4ETK: Crystal Structure Of E6a/l130d/a155h Variant Of De Novo Designed Serine Hydrolase, Northeast Structural Genomics Consortium (nesg) Target Or186

Citation:
Abstract
A challenge in the computational design of enzymes is that multiple properties, including substrate binding, transition state stabilization and product release, must be simultaneously optimized, and this has limited the absolute activity of successful designs. Here, we focus on a single critical property of many enzymes: the nucleophilicity of an active site residue that initiates catalysis. We design proteins with idealized serine-containing catalytic triads and assess their nucleophilicity directly in native biological systems using activity-based organophosphate probes. Crystal structures of the most successful designs show unprecedented agreement with computational models, including extensive hydrogen bonding networks between the catalytic triad (or quartet) residues, and mutagenesis experiments demonstrate that these networks are critical for serine activation and organophosphate reactivity. Following optimization by yeast display, the designs react with organophosphate probes at rates comparable to natural serine hydrolases. Co-crystal structures with diisopropyl fluorophosphate bound to the serine nucleophile suggest that the designs could provide the basis for a new class of organophosphate capture agents.
PDB ID: 4ETKDownload
MMDB ID: 100574
PDB Deposition Date: 2012/4/24
Updated in MMDB: 2012/06
Experimental Method:
x-ray diffraction
Resolution: 2.7  Å
Source Organism:
Similar Structures:
Biological Unit for 4ETK: monomeric; determined by author and by software (PISA)
Molecular Components in 4ETK
Label Count Molecule
Protein (1 molecule)
1
DE Novo Designed Serine Hydrolase
Molecule annotation
Chemical (1 molecule)
1
1
* Click molecule labels to explore molecular sequence information.

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