9QUI

Ni(II)-bound de novo protein scaffold TFD-EH

Summary for 9QUI

• Entry DOI: 10.2210/pdb9qui/pdb
• Related: 6ZV9
• Descriptor: TFD-EH, NICKEL (II) ION, IMIDAZOLE, ... (6 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: 19320.02

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, Last modification date: 2026-01-21)

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, 34:32-44.e6, 2026

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: 41197620
DOI: 10.1016/j.str.2025.10.010

Experimental method

X-RAY DIFFRACTION (2.1 Å)