6GBJ

Repertoires of functionally diverse enzymes through computational design at epistatic active-site positions

Summary for 6GBJ

• Entry DOI: 10.2210/pdb6gbj/pdb
• Descriptor: Parathion hydrolase, FORMIC ACID, ZINC ION, ... (6 entities in total)
• Functional Keywords: phosphotriesterase, hydrolase
• Biological source: Brevundimonas diminuta (Pseudomonas diminuta)
• Total number of polymer chains: 1
• Total formula weight: 37676.99

Authors

Khersonsky, O.,Lipsh, R.,Avizemer, Z.,Goldsmith, M.,Ashani, Y.,Leader, H.,Dym, O.,Rogotner, S.,Trudeau, D.,Tawfik, D.S.,Fleishman, S.J. (deposition date: 2018-04-15, release date: 2018-10-24, Last modification date: 2024-01-17)

Primary citation

Khersonsky, O.,Lipsh, R.,Avizemer, Z.,Ashani, Y.,Goldsmith, M.,Leader, H.,Dym, O.,Rogotner, S.,Trudeau, D.L.,Prilusky, J.,Amengual-Rigo, P.,Guallar, V.,Tawfik, D.S.,Fleishman, S.J.
Automated Design of Efficient and Functionally Diverse Enzyme Repertoires.
Mol. Cell, 72:178-186.e5, 2018

PubMed Abstract: Substantial improvements in enzyme activity demand multiple mutations at spatially proximal positions in the active site. Such mutations, however, often exhibit unpredictable epistatic (non-additive) effects on activity. Here we describe FuncLib, an automated method for designing multipoint mutations at enzyme active sites using phylogenetic analysis and Rosetta design calculations. We applied FuncLib to two unrelated enzymes, a phosphotriesterase and an acetyl-CoA synthetase. All designs were active, and most showed activity profiles that significantly differed from the wild-type and from one another. Several dozen designs with only 3-6 active-site mutations exhibited 10- to 4,000-fold higher efficiencies with a range of alternative substrates, including hydrolysis of the toxic organophosphate nerve agents soman and cyclosarin and synthesis of butyryl-CoA. FuncLib is implemented as a web server (http://FuncLib.weizmann.ac.il); it circumvents iterative, high-throughput experimental screens and opens the way to designing highly efficient and diverse catalytic repertoires.

PubMed: 30270109
DOI: 10.1016/j.molcel.2018.08.033

Experimental method

X-RAY DIFFRACTION (1.63 Å)