47-60.

4. Lecker, S. H., Goldberg, A. L., & Mitch, W. E. (2006). Protein degradation by the ubiquitin-proteasome pathway in normal and disease states. Journal of the American Society of Nephrology: JASN, 17(7), 1807–1819. https://doi.org/10.1681/ASN.2006010083