7t7y

From Proteopedia

The crystal structure of family 8 carbohydrate-binding module from Dictyostelium discoideum complexed with iodine atoms

Structural highlights

Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.81Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Deciphering how enzymes interact, modify, and recognize carbohydrates has long been a topic of interest in academic, pharmaceutical, and industrial research. Carbohydrate-binding modules (CBMs) are non-catalytic globular protein domains attached to carbohydrate-active enzymes (CAZymes) that strengthen enzyme affinity to substrates and increase enzymatic efficiency via targeting and proximity effects. CBMs are considered auspicious for various biotechnological purposes in textile, food, and feed industries, representing valuable tools in basic science research and biomedicine. Here, we present the first crystallographic structure of a CBM8 family member (CBM8), DdCBM8 from the slime mold Dictyostelium discoideum, which was identified attached to an endo-beta-1,4-glucanase (glycoside hydrolase family 9). We show that the planar carbohydrate binding site of DdCBM8, composed of aromatic residues, is similar to type A CBMs that are specific for crystalline (multi-chain) polysaccharides. Accordingly, pull-down assays indicated that DdCBM8 was able to bind insoluble forms of cellulose. However, affinity gel electrophoresis demonstrated that DdCBM8 also bound to soluble (single chain) polysaccharides, especially glucomannan, similar to type B CBMs, although it had no apparent affinity for oligosaccharides. Therefore, the structural characteristics and broad specificity of DdCBM8 represent exceptions to the canonical CBM classification. In addition, mutational analysis identified specific amino acid residues involved in ligand recognition, which are conserved throughout the CBM8 family. This advancement in the structural and functional characterization of CBMs contributes to our understanding of CAZymes and protein-carbohydrate interactions, pushing forward protein engineering strategies and enhancing the potential biotechnological applications of glycoside hydrolase accessory modules.

Unique properties of a Dictyostelium discoideum carbohydrate-binding module expand our understanding of CBM-ligand interactions.,Liberato MV, Campos BM, Tomazetto G, Crouch LI, Garcia W, Zeri ACM, Bolam DN, Squina FM J Biol Chem. 2022 Apr 1:101891. doi: 10.1016/j.jbc.2022.101891. PMID:35378128^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Liberato MV, Campos BM, Tomazetto G, Crouch LI, Garcia W, Zeri ACM, Bolam DN, Squina FM. Unique properties of a Dictyostelium discoideum carbohydrate-binding module expand our understanding of CBM-ligand interactions. J Biol Chem. 2022 Apr 1:101891. doi: 10.1016/j.jbc.2022.101891. PMID:35378128 doi:http://dx.doi.org/10.1016/j.jbc.2022.101891