9HVB

High-efficiency Kemp eliminases by complete computational design

Summary for 9HVB

• Entry DOI: 10.2210/pdb9hvb/pdb
• Descriptor: Kemp eliminase, SULFATE ION (3 entities in total)
• Functional Keywords: inhibitor, lyase
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 28370.31

Authors

Listov, D.,Dym, O.,Vos, E.,Hoffka, G.,Berg, A.,Rogotner, S.,Caroline, s.,Kamerlin, L.,Fleishman, S.J. (deposition date: 2024-12-26, release date: 2025-06-11, Last modification date: 2025-08-13)

Primary citation

Listov, D.,Vos, E.,Hoffka, G.,Hoch, S.Y.,Berg, A.,Hamer-Rogotner, S.,Dym, O.,Kamerlin, S.C.L.,Fleishman, S.J.
Complete computational design of high-efficiency Kemp elimination enzymes.
Nature, 643:1421-1427, 2025

PubMed Abstract: Until now, computationally designed enzymes exhibited low catalytic rates and required intensive experimental optimization to reach activity levels observed in comparable natural enzymes. These results exposed limitations in design methodology and suggested critical gaps in our understanding of the fundamentals of biocatalysis. We present a fully computational workflow for designing efficient enzymes in TIM-barrel folds using backbone fragments from natural proteins and without requiring optimization by mutant-library screening. Three Kemp eliminase designs exhibit efficiencies greater than 2,000 M s. The most efficient shows more than 140 mutations from any natural protein, including a novel active site. It exhibits high stability (greater than 85 °C) and remarkable catalytic efficiency (12,700 M s) and rate (2.8 s), surpassing previous computational designs by two orders of magnitude. Furthermore, designing a residue considered essential in all previous Kemp eliminase designs increases efficiency to more than 10 M s and rate to 30 s, achieving catalytic parameters comparable to natural enzymes and challenging fundamental biocatalytic assumptions. By overcoming limitations in design methodology, our strategy enables programming stable, high-efficiency, new-to-nature enzymes through a minimal experimental effort.

PubMed: 40533551
DOI: 10.1038/s41586-025-09136-2

Experimental method

X-RAY DIFFRACTION (2 Å)