Carbohydrate Binding Module Family 8

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• Author: Elizabeth Ficko-Blean
• Responsible Curator: Elizabeth Ficko-Blean

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CAZy DB link

https://www.cazy.org/CBM08.html

Ligand specificities

These CBMs were originally called CBDVIII (family 8 cellulose-binding domains). DdCBM8, from the slime mold Dictyostelium discoideum CelA enzyme (270-6) binds insoluble forms of cellulose and xyloglucan, glucomannan, β-glucan, and hydroxyethyl cellulose (HEC), but not xylan[1]. Binding was detected using affinity gel electrophoresis, ITC and intrinsic fluorescence microscopy[1]. There is no evidence for binding to oligosaccharides [1].

Structural Features

[[File:DdCBM8.png|thumb|300px|right|Figure 1. A secondary structure representation of the Dictyostelium discoideum DdCBM8 from the CelA enzyme 7T7Z showing the hydrophobic platform which is its predicted planar binding site [1].

DdCBM8 is found C-terminal to the GH9 endo-(1,4)-beta-D-glucanase (cellulase) catalytic module of the CelA enzyme (270–6) and connected via a Thr-Glu-Thr-Pro type repeat linker [1, 2].

DdCBM8 has a beta-sandwich fold. W572, W574, and Y600 form a planar surface, akin to type A CBMs[1]. These residues align with the CBM29-2 1GWM binding site [3].

DdCBM8 appears to be broadly specific with both type A and type B CBM characteristics as it binds crystalline cellulose with a planar binding site, but has higher affinity for soluble glycans[1].

Content in this section should include, in paragraph form, a description of:

• Fold: Structural fold (beta trefoil, beta sandwich, etc.)
• Type: Include here Type A, B, or C and properties
• Features of ligand binding: Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc.

Functionalities

CelA and CelB (a cellulose binding domain with no known cellulase activity[4]) from Dictyostelium discoideum are predicted to be important for amoebae release from spores as transcriptomic experiments show that their mRNA levels are low in dormant spores, they rise during germination and then rapidly disappear after germination [2]. Cellulase activities from differently sized cellulases are also shown to increase during spore germination [5]. It is suggested that CelB might improve the substrate accessibility for CelA due to their concomitant expression during germination [4].

Content in this section should include, in paragraph form, a description of:

• Functional role of CBM: Describe common functional roles such as targeting, disruptive, anchoring, proximity/position on substrate.
• Most Common Associated Modules: 1. Glycoside Hydrolase Activity; 2. Additional Associated Modules (other CBM, FNIII, cohesin, dockerins, expansins, etc.)
• Novel Applications: Include here if CBM has been used to modify another enzyme, or if a CBM was used to label plant/mammalian tissues? Etc.

Family Firsts

First Identified

The first suggestion of binding to cellulose for the CBM8 family was determined by affinity gels in the absence of the CBM8 from CelA from Dictyostelium discoideum [2]. Clear binding studies were presented in [1].

First Structural Characterization

The first crystal structures are from DdCBM8, from the slime mold Dictyostelium discoideum [1], see 7T7Y and 7T7Z.

References

1. Liberato MV, Campos BM, Tomazetto G, Crouch LI, Garcia W, Zeri ACM, Bolam DN, and Squina FM. (2022). Unique properties of a Dictyostelium discoideum carbohydrate-binding module expand our understanding of CBM-ligand interactions. J Biol Chem. 2022;298(5):101891. DOI:10.1016/j.jbc.2022.101891 |
2. Ramalingam R, Blume JE, and Ennis HL. (1992). The Dictyostelium discoideum spore germination-specific cellulase is organized into functional domains. J Bacteriol. 1992;174(23):7834-7. DOI:10.1128/jb.174.23.7834-7837.1992 |
3. Charnock SJ, Bolam DN, Nurizzo D, Szabó L, McKie VA, Gilbert HJ, and Davies GJ. (2002). Promiscuity in ligand-binding: The three-dimensional structure of a Piromyces carbohydrate-binding module, CBM29-2, in complex with cello- and mannohexaose. Proc Natl Acad Sci U S A. 2002;99(22):14077-82. DOI:10.1073/pnas.212516199 |
4. Ramalingam R and Ennis HL. (1997). Characterization of the Dictyostelium discoideum cellulose-binding protein CelB and regulation of gene expression. J Biol Chem. 1997;272(42):26166-72. DOI:10.1074/jbc.272.42.26166 |
5. Blume JE and Ennis HL. (1991). A Dictyostelium discoideum cellulase is a member of a spore germination-specific gene family. J Biol Chem. 1991;266(23):15432-7. | Google Books | Open Library
6. Tomme P, Boraston A, McLean B, Kormos J, Creagh AL, Sturch K, Gilkes NR, Haynes CA, Warren RA, and Kilburn DG. (1998). Characterization and affinity applications of cellulose-binding domains. J Chromatogr B Biomed Sci Appl. 1998;715(1):283-96. DOI:10.1016/s0378-4347(98)00053-x |

7. P. Tomme, R.A.J. Warren, R.C. Miller Jr., D.G. Kilburn, N.R. Gilkes, in: J.N. Saddler, M.H. Penner (Eds.), Enzymatic Degradation of Insoluble Carbohydrates, American Chemical Society Symposium Series, 1995, p. 142.