8Z2K
Substrate analog a013 bound form of PET-degrading cutinase mutant Cut190**SS_S176A
This is a non-PDB format compatible entry.
Summary for 8Z2K
| Entry DOI | 10.2210/pdb8z2k/pdb |
| Descriptor | Alpha/beta hydrolase family protein, 4-[oxidanyl(2-phenylmethoxyethoxy)phosphoryl]benzoic acid, CALCIUM ION, ... (4 entities in total) |
| Functional Keywords | protein engineering, polyesterase, metal binding, aromatic ligand, hydrolase |
| Biological source | Saccharomonospora viridis |
| Total number of polymer chains | 2 |
| Total formula weight | 57778.83 |
| Authors | Numoto, N.,Kondo, F.,Bekker, G.J.,Liao, Z.,Yamashita, M.,Iida, A.,Ito, N.,Kamiya, N.,Oda, M. (deposition date: 2024-04-12, release date: 2024-11-06) |
| Primary citation | Numoto, N.,Kondo, F.,Bekker, G.J.,Liao, Z.,Yamashita, M.,Iida, A.,Ito, N.,Kamiya, N.,Oda, M. Structural dynamics of the Ca 2+ -regulated cutinase towards structure-based improvement of PET degradation activity. Int.J.Biol.Macromol., 281:136597-136597, 2024 Cited by PubMed Abstract: We previously revealed the structural basis of Ca 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. 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-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. PubMed: 39419144DOI: 10.1016/j.ijbiomac.2024.136597 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.2 Å) |
Structure validation
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