In this study we report the crystal structure of a laccase-like multi copper oxidase (LMCO) from the thermophilic fungus Thermothelomyces thermophila, named TtLMCO1, which is an enzyme with no close structural homologues. As a three-domain laccase, TtLMCO1 structure indicates that the enzyme combines distinct characteristics of different members of the MCO superfamily. TtLMCO1 shares a similar substrate-binding site architecture with ascorbate oxidase of Curcubita pepo. At the same time, as a fungal LMCO, TtLMCO1 is able to oxidize a wide spectrum of phenolic compounds. Docking simulations with substrates that are oxidized by TtLMCO1 provide evidence that substrate specificity of these metallo-proteins is not exclusively related to their redox potential but also on the architecture of the binding site and the side chain flexibility of specific amino acids.