7K4S

Crystal structure of Kemp Eliminase HG3.7

Summary for 7K4S

• Entry DOI: 10.2210/pdb7k4s/pdb
• Descriptor: Endo-1,4-beta-xylanase, SULFATE ION (3 entities in total)
• Functional Keywords: kemp elimination, directed evolution, hydrolase
• Biological source: Thermoascus aurantiacus
• Total number of polymer chains: 1
• Total formula weight: 33693.73

Authors

Padua, R.A.P.,Otten, R.,Bunzel, A.,Nguyen, V.,Pitsawong, W.,Patterson, M.,Sui, S.,Perry, S.L.,Cohen, A.E.,Hilvert, D.,Kern, D. (deposition date: 2020-09-16, release date: 2020-12-02, Last modification date: 2023-10-18)

Primary citation

Otten, R.,Padua, R.A.P.,Bunzel, H.A.,Nguyen, V.,Pitsawong, W.,Patterson, M.,Sui, S.,Perry, S.L.,Cohen, A.E.,Hilvert, D.,Kern, D.
How directed evolution reshapes the energy landscape in an enzyme to boost catalysis.
Science, 370:1442-1446, 2020

PubMed 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.

PubMed: 33214289
DOI: 10.1126/science.abd3623

Experimental method

X-RAY DIFFRACTION (2 Å)