A non-canonical nucleophile unlocks a new mechanistic pathway in a designed enzyme

Amy E. Hutton, Jake Foster, Rebecca Crawshaw, Florence J. Hardy, Linus O. Johannissen, Thomas M. Lister, Emilie F. Gérard, Zachary Birch-Price, Richard Obexer, Sam Hay and Anthony P. Green ()
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Amy E. Hutton: The University of Manchester
Jake Foster: The University of Manchester
Rebecca Crawshaw: The University of Manchester
Florence J. Hardy: The University of Manchester
Linus O. Johannissen: The University of Manchester
Thomas M. Lister: The University of Manchester
Emilie F. Gérard: The University of Manchester
Zachary Birch-Price: The University of Manchester
Richard Obexer: The University of Manchester
Sam Hay: The University of Manchester
Anthony P. Green: The University of Manchester

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: Abstract Directed evolution of computationally designed enzymes has provided new insights into the emergence of sophisticated catalytic sites in proteins. In this regard, we have recently shown that a histidine nucleophile and a flexible arginine can work in synergy to accelerate the Morita-Baylis-Hillman (MBH) reaction with unrivalled efficiency. Here, we show that replacing the catalytic histidine with a non-canonical Nδ-methylhistidine (MeHis23) nucleophile leads to a substantially altered evolutionary outcome in which the catalytic Arg124 has been abandoned. Instead, Glu26 has emerged, which mediates a rate-limiting proton transfer step to deliver an enzyme (BHMeHis1.8) that is more than an order of magnitude more active than our earlier MBHase. Interestingly, although MeHis23 to His substitution in BHMeHis1.8 reduces activity by 4-fold, the resulting His containing variant is still a potent MBH biocatalyst. However, analysis of the BHMeHis1.8 evolutionary trajectory reveals that the MeHis nucleophile was crucial in the early stages of engineering to unlock the new mechanistic pathway. This study demonstrates how even subtle perturbations to key catalytic elements of designed enzymes can lead to vastly different evolutionary outcomes, resulting in new mechanistic solutions to complex chemical transformations.

Date: 2024
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DOI: 10.1038/s41467-024-46123-z

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