Download MendeleyStructural dynamics of the Ca 2+ -regulated cutinase towards structure-based improvement of PET degradation activity.
Numoto, N., Kondo, F., Bekker, G.J., Liao, Z., Yamashita, M., Iida, A., Ito, N., Kamiya, N., Oda, M.(2024) Int J Biol Macromol 281: 136597-136597
- PubMed: 39419144
- DOI: https://doi.org/10.1016/j.ijbiomac.2024.136597
- Primary Citation of Related Structures:
8Z2G, 8Z2H, 8Z2I, 8Z2J, 8Z2K - PubMed Abstract:
We previously revealed the structural basis of Ca 2+ dependent regulation of a polyethylene terephthalate (PET)-degrading enzyme, Cut190, and proposed a unique reaction cycle in which the enzyme repeatedly binds and releases Ca 2+ . Here, we report crystal structures of Cut190 mutants with high thermal stability complexed with PET-like ligands that contain aromatic rings. The structural information has allowed us to perform further computational analyses using a PET-trimer bound model. Our multicanonical molecular dynamics simulations and subsequent analyses of the free energy landscapes revealed a novel intermediate form that occurs during the enzymatic reaction cycle. Furthermore, the computational analyses were used to investigate the effect of the point mutations F77L and F81L in the Ca 2+ -binding site, which showed that the former stabilizes the engaged and open forms to improve transition between the open and active forms, while the latter extremely increases the open form. Subsequent experiments showed that the F77L mutation increased the activity, while the F81L mutation decreased the activity. Our computational analysis has enabled us to explore the dynamics of Cut190 on a completely new level, providing key insights into how the balance between the various conformations influences the reaction cycle and ultimately how to improve the reaction cycle.
Organizational Affiliation:
Medical Research Laboratory, Institute of Integrated Research, Institute of Science Tokyo, 1-5-45 Yushima Bunkyo-ku, Tokyo 113-8510, Japan; International Center for Structural Biology, Research Institute for Interdisciplinary Science, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.
