6R3M

Family 11 Carbohydrate-Binding Module from Clostridium thermocellum in complex with beta-1,3-1,4-mixed-linked tetrasaccharide

Summary for 6R3M

• Entry DOI: 10.2210/pdb6r3m/pdb
• Related: 1V0A
• Descriptor: Endoglucanase H, beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-beta-D-glucopyranose, CALCIUM ION, ... (7 entities in total)
• Functional Keywords: ctcbm11 beta-1, 3-1, 4-mixed-linked glucan clostridium thermocellum, sugar binding protein
• Biological source: Hungateiclostridium thermocellum ATCC 27405
• Total number of polymer chains: 1
• Total formula weight: 21157.80

Authors

Ribeiro, D.O.,Carvalho, A.L. (deposition date: 2019-03-20, release date: 2020-02-05, Last modification date: 2024-01-24)

Primary citation

Ribeiro, D.O.,Viegas, A.,Pires, V.M.R.,Medeiros-Silva, J.,Bule, P.,Chai, W.,Marcelo, F.,Fontes, C.M.G.A.,Cabrita, E.J.,Palma, A.S.,Carvalho, A.L.
Molecular basis for the preferential recognition of beta 1,3-1,4-glucans by the family 11 carbohydrate-binding module from Clostridium thermocellum.
Febs J., 287:2723-2743, 2020

PubMed Abstract: Understanding the specific molecular interactions between proteins and β1,3-1,4-mixed-linked d-glucans is fundamental to harvest the full biological and biotechnological potential of these carbohydrates and of proteins that specifically recognize them. The family 11 carbohydrate-binding module from Clostridium thermocellum (CtCBM11) is known for its binding preference for β1,3-1,4-mixed-linked over β1,4-linked glucans. Despite the growing industrial interest of this protein for the biotransformation of lignocellulosic biomass, the molecular determinants of its ligand specificity are not well defined. In this report, a combined approach of methodologies was used to unravel, at a molecular level, the ligand recognition of CtCBM11. The analysis of the interaction by carbohydrate microarrays and NMR and the crystal structures of CtCBM11 bound to β1,3-1,4-linked glucose oligosaccharides showed that both the chain length and the position of the β1,3-linkage are important for recognition, and identified the tetrasaccharide Glcβ1,4Glcβ1,4Glcβ1,3Glc sequence as a minimum epitope required for binding. The structural data, along with site-directed mutagenesis and ITC studies, demonstrated the specificity of CtCBM11 for the twisted conformation of β1,3-1,4-mixed-linked glucans. This is mediated by a conformation-selection mechanism of the ligand in the binding cleft through CH-π stacking and a hydrogen bonding network, which is dependent not only on ligand chain length, but also on the presence of a β1,3-linkage at the reducing end and at specific positions along the β1,4-linked glucan chain. The understanding of the detailed mechanism by which CtCBM11 can distinguish between linear and mixed-linked β-glucans strengthens its exploitation for the design of new biomolecules with improved capabilities and applications in health and agriculture. DATABASE: Structural data are available in the Protein Data Bank under the accession codes 6R3M and 6R31.

PubMed: 31794092
DOI: 10.1111/febs.15162

Experimental method

X-RAY DIFFRACTION (1.45 Å)