Difference between revisions of "Part:BBa K3979004:Design"
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<h2>Design Considerations</h2>
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__NOTOC__
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<partinfo>BBa_K3979004 short</partinfo>
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<partinfo>BBa_K3979004 SequenceAndFeatures</partinfo>
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===Design Notes===
 
This is a chitinase gene designed using the catalytic domain(CD) of ChiB from Pseudoalteromonas sp. DL-6 and the chitin-binding domain (CBD) of ChiB (Uniprot ID: P11797) from Serratia marcescens. The domains mentioned above are linked without any extra linking residues because CBD of  Pseudoalteromonas chitinase is not yet annotated. CD-CBD makes a basic chitinase gene framework. The protein sequences were linked initially and then reverse translated to nucleotide sequences(stop codon inclusive) along with codon optimization for E.coli expression using the BOOST Juggler tool. BamHI and HindIII sites were added at the 5’ and 3’ end of the gene, respectively.
 
This is a chitinase gene designed using the catalytic domain(CD) of ChiB from Pseudoalteromonas sp. DL-6 and the chitin-binding domain (CBD) of ChiB (Uniprot ID: P11797) from Serratia marcescens. The domains mentioned above are linked without any extra linking residues because CBD of  Pseudoalteromonas chitinase is not yet annotated. CD-CBD makes a basic chitinase gene framework. The protein sequences were linked initially and then reverse translated to nucleotide sequences(stop codon inclusive) along with codon optimization for E.coli expression using the BOOST Juggler tool. BamHI and HindIII sites were added at the 5’ and 3’ end of the gene, respectively.
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===Source===
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Chitinase B Serratia marcescens
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GenBank ID: P11797
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Chitinase from Pseudoalteromonas sp. DL-6
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GenBank ID: AGU01016.1
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===References===
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<br/>
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<ul>
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<li>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.</li>
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<li>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.</li>
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</ul>

Revision as of 01:36, 20 October 2021

Bacterial Chitinase Combo 1


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 1813
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 1567
    Illegal AgeI site found at 520
    Illegal AgeI site found at 1612
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI.rc site found at 517
    Illegal SapI.rc site found at 775


Design Notes

This is a chitinase gene designed using the catalytic domain(CD) of ChiB from Pseudoalteromonas sp. DL-6 and the chitin-binding domain (CBD) of ChiB (Uniprot ID: P11797) from Serratia marcescens. The domains mentioned above are linked without any extra linking residues because CBD of Pseudoalteromonas chitinase is not yet annotated. CD-CBD makes a basic chitinase gene framework. The protein sequences were linked initially and then reverse translated to nucleotide sequences(stop codon inclusive) along with codon optimization for E.coli expression using the BOOST Juggler tool. BamHI and HindIII sites were added at the 5’ and 3’ end of the gene, respectively.


Source

Chitinase B Serratia marcescens GenBank ID: P11797

Chitinase from Pseudoalteromonas sp. DL-6 GenBank ID: AGU01016.1

References


  • 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.