Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism

• Published in: Scientific reports Vol. 6; no. 1; p. 23473
• Main Authors: Liberato, Marcelo V., Silveira, Rodrigo L., Prates, Érica T., de Araujo, Evandro A., Pellegrini, Vanessa O. A., Camilo, Cesar M., Kadowaki, Marco A., Neto, Mario de O., Popov, Alexander, Skaf, Munir S., Polikarpov, Igor
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 01-04-2016; Nature Publishing Group
• Subjects: 119/118; 631/114/2410; 631/45/607; 631/535/1266; Amino Acid Sequence; Bacillus licheniformis - enzymology; Bacterial Proteins - chemistry; Binding Sites; Biodiesel fuels; Biofuels; Biomass; Biomaterials; Carbohydrates; Catalytic Domain; Cellulase; Cellulose; Cellulose - analogs & derivatives; Cellulose - metabolism; Consensus Sequence; Crystal structure; Crystallography; Crystallography, X-Ray; Enzymes; Glycoside hydrolase; Humanities and Social Sciences; Hydrolase; Immunoglobulins; Life Sciences; Ligands; Lignocellulose; Models, Molecular; Molecular Dynamics Simulation; Motion; multidisciplinary; Mutagenesis, Site-Directed; Packing; Phylogeny; Protein Conformation; Protein Domains; Recombinant Proteins - chemistry; Scattering, Small Angle; Science; Sequence Alignment; Sequence Homology, Amino Acid; Substrate Specificity; Tetroses - metabolism; X-ray crystallography; X-Ray Diffraction; X-ray scattering
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/srep23473

Glycoside hydrolases (GHs) play fundamental roles in the decomposition of lignocellulosic biomaterials. Here, we report the full-length structure of a cellulase from
Bacillus licheniformis
(
Bl
Cel5B), a member of the GH5 subfamily 4 that is entirely dependent on its two ancillary modules (Ig-like module and CBM46) for catalytic activity. Using X-ray crystallography, small-angle X-ray scattering and molecular dynamics simulations, we propose that the C-terminal CBM46 caps the distal N-terminal catalytic domain (CD) to establish a fully functional active site via a combination of large-scale multidomain conformational selection and induced-fit mechanisms. The Ig-like module is pivoting the packing and unpacking motions of CBM46 relative to CD in the assembly of the binding subsite. This is the first example of a multidomain GH relying on large amplitude motions of the CBM46 for assembly of the catalytically competent form of the enzyme.