Structure of an iminosugar complex of a glycoside hydrolase family 5 lichenase provides insights into the active site

TmCel5B is a lichenase belonging to glycoside hydrolase family 5 subfamily 36 (GH5_36). To gain insights into the active site of this subfamily which contains multifunctional endoglycanases, we determined the crystal structure of TmCel5B in complex with an iminosugar, 1-deoxynojiromycin (DNJ). DNJ is bound to the -1 subsite, making a network of non-covalent interactions with the acid/base residue Glu139, the nucleophile Glu259, and with other residues that are conserved across the GH5 family. The catalytic site displayed a Glu-Arg-Glu triad of the catalytic glutamates that is unique to the GH5_36 subfamily. Structural comparison of active sites of GH5_36 homologs revealed divergent residues and loop regions that are likely molecular determinants of homolog-specific properties. Furthermore, a comparative analysis of the binding modes of iminocyclitol complexes of GH5 homologs revealed the structural basis of their binding to GH5 glycosidases, in which the subsite binding location, the interactions of the ligand with specific conserved residues, and the electrostatic interactions of the catalytic glutamates with the ring nitrogen, are crucial. (c) 2022 Elsevier B.V. and Societe Francaise de Biochimie et Biologie Moleculaire (SFBBM). All rights reserved.

Automated summary

TmCel5B is a lichenase that belongs to glycoside hydrolase family 5 subfamily 36 (GH5_36). The crystal structure of TmCel5B in complex with 1-deoxynojiromycin (DNJ) was determined to gain insights into the active site of this multifunctional endoglycanase-containing subfamily. The binding of DNJ to the -1 subsite involves non-covalent interactions with conserved residues and a unique Glu-Arg-Glu triad in the catalytic site. Comparative analysis further revealed molecular determinants of homolog-specific properties and the structural basis of iminocyclitol binding to GH5 glycosidases.