Carbohydrate Binding Module Family 100

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• Author: Guanchen Liu
• Responsible Curator: Yaoguang Chang

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CAZy DB link

https://www.cazy.org/CBM100.html

Ligand specificities

Figure 1. Domain analysis of the parent enzyme of PhCBM100.The enzyme consists of a signal peptide (1-23 amino acids), a PL29 domain (68-399 amino acids), a CBM100 domain (viz., PhCBM100; 555-785 amino acids) and a C-terminal sorting domain (786-851 amino acids).

The first characterized member of the CBM100 family, PhCBM100[1], was found in a PL29 putative chondroitin lyase from Polaribacter haliotis. PhCBM100 bound specifically to chondroitin sulfates (CSs) including CS-A, CS-C and fucosylated chondroitin sulfate from sea cucumber Apostichopus japonicus, whereas incapable of binding to other glycosaminoglycans or polyuronic acids. By affinity electrophoresis assays, PhCBM100 displays high affinity for CS-A and CS-C with the K_a values of 2.1×10⁶ M^-1 and 6.0×10⁶ M^-1, respectively.

Structural Features

Figure 2. Structure of PhCBM100. (A) Schematic representation of PhCBM100 showing helices in yellow and strands in cyan. (B) Detailed view of the putative PhCBM100 binding site. The surface is colored by electrostatic potential, from blue (positive charge) to red (negative charge).

The 1.55 Å resolution X-ray crystal structure of PhCBM100 (PDB 8jiy) exhibited a β-sandwich fold formed by two antiparallel comprised of 10 β-strands and 2 helices. A groove with both a distinct positive charge and a high degree of conserved residues is proposed as the binding site, enriched with hydrophilic amino acids. As the result of molecular docking, the basic amino acid residues (e.g., Lys-40, Arg-122 and Arg-201) of PhCBM100 may contribute to CS binding through the ionic contacts.

Functionalities

PhCBM100 is a component of a PL29 enzyme that displays chondroitin-sulfate ABC endolyase activity, consistent with the PhCBM100 specificity. The in situ visualization of chondroitin sulfate in animal tissues (e.g., chicken cartilage, bovine muscle, and porcine laryngeal cartilage) was realized by utilizing a fluorescent probe constructed by fusing PhCBM100 with a green fluorescent protein.

Family Firsts

First Identified

The chondroitin sulfate binding PhCBM100 from the P. haliotis PL29 putative chondroitin lyase was the first member of the family to be identified and characterized.

First Structural Characterization

PhCBM100 was also the first structurally characterized CBM100.

References

1. Liu G, Chang Y, Mei X, Chen G, Zhang Y, Jiang X, Tao W, and Xue C. (2024). Identification and structural characterization of a novel chondroitin sulfate-specific carbohydrate-binding module: The first member of a new family, CBM100. Int J Biol Macromol. 2024;255:127959. DOI:10.1016/j.ijbiomac.2023.127959 |