Part:BBa_K4179016

flavin-dependent monooxygenase - XimD

Figure 1: Decursinol and mamesin synthesis pathway

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Figure 2: PDB file of XimD created with Phyre2[4] and visualized in ChimeraX[5]

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XimD is part of the xiamenmycin biosynthesis gene cluster in addition to XimA, XimB, XimC, and XimE[1]. Xiamenmycin is a benzopyran compound that was shown as having anti fibrotic and anti-inflammatory activity[1]. XimD is an flavin-dependent monooxygenase that catalyzes the formation of an epoxide intermediate[2]. This intermediate, in turn, can be catalyzed by XimE(Part:BBa_K4179018) to a pyran product[2]. Alternatively, the epoxide intermediate can spontaneously undergo 5-exo-tet-cyclization to produce furan[2].

Use and purpose

The team of Technion 2022 used this part in a construct (Part:BBa_K4179019). The purpose of the composite part is to introduce XimD and XimE into E. coli to allow the formation of decursinol (a pyran) from 7-methyldesuberosin. To ensure the pyran product (decursinol) is favorable in comparison with the furan product (marmesin), the team constrained a surplus of XimE via genetic manipulations. The sequence of this part was taken from a previous workthe work of Bu et al.[3].

Sequence and Features

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  COMPATIBLE WITH RFC[12]
• 21
  INCOMPATIBLE WITH RFC[21]

  Illegal BamHI site found at 1385
  Illegal XhoI site found at 1117
  
• 23
  COMPATIBLE WITH RFC[23]
• 25
  INCOMPATIBLE WITH RFC[25]

  Illegal NgoMIV site found at 106
  Illegal NgoMIV site found at 1165
  
• 1000
  COMPATIBLE WITH RFC[1000]

References

1. Yang, Y., Fu, L., Zhang, J., Hu, L., Xu, M., & Xu, J. (2014). Characterization of the xiamenmycin biosynthesis gene cluster in Streptomyces xiamenensis 318. PLoS One, 9(6), e99537.

2. He, B. B., Zhou, T., Bu, X. L., Weng, J. Y., Xu, J., Lin, S., ... & Xu, M. J. (2019). Enzymatic pyran formation involved in xiamenmycin biosynthesis. ACS Catalysis, 9(6), 5391-5399.

3. Bu, X. L., He, B. B., Weng, J. Y., Jiang, C. C., Zhao, Y. L., Li, S. M., ... & Xu, M. J. (2020). Constructing microbial hosts for the production of benzoheterocyclic derivatives. ACS Synthetic Biology, 9(9), 2282-2290.

4. Kelley, Lawrence A, et al. “The PHYRE2 Web Portal for Protein Modeling, Prediction and Analysis.” Nature Protocols, vol. 10, no. 6, 2015, pp. 845–858., https://doi.org/10.1038/nprot.2015.053.

5. Pettersen, Eric F., et al. “UCSF Chimerax: Structure Visualization for Researchers, Educators, and Developers.” Protein Science, vol. 30, no. 1, 2020, pp. 70–82., https://doi.org/10.1002/pro.3943.