How can databases contribute to a solution of the plastics waste problem?
For an efficient enzymatic degradation of plastics, we see four challenges. First, enzyme families other than α/β-hydrolases should be considered. For instance, laccases or peroxidases can also act on PUR41. First reports have been published but fell short in the identification of proteins and genes. Enzymatic or non-enzymatic degradation of other plastics components such as dyes or additives from commercial sources might need further investigations, too. Second, there is an increasing need for comparable data on plastics degradation. The comparability and reproducibility of data on enzymatic plastics degradation is impeded by the variety of possible substrates, e.g., in case of plastics built from several types of monomers. Furthermore, physical properties of plastic materials can differ remarkably among different commercial suppliers, e.g., thickness of plastic foils, number of additives, or crystallinity. Finally, incorrect annotation of genome and metagenome datasets has resulted in the accumulation of many false positive plastic degrading enzymes in various publications but also in PMBD. Removing these from the data bases is a major task.
Within this setting the PAZy database provides information on several well studied enzymes supplemented by the protein sequences and structures of homologous sequences, which enables the search for novel candidates and the design of enzyme variants. Most protein sequences and functional data are available for PETases, for which several positions were already assessed experimentally for substrate binding or thermostability in earlier studies from literature (Table 2 ). The standard numbering scheme of PETase homologues facilitates the comparison of different amino acid positions from literature and the identification of sequence motifs for PETases, as shown for the comparison between Is PETase, LCC, and other PETase homologues. In upcoming studies, the PAZy database will be updated to cover sequences from other protein family databases than the LED, depending on the availability of structures and biochemical data. Finally, the underlying web platform of the PAZy database makes it easier to share knowledge on various plastics degrading enzymes in a more comparable way. Thus, it can be expected that the suggested sequence motifs for PETases or PURases will be refurbished, as more experimental data on residues for substrate binding or thermostability are made available in the future.