Docking simulation and competitive experiments validate the interaction between the 2,5-xylidine inhibitor and Rigidoporus lignosus laccase.
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.
Cambria
Maria Teresa
MT
Dipartimento di Scienze Chimiche, Universitá degli Studi di Catania, Viale A. Doria 6, Ed. 2 Citá Universitaria, I-95125 Catania, Italy.
Di Marino
Daniele
D
Falconi
Mattia
M
Garavaglia
Silvia
S
Cambria
Antonio
A
D000595:Amino Acid Sequence; D000814:Aniline Compounds / Q000737:chemistry* / Q000378:metabolism*; D001487:Basidiomycota / Q000737:chemistry / Q000201:enzymology* / Q000235:genetics; D001665:Binding Sites; D001667:Binding, Competitive; D020134:Catalytic Domain; D003198:Computer Simulation; D003460:Crystallization; D018360:Crystallography, X-Ray; D042845:Laccase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid
D000814:Aniline Compounds; C016835:2,5-xylidene; D042845:Laccase