Molecule of the Month: Biodegradable Plastic
Bacteria build biodegradable plastic that could be better for the environment
Exploring the Structure
Since bacteria use plastic as a way to store energy, they also need an enzyme to degrade it when energy is needed. This is serendipitous for us, since these bacteria can also use this enzyme to break down bioplastics in landfills. The enzyme PHB depolymerase (PDB entry 2d81) is similar to our serine protease digestive enzymes, using an activated serine amino acid to chop the bioplastic chain into its component pieces. In this structure, researchers have mutated the serine to inactivate the enzyme, so they could visualize the molecular details of the complex between PHB depolymerase and a fragment of bioplastic.
Topics for Further Discussion
- Acetyl-CoA is used by many enzymes in the cell. Use the Ligand page for “ACO” to explore the structure of acetyl-CoA and find some of the PDB entries that include it.
- You can use the Structure Alignment View to compare the structures of PhaC from two different bacteria, PDB entries 5t6o and 5xav.
Related PDB-101 Resources
- Browse Biotechnology
- Browse Molecules and the Environment
- Browse Biological Energy
- R Geyer, J. Jambeck & KL Law (2017) Production, use, and fate of all plastics ever made. Scientific Advances 3, e1700782.
- V Urtuvia, P Villegas, M González & M Seeger (2014) Bacterial production of the biodegradable plastics polyhydroxyalkanoates. International Journal of Biological Macromolecules 70, 208-213.
- GQ Chen. (2009) A microbial polyhydroxyalkanoates (PHA) based bio- and materials industry. (2009) Chemical Society Reviews 38, 2434-2446.
- 5t6o: EC Wittenborn, M Jost, Y We, J Stubbe & CL Drennan (2016) Structure of the catalytic domain of the class I polyhydroxybutyrate synthase from Cupriavidus necator. Journal of Biological Chemistry 291, 25264-25277.
- 2d81: T Hisano, K Kasuya, Y Tezuka, N Ishii, T Kobayashi, M Shiraki, E Oroudjev, H Hansma, T Iwata, Y Doi, T Saito & K Miki (2006) The crystal structure of polyhydroxybutyrate depolymerase from Penicillium funiculosum provides insights into the recognition and degradation of biopolyesters. Journal of Molecular Biology 356, 993-1004.
- 4o9c: EJ Kim & KJ Kim (2014) Crystal structure and biochemical characterization of PhaA from Ralstonia eutropha, a polyhydroxyalkanoate-producing bacterium. Biochemical and Biophysical Research Communications 452, 124-129.
- 3vzs: K Matsumoto, Y Tanaka, T Watanabe, R Motohashi, K Ikeda, K Tobitani, M Yao, I Tanaka & S Taguchi (2013) Directed evolution and structural analysis of NADPH-dependent acetoacetyl coenzyme A (acetoacetyl-CoA) reductase from Ralstonia eutropha reveals two mutations responsible for enhanced kinetics. Applied Environmental Microbiology 79, 6134-6139.
- 5hz2: J Kim, YJ Kim, SY Choi, SY Lee & KJ Kim (2017) Crystal structure of Ralstonia eutropha polyhydroxyalkanoate synthase C-terminal domain and reaction mechanisms. Biotechnology Journal 12, 1600648.
- 5xav: MF Chek, SY Kim, T Mori, H Arsad, MR Samian, K Sudesh & T Hakoshima (2017) Structure of polyhydroxyalkanoate (PHA) synthase PhaC from Chromobacterium sp. USM2, producing biodegradable plastics. Scientific Reports 7, 5312.
December 2017, Luigi Di Costanzo & David S. Goodsellhttp://doi.org/10.2210/rcsb_pdb/mom_2017_12