Docking Simulation and Competitive Experiments Validate the Interaction Between the 2,5-Xylidine Inhibitor and Rigidoporus lignosus Laccase |
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Authors: | Maria Teresa Cambria Daniele Di Marino Mattia Falconi Silvia Garavaglia Antonio Cambria |
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Affiliation: | 1. Dipartimento di Scienze Chimiche , Università degli Studi di Catania , Viale A. Doria 6, Ed. 2, Città Universitaria, I-95125 , Catania , Italy;2. Dipartimento di Biologia, Università Roma “Tor Vergata” and CIBB, Centro Interdipartimentale di Biostatistica e Bioinformatica , Via della Ricerca Scientifica, 1, 00133 , Rome , Italy;3. DISCAFF-INFM, Università del Piemonte orientale “A. Avogadro” , 28100 , Novara , Italy;4. Istituto Nazionale Biostrutture e Biosistemi , Consorzio Interuniversitario, Viale medaglie d'Oro 305, I-00136 , Roma , Italy |
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Abstract: | Abstract Laccases are polyphenol oxidases which oxidize a broad range of reducing substrates, preferably phenolic compounds, and their use in biotechnological applications is increasing. Recently, the first X-ray structure of active laccase from white rot fungus Rigidoporus lignosus has been reported containing a full complement of copper ions. Comparison among selected fungal laccases of known 3D structure has shown that the Rigidoporus lignosus laccase has a very high similarity with the Trametes versicolor laccase that, being co-crystallized with 2,5-xylidine, shows a well defined binding pocket for the substrate. Global sequence alignment between Rigidoporus lignosus and Trametes versicolor laccases shows 73% of identity but, surprisingly, there is no identity and neither conservative substitutions between the residues composing the loops directly contacting the 2,5-xylidine. Moreover the structural alignment of these two enzymes identifies in these loops a striking structural similarity proposing the question if 2,5-xylidine may bind in same enzyme pocket. Here we report the protein-ligand docking simulation of 3D structure of Rigidoporus lignosus laccase and 2,5-xylidine. Docking simulation analyses show that spatial conformation of the two 2,5-xylidine binding pockets, despite differences in the residues directly contacting the ligand, may arrange a similar pocket that allows a comparable accommodation of the inhibitor. To validate these results the binding of 2,5-xylidine in the substrate cavity has been confirmed by kinetic competitive experiments. |
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