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PETase site-directed mutant I208V

This is one of the site-directed mutants of the PETase we designed, we change the 208th amino acid isoleucine(I) with valine(V). The module is the Saccharomyces cerevisiae codon optimization version of PETase gene. We used site-directed mutagenesis PCR to obtain this mutant.

Sequence and Features

Results

Rational Design

Serine-based Catalytic Triad Mechanism & 3D Model Simulation

Since PETase was found to contain a GWSMG motif in accordance with the GXGXG motif^[2], which is characteristic and highly conserved in α/β hydrolase fold family, we simulated a best fit model for PETase by SWISSMODEL with a template as Thc_Cut2. As expected, the homology model of PETase displays a canonical α/β hydrolase fold with a Ser¹⁶¹-His²³⁷-Asp²³⁷ catalytic triad and a preformed oxyanion hole (Fig.1), suggesting a classic serine hydrolase mechanism.

Mutation Design

Based on the simulated 3D structure, we found the 208th (with signal peptide excluded) amino acid residue situates right over the catalytic triad, which is an isoleucine(Fig.2). It is apperant that the interaction of catalytic triad with substrate would be inhibited due to the space oppcupied by 208th isoleucine. So we decided to substitue 208th isoleucine with another smaller amino acid.

However, as the isoleucine is the most hydrophobic amino acid, it takes risk to substitue it with another one, as it may lead to the hydrophobic amino acid decreasing. On balance, we chose valine as substitution, for its hydrophobicity is quite close to isoleucine, and the volume of valine is much smaller than that of isoleucine.

The 3D structure of mutant I208V is as Fig.3. Comparing to wild-type PETase(Fig.2), the mutant I208V exposes the catalytic triad much more widely. And the assay shows the stratety worked well for improving PET hydrolysis activity. The results are as follows.

Assay system—CFPS system

CFPS system

Cell-free protein synthesis(CFPS) is a widely used method in molecular biology. Production of proteins using cell-free protein synthesis usually takes a few hours, in contrast to production of proteins in cells, which typically takes days to weeks. In fact, even first-time users can often obtain newly synthesized proteins in one day using a commercial system.

The diversity of the cell-free systems allows in vitro synthesis of a wide range of proteins for a variety of downstream applications, such as screeening of enzymes activities. In the post-genomic era, cell-free protein synthesis has rapidly become the preferred approach for high-throughput functional and structural studies of proteins and a versatile tool for in vitro protein evolution and synthetic biology^[1].

Plasmid construction and expression in CFPS system

Ligaion of digested pRset_CFP-1, digested CFP gene and digested PETase(I208V) gene in accordance with the 1:5:5 molecular ratio. The newly constructed plasmid is called pRset_CFP-1_PETase-I208V. Than , the plasmids pRset_CFP-1_PETase-I208V was put into the CFPS(Cell-Free Protein Synthesis) to synthesis the enzymes we expected.

Degradation data

After the enzymes were expressed in the system successfully, we used the proteins we got to degrade PET and detected the degradation product, MHET, which has no other characteristic adsorption peak except at 260nm.

Reference

[1]Shaorong Chong. Overview of Cell-Free Protein Synthesis: Historic Landmarks, Commercial Systems, and Expanding Applications. Current Protocols in Molecular Biology 16.30.1-16.30.11, October 2014 DOI: 10.1002/0471142727.mb1630s108