4O5S

Crystal structure of Diels-Alderase CE11

Summary for 4O5S

• Entry DOI: 10.2210/pdb4o5s/pdb
• Related: 1E1A 3I1C 3U0S 4O5T
• Descriptor: Diisopropyl-fluorophosphatase (2 entities in total)
• Functional Keywords: protein engineering, computer-aided design, diels-alder reaction, enzyme design, directed evolution, substrate specificity, beta-propeller, helix-loop-helix, de novo protein, artificial catalyst, diels-alderase, catalyst for cycloaddition, hydrolase
• Biological source: Loligo vulgaris (Common European squid)
• Total number of polymer chains: 2
• Total formula weight: 74516.42

Authors

Beck, T.,Preiswerk, N.,Mayer, C.,Hilvert, D. (deposition date: 2013-12-20, release date: 2014-06-04, Last modification date: 2023-11-08)

Primary citation

Preiswerk, N.,Beck, T.,Schulz, J.D.,Milovnik, P.,Mayer, C.,Siegel, J.B.,Baker, D.,Hilvert, D.
Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase.
Proc.Natl.Acad.Sci.USA, 111:8013-8018, 2014

PubMed Abstract: By combining targeted mutagenesis, computational refinement, and directed evolution, a modestly active, computationally designed Diels-Alderase was converted into the most proficient biocatalyst for [4+2] cycloadditions known. The high stereoselectivity and minimal product inhibition of the evolved enzyme enabled preparative scale synthesis of a single product diastereomer. X-ray crystallography of the enzyme-product complex shows that the molecular changes introduced over the course of optimization, including addition of a lid structure, gradually reshaped the pocket for more effective substrate preorganization and transition state stabilization. The good overall agreement between the experimental structure and the original design model with respect to the orientations of both the bound product and the catalytic side chains contrasts with other computationally designed enzymes. Because design accuracy appears to correlate with scaffold rigidity, improved control over backbone conformation will likely be the key to future efforts to design more efficient enzymes for diverse chemical reactions.

PubMed: 24847076
DOI: 10.1073/pnas.1401073111

Experimental method

X-RAY DIFFRACTION (1.8 Å)