Difference between revisions of "Part:BBa K3493000:Design"

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===Design Notes===
 
===Design Notes===
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Codon optimization for E. coli. Following reports that the Streptococcus mutans homologous dextranase has a higher activity and resistance to proteolysis when its N terminal (residues 1-99) and C-terminal (residues 733-850) are deleted (Kim et al. 2011. Appl. Microbiol. Biotechnol.), we removed them from the CDS submitted to the registry. Accordingly, our final CDS has the contains the region of the G. algens dextranase sequence that aligns to residues 104 - 734 of the PDB structure of the S. mutans dextranase (Suzuki, et al. 2012. J. Biol. Chem.).
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This part is the CDS of a dextranase from a psychrophile organism (Gelidibacter algens) codon optimized for expression in Escherichia coli. Following reports that the Streptococcus mutans homologous dextranase has a higher activity when its N terminal (residues 1-99) and C-terminal (residues 733-850) are deleted (Kim et al., 2011), we removed them from the CDS submitted to the registry. Accordingly, our final CDS contains the region of the G. algens dextranase sequence that aligns to residues 104 - 734 of the PDB structure of the S. mutans dextranase (Suzuki et al., 2012). The dextranase of G. algens was successfully expressed in E. coli using the pET28a expression vector.  
  
 
===Source===
 
===Source===
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===References===
 
===References===
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Kim, Y.-M., Shimizu, R., Nakai, H., Mori, H., Okuyama, M., Kang, M.-S., Fujimoto, Z., Funane, K., Kim, D., & Kimura, A. (2011). Truncation of N- and C-terminal regions of Streptococcus mutans dextranase enhances catalytic activity. Applied Microbiology and Biotechnology, 91(2), 329–339.
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Suzuki, N., Kim, Y.-M., Fujimoto, Z., Momma, M., Okuyama, M., Mori, H., Funane, K., & Kimura, A. (2012). Structural elucidation of dextran degradation mechanism by streptococcus mutans dextranase belonging to glycoside hydrolase family 66. The Journal of Biological Chemistry, 287(24), 19916–19926.

Latest revision as of 22:42, 18 October 2021


G. algens dextranase CDS


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal PstI site found at 385
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal PstI site found at 385
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal PstI site found at 385
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal PstI site found at 385
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

This part is the CDS of a dextranase from a psychrophile organism (Gelidibacter algens) codon optimized for expression in Escherichia coli. Following reports that the Streptococcus mutans homologous dextranase has a higher activity when its N terminal (residues 1-99) and C-terminal (residues 733-850) are deleted (Kim et al., 2011), we removed them from the CDS submitted to the registry. Accordingly, our final CDS contains the region of the G. algens dextranase sequence that aligns to residues 104 - 734 of the PDB structure of the S. mutans dextranase (Suzuki et al., 2012). The dextranase of G. algens was successfully expressed in E. coli using the pET28a expression vector.

Source

The protein sequence is available at NCBI (https://www.ncbi.nlm.nih.gov/protein/WP_066432599.1?report=genbank&log$=prottop&blast_rank=700&RID=MZBBN4NZ014). The gene sequence was inferred from the protein sequence using codon optimization for E. coli.

References

Kim, Y.-M., Shimizu, R., Nakai, H., Mori, H., Okuyama, M., Kang, M.-S., Fujimoto, Z., Funane, K., Kim, D., & Kimura, A. (2011). Truncation of N- and C-terminal regions of Streptococcus mutans dextranase enhances catalytic activity. Applied Microbiology and Biotechnology, 91(2), 329–339.

Suzuki, N., Kim, Y.-M., Fujimoto, Z., Momma, M., Okuyama, M., Mori, H., Funane, K., & Kimura, A. (2012). Structural elucidation of dextran degradation mechanism by streptococcus mutans dextranase belonging to glycoside hydrolase family 66. The Journal of Biological Chemistry, 287(24), 19916–19926.