Coding
ChiB

Part:BBa_K3979009:Design

Designed by: Akshay J, Abhishek Raghunathan   Group: iGEM21_IISER_TVM   (2021-10-19)


ChiB gene of Serratia marcescens of QMB1466


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 7
    Illegal XhoI site found at 1519
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

While designing the sequence of the recombinant chitinase, there were several considerations that we needed to keep in mind. Firstly, since we planned to express the chitinase in E. coli, it became necessary that the final molecular weight was less than 100 kDa to enable robust protein folding post expression in the chassis. This imposed a constraint on the size and number of wild-type domains we could join. Secondly, since we aimed to use the chitinase as a therapeutic, the activity of our enzyme as a function of temperature and pH were essential parameters to keep in mind. Our interactions with distinguished crystallographers made us realize that these parameters would depend heavily on the temperature and pH activity curves of the wild-type chitinases we chose. Hence, we decided on wild-type enzymes that retained a significant fraction of their activities at physiological temperatures and pH.



Source

Chitinase B gene of Serratia marcescens of QMB1466 GenBank ID: P11797


References


  • Pseudoalteromonas sp DL-6: Wang X, Zhao Y, Tan H, Chi N, Zhang Q, Du Y, Yin H. Characterisation of a chitinase from Pseudoalteromonas sp. DL-6, a marine psychrophilic bacterium. Int J Biol Macromol. 2014 Sep;70:455-62. doi: 10.1016/j.ijbiomac.2014.07.033. Epub 2014 Jul 23. PMID: 25064555.
  • Serratia marcescens: Li J, Zheng J, Liang Y, Yan R, Xu X, Lin J. Expression and characterization of a chitinase from Serratia marcescens. Protein Expr Purif. 2020 Jul;171:105613. doi: 10.1016/j.pep.2020.105613. Epub 2020 Feb 23. PMID: 32097727.
  • Saima, & Kuddus, Mohammed & Roohi, & Ahmad, Iffat. (2013). Isolation of novel chitinolytic bacteria and production optimization of extracellular chitinase. Journal of Genetic Engineering and Biotechnology. 11. 39–46. 10.1016/j.jgeb.2013.03.001.
  • O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461 DOI 10.1002/jcc.21334