Polyphenol oxidases (PPOs) are a group of Cu-containing enzymes distributed from bacteria to humans, exhibiting two activities, catechol oxidase and tyrosinase. However, their precise mechanism of action and the structural elements that determine the distinction between the two activities are yet to be fully understood. In nature, PPOs catalyse the oxidation of several phenols to o-quinones, considerably affecting colour, flavour, nutritional properties, shelf life and therefore market values of numerous vegetables and fruits. On the other hand, PPOs have been widely employed as biocatalysts in many reactions, with a vast spectrum of applications in food, pharmaceutical, and cosmetic industries. One of the most important although least studied application of PPOs is as sensitive detectors of phenol derivatives in polluted waters as well as efficient tools towards biodegradation of these substances.

In a previous work, the use of a PPO from the thermophilic fungus Thermothelomyces thermophila (TtPPO), for the degradation of chlorophenols (CPs), contagious by-products of various pesticides, was presented and evaluated. Based on a homology model and available literature on PPO structure-function relations, point mutations were designed, that led to TtPPO variants with altered activity. In order to shed light on the structure-function relations of TtPPO, we solved the structure of specific TtPPO mutant (G292N) (PDB code 6Z1S). Unfortunately, subsequent efforts to determine TtPPO structure in complex with various ligands or substrate analogues have not been yet successful.

The present work attempts to shed light on the structural determinants of TtPPO function, by performing protein-ligand docking experiments via YASARA software. The docking results are compared with the biochemical data, and the role of specific aminoacids in TtPPO function is discussed. Observations concerning the binding of the different substrates to the active site of the enzyme, i.e the identification of the amino acids involved in this process, extracted form high-resolution structural models, would allow for structure-based design and production of a more potent biocatalyst for the bioremediation of CPs, providing an economic, effective and sustainable tool for wastewater treatment.