5RG6 image
Entry Detail
PDB ID:
5RG6
Keywords:
Title:
Crystal Structure of Kemp Eliminase HG3.7 in unbound state, 277K
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2020-03-19
Release Date:
2020-07-22
Method Details:
Experimental Method:
Resolution:
1.35 Å
R-Value Free:
0.14
R-Value Work:
0.12
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Kemp Eliminase HG3
Mutations:V6I Q37K Q42M T44W K50Q R81G H83G T84C S89R Q90H A125N N130G N172M A234S T236L E237M W267F
Chain IDs:A, B
Chain Length:318
Number of Molecules:2
Biological Source:Thermoascus aurantiacus
Ligand Molecules
Primary Citation
Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico.
Nat Commun 11 4808 4808 (2020)
PMID: 32968058 DOI: 10.1038/s41467-020-18619-x

Abstact

The creation of artificial enzymes is a key objective of computational protein design. Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve activity. Here, we use room-temperature X-ray crystallography to study changes in the conformational ensemble during evolution of the designed Kemp eliminase HG3 (kcat/KM 146 M-1s-1). We observe that catalytic residues are increasingly rigidified, the active site becomes better pre-organized, and its entrance is widened. Based on these observations, we engineer HG4, an efficient biocatalyst (kcat/KM 103,000 M-1s-1) containing key first and second-shell mutations found during evolution. HG4 structures reveal that its active site is pre-organized and rigidified for efficient catalysis. Our results show how directed evolution circumvents challenges inherent to enzyme design by shifting conformational ensembles to favor catalytically-productive sub-states, and suggest improvements to the design methodology that incorporate ensemble modeling of crystallographic data.

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