Abstract
Biomass can be converted into sugars by a series of lignocellulolytic enzymes, which belong to the glycoside hydrolase (GH) families summarized in CAZy databases. Here, using a structural bioinformatics method, we analyzed the active site architecture of the main lignocellulolytic enzyme families. The aromatic amino acids Trp/Tyr and polar amino acids Glu/Asp/Asn/Gln/Arg occurred at higher frequencies in the active site architecture than in the whole enzyme structure. And the number of potential subsites was significantly different among different families. In the cellulase and xylanase families, the conserved amino acids in the active site architecture were mostly found at the −2 to +1 subsites, while in β-glucosidase they were mainly concentrated at the −1 subsite. Families with more conserved binding amino acid residues displayed strong selectivity for their ligands, while those with fewer conserved binding amino acid residues often exhibited promiscuity when recognizing ligands. Enzymes with different activities also tended to bind different hydroxyl oxygen atoms on the ligand. These results may help us to better understand the common and unique structural bases of enzyme-ligand recognition from different families and provide a theoretical basis for the functional evolution and rational design of major lignocellulolytic enzymes.
Highlights
Recognition between enzymes and their ligands is the most likely mechanism to cause promiscuity[17]
Among all of the components in lignocellulose, only cellulose and hemicellulose can be converted into fermentable sugars using microbial cellulase and hemicellulase[1], which include a variety of enzymes
GH5, GH6, GH7, GH9 and GH12 were selected as the target families of cellulase with 522, 63, 82, 157 and 65 sequences, respectively; GH10 had 335 sequences and GH11 had 267 sequences to represent xylanase; GH1 and GH3 contained 331 and 278 sequences to represent β -glucosidase (Supplementary Table S1, all data above was valid to October 2015)
Summary
Recognition between enzymes and their ligands is the most likely mechanism to cause promiscuity[17]. Three representative enzymes were selected, cellulase, xylanase and β -glucosidase, and statistical analyses of the biological information on their active site architectures were performed.
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