The crystal structure of LC-cutinase with PET-degrading activity was determined. Then, the mutations were introduced into LC-cutinase and two proteases (Tk-subtilisin and Tk-SP) with abnormal prion-degrading activity based on their structures to improve their enzymatic properties. As a result, the LC-cutinase derivative with enhanced stability, the Tk-subtilisin derivative with increased maturation rate, and the Tk-SP derivative with high stability in the presence of EDTA were constructed. In addition, two thermostable cellulases were isolated from leaf-branch compost by a metagenomic approach and their crystal structures were determined.