8PEC image
Entry Detail
PDB ID:
8PEC
Keywords:
Title:
OXA-48_Q5-CAZ. Epistasis Arises from Shifting the Rate-Limiting Step during Enzyme Evolution
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2023-06-13
Release Date:
2024-02-14
Method Details:
Experimental Method:
Resolution:
2.66 Å
R-Value Free:
0.27
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 61
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Beta-lactamase
Mutations:A33V, K51E, F72L, S212A, T213A
Chain IDs:A, B, C, D
Chain Length:242
Number of Molecules:4
Biological Source:Klebsiella pneumoniae
Primary Citation
Epistasis arises from shifting the rate-limiting step during enzyme evolution of a beta-lactamase.
Nat Catal 7 499 509 (2024)
PMID: 38828429 DOI: 10.1038/s41929-024-01117-4

Abstact

Epistasis, the non-additive effect of mutations, can provide combinatorial improvements to enzyme activity that substantially exceed the gains from individual mutations. Yet the molecular mechanisms of epistasis remain elusive, undermining our ability to predict pathogen evolution and engineer biocatalysts. Here we reveal how directed evolution of a β-lactamase yielded highly epistatic activity enhancements. Evolution selected four mutations that increase antibiotic resistance 40-fold, despite their marginal individual effects (≤2-fold). Synergistic improvements coincided with the introduction of super-stochiometric burst kinetics, indicating that epistasis is rooted in the enzyme's conformational dynamics. Our analysis reveals that epistasis stemmed from distinct effects of each mutation on the catalytic cycle. The initial mutation increased protein flexibility and accelerated substrate binding, which is rate-limiting in the wild-type enzyme. Subsequent mutations predominantly boosted the chemical steps by fine-tuning substrate interactions. Our work identifies an overlooked cause for epistasis: changing the rate-limiting step can result in substantial synergy that boosts enzyme activity.

Legend

Protein

Chemical

Disease

Primary Citation of related structures