9QUC
Metal-free de novo protein scaffold TFD-EH
Summary for 9QUC
| Entry DOI | 10.2210/pdb9quc/pdb |
| Related | 6ZV9 |
| Descriptor | TFD-EH, CITRIC ACID, 1,2-ETHANEDIOL, ... (4 entities in total) |
| Functional Keywords | tim barrel, enzyme engineering, metal coordination, conformational dynamics, de novo protein |
| Biological source | synthetic construct |
| Total number of polymer chains | 1 |
| Total formula weight | 19480.51 |
| Authors | Wagner Egea, P.,Delhommel, F.,Mustafa, G.,Leiss-Maier, F.,Klimper, L.,Badmann, T.,Heider, A.,Wille, I.C.,Groll, M.,Sattler, M.,Zeymer, C. (deposition date: 2025-04-10, release date: 2025-11-19) |
| Primary citation | Wagner Egea, P.,Delhommel, F.,Mustafa, G.,Leiss-Maier, F.,Klimper, L.,Badmann, T.,Heider, A.,Wille, I.,Groll, M.,Sattler, M.,Zeymer, C. Modular protein scaffold architecture and AI-guided sequence optimization facilitate de novo metalloenzyme engineering. Structure, 2025 Cited by PubMed Abstract: Incorporating metal cofactors into computationally designed protein scaffolds provides a versatile route to novel protein functions, including the potential for new-to-nature enzyme catalysis. However, a major challenge in protein design is to understand how the scaffold architecture influences conformational dynamics. Here, we characterized structure and dynamics of a modular de novo scaffold with flexible inter-domain linkers. Three rationally engineered variants with different metal specificity were studied by combining X-ray crystallography, NMR spectroscopy, and molecular dynamics simulations. The lanthanide-binding variant was initially trapped in an inactive conformational state, which impaired efficient metal coordination and cerium-dependent photocatalytic activity. Stabilization of the active conformation by AI-guided sequence optimization using ProteinMPNN led to accelerated lanthanide binding and a 10-fold increase in k/K for a photoenzymatic model reaction. Our results suggest that modular scaffold architectures provide an attractive starting point for de novo metalloenzyme engineering and that ProteinMPNN-based sequence redesign can stabilize desired conformational states. PubMed: 41197620DOI: 10.1016/j.str.2025.10.010 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.6 Å) |
Structure validation
Download full validation report
