Virtual investigation of the biomass conversion efficiency of three Streptomyces species

Abstract

Global worries about the gradual depletion of the non-renewable fossil fuel reserves, as well as the problem of environmental pollution, and global warming have prompted researchers to opt for more sustainable and environmentally friendly solutions. Converting biomass to bioethanol is a cost effective and inexpensive alternative to produce energy. The lytic polysaccharide monooxygenase (LPMO) enzyme of microbial origin represents an ideal solution because of their catalytic potential for the cleavage of the cellulosic biomass and the production of simple fermentable sugars. Here, we have described the 3D structures, the molecular functioning, as well as the cellulosic biomass conversion efficiency of three LPMOs belonging to three species of Streptomyces, S. albidoflavus, S. flaveus, and S. griseus. Analysis of the conserved domains of the amino acid sequences showed that the three enzymes belong to the LPMO-10 family and include an LPMO domain and a carbohydrate-binding domain. The enzyme of the species S. griseus further comprises two cellulose binding domain and cellulase/cellobiase CelA1 (Carbohydrate transport and metabolism) domain. Homology modeling of the 3D structures of the three enzymes was carried out by the SwissModel program, the models are then checked and validated. The analysis of the interactions at the active site level of the three modeled LPMOs showed the presence of conserved amino acids in all the studied enzymes, specially the His-His brace located around the copper ion. The result of the molecular docking with the cellotetraose substrate shows very close binding energies for the three LPMOs (-5.5 kcal/mol for S. griseus, and −5.3 kcal/mol for S. albidoflavus and S. flaveus) indicating the same affinities of these enzymes to the cellulosic substrates. The visualization of the interactions of cellotetraose within the catalytic sites of the enzymes showed the involvement of the amino acids His, Ala, Trp, Tyr, Phe, and Glu, which are well conserved in the two LPMOs of S. griseus and S. albidoflavus species suggesting a C1 oxidizing activity, whereas for the LPMO of S. flaveus, the Phe and Glu are replaced by Tyr and Gln, respectively suggesting a C1/C4 oxidizing AA10. The molecular information obtained during this study confirms the cellulose degradation potential of Streptomyces LPMOs, as well as their different modes of cellulose oxidation and provides strong evidence of the interest of these enzymes in the biomass conversion.