PDBsum entry 7k4x

Hydrolase

PDB id: 7k4x

Contents

Protein chains

302 a.a.

Ligands

6NT ×2

ACT ×4

SO4 ×6

Waters ×516

References listed in PDB file

Key reference

• Title: How directed evolution reshapes the energy landscape in an enzyme to boost catalysis.
• Authors: R.Otten, R.A.P.Pádua, H.A.Bunzel, V.Nguyen, W.Pitsawong, M.Patterson, S.Sui, S.L.Perry, A.E.Cohen, D.Hilvert, D.Kern.
• Ref.: Science, 2020, 370, 1442-1446. [DOI no: 10.1126/science.abd3623]
• PubMed id: 33214289

Abstract

The advent of biocatalysts designed computationally and optimized by laboratory evolution provides an opportunity to explore molecular strategies for augmenting catalytic function. Applying a suite of nuclear magnetic resonance, crystallography, and stopped-flow techniques to an enzyme designed for an elementary proton transfer reaction, we show how directed evolution gradually altered the conformational ensemble of the protein scaffold to populate a narrow, highly active conformational ensemble and accelerate this transformation by nearly nine orders of magnitude. Mutations acquired during optimization enabled global conformational changes, including high-energy backbone rearrangements, that cooperatively organized the catalytic base and oxyanion stabilizer, thus perfecting transition-state stabilization. The development of protein catalysts for many chemical transformations could be facilitated by explicitly sampling conformational substates during design and specifically stabilizing productive substates over all unproductive conformations.