Part:BBa_K2201301

modeled aminoacyl-tRNA synthetase 4 for the incorporation of CBT-asparagine

This aminoacyl-tRNA synthetase was designed with the ROSETTA enzym design protocol. The basis is the tyrosyl-tRNA synthetase 1J1U of Methanococcus jannaschii with the novel amino acid N^γ‑2‑cyanobenzothiazol‑6‑yl‑L‑asparagine (CBT-asparagine) as ligand. We chose three synthetases based on a good ligand score generated by ROSETTA. Additionally, we ensured that CBT-asparagine fits to the binding pocket by visuel control. Thus, we selected the synthetases 2, 4 and 5 which have following ligand binding and total scores:

• BBa_K2201300 - ligand binding score: -6.56, total score: 38.01
• BBa_K2201301 - ligand binding score: -4.37, total score: 58.45
• BBa_K2201302 - ligand binding score: -4.25, total score: 109.13

Please note that the scores are relative badness-of-fit measures and thus only comparable between score values.

Compared with the wild type, the modeled sequences show several mutations. Following figure shows a schematic overview of these mutations.

Multiple alignment of the peptide sequence of the modeled synthetase sequences and the synthetase sequence of the wild type 1J1U. The 7 mutations are between the positions 30 and 40, 60 and 80, 110 and 120, 130 and 140, 150 and 160 and at the positions 173 and 176. Between the positions 203 and 211 is a deletion.

Additionally, the following figure shows the distances between the peptide sequences of the modeled synthetases and the wild type 1J1U.

Distances between the modeled synthetase sequences and the synthetase sequence of the wild type 1J1U.

Sequence and Features

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  COMPATIBLE WITH RFC[12]
• 21
  COMPATIBLE WITH RFC[21]
• 23
  COMPATIBLE WITH RFC[23]
• 25
  COMPATIBLE WITH RFC[25]
• 1000
  INCOMPATIBLE WITH RFC[1000]

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