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.