Molecule of the Month: Plastic-eating Enzymes
Researchers are looking to Nature to find ways to dispose of discarded plastic.
Exploring the Structure
Engineered PET Hydrolase
PDB ID 7vve includes an engineered PET-breaking enzyme with enhanced plastic-digesting ability and greater thermal stability. The structure includes MHET bound in the active site and reveals how several mutations can enhance the activity of the enzyme. Two neighboring positions are changed to cysteine, which together form a disulfide bridge that makes the enzyme more stable to heat. Two other changes reduce the size of amino acids flanking the active site, presumably making it more accessible to plastic polymer chains. The enzyme uses a classic serine-histidine-aspartate catalytic triad like those seen in serine proteases. In order to determine the structure with the plastic fragment bound in the active site, the serine was changed to alanine. To explore this structure in more detail and compare it with the wild type cutinase enzyme (PDB ID 4eb0), click on the image for an interactive JSmol.
Topics for Further Discussion
- Many structures of engineered plastic-eating enzymes are available in the PDB archive. To find them, start with any structure of the enzyme and then use the “Find similar proteins by: Sequence” (in the “Macromolecules” section of each Structure Summary Page). The changes are typically minimal, so a 80% or 90% sequence identity will return a useful list.
- You can easily compare engineered structures and the wild type structures using the “Pairwise Structure Alignment” feature in the “Analyze” tab.
Related PDB-101 Resources
- Browse Biotechnology
- Browse Molecules and the Environment
- Chow, J., Perez-Garcia, P., Dierkes, R., Streit, W.R. (2022) Microbial enzymes will offer limited solutions to the global plastic pollution crisis. Microbial Biotechnology doi: 10.1111/1751-7915.14135
- 7vve: Zeng, W., Li, X., Yang, Y., Min, J., Huang, J.-W., Liu, W., Niu, D., Yang, X., Han, X., Zhang, L., Dai, L., Chen, C.-C., Guo, R.-T. (2022) Substrate-Binding Mode of a Thermophilic PET Hydrolase and Engineering the Enzyme to Enhance the Hydrolytic Efficacy. ACS Catal 12: 3033-3040
- 6qga: Palm, G.J., Reisky, L., Bottcher, D., Muller, H., Michels, E.A.P., Walczak, M.C., Berndt, L., Weiss, M.S., Bornscheuer, U.T., Weber, G. (2019) Structure of the plastic-degrading Ideonella sakaiensis MHETase bound to a substrate. Nat Commun 10: 1717
- 5y0m: Negoro, S., Shibata, N., Lee, Y.H., Takehara, I., Kinugasa, R., Nagai, K., Tanaka, Y., Kato, D.I., Takeo, M., Goto, Y., Higuchi, Y. (2018) Structural basis of the correct subunit assembly, aggregation, and intracellular degradation of nylon hydrolase. Sci Rep 8: 9725-9725
- 5xh3: Han, X., Liu, W., Huang, J.W., Ma, J., Zheng, Y., Ko, T.P., Xu, L., Cheng, Y.S., Chen, C.C., Guo, R.T. (2017) Structural insight into catalytic mechanism of PET hydrolase. Nat Commun 8: 2106-2106
- 2zm0: Kawashima, Y., Ohki, T., Shibata, N., Higuchi, Y., Wakitani, Y., Matsuura, Y., Nakata, Y., Takeo, M., Kato, D., Negoro, S. (2009) Molecular design of a nylon-6 byproduct-degrading enzyme from a carboxylesterase with a beta-lactamase fold. FEBS J 276: 2547-2556
January 2023, David Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2023_1