Carbohydrate Binding Module Family 62

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• Author: ^^^Cedric Montanier^^^
• Responsible Curator: ^^^Harry Gilbert^^^

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CAZy DB link

https://www.cazy.org/CBM62.html

Ligand specificities

The only known crystallographic structure of a carbohydrate-binding module of family 62 is the CtCBM62 one. Moreover, its structure has been solved in complex with a xyloglucan oligosaccharide, a 61-α-D-galactosyl mannotriose (GM3) or arabinose. Those sugar complexed crystal structures of CtCBM62 revealed that the interactions between the protein and the α-L pyranose form of the pentose sugar arabinose and galactose are highly conserved. Recognition of an axial O4 is thus a key determinant for the specificity of CtCBM62 for galactose and arabinopyranose, as opposed to mannose, glucose and xylose. Isothermal titration calorimetry revealed affinity for a wild set of galactose and/or arabinose containing polysaccharides such as galactomannan, xyloglucan, arabinogalactan and arabinan. Regarding the location of the ligand-binding site, in the loops that connect the β-sheets, CtCBM62 recognises terminal sugars.

Mention here all major natural ligand specificities that are found within a given family (also plant or mammalian origin). Certain linkages and promiscuity would also be mentioned here if biologically relevant.

Note: Here is an example of how to insert references in the text, together with the "biblio" section below: Please see these references for an essential introduction to the CAZy classification system: [1, 2]. CBMs, in particular, have been extensively reviewed [3, 4, 5, 6].

Structural Features

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

• Fold:

The crystal structure of CtCBM62 presents a classic β-jelly-roll fold, consisting of five major antiparallel β-strands on one face (β1, 2, 4, 5 and 7) and three antiparallel β-strands on the other face (β3, 6 and 8). Two α-helixes and five loops on the top of the β-jelly-roll complete the structure. A single structural calcium ion is found between the beginning of strand β-8 and the end of helix α-1. It displays typical hepta-coordination and is coordinated to the main-chain O of residues Lys 27, Asp 32 and Ala 132, the Oε2 of Asp 30 and Glu 133, and a bidentate interaction with both the main-chain carbonyl and Oε2 of Thr 35. The calcium ions in each molecule in the asymmetric unit are face to face (distant of 12.33 Å), positioning the loops containing the residues Asp 30, Gly 31 and Asp 32 opposite each other and at a distance of ≈ 4 Å.

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

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

Insert archetype here, possibly including very brief synopsis.

First Structural Characterization

Insert archetype here, possibly including very brief synopsis.

References

1. Davies, G.J. and Sinnott, M.L. (2008) Sorting the diverse: the sequence-based classifications of carbohydrate-active enzymes. Biochem. J. (BJ Classic Paper, online only). DOI: 10.1042/BJ20080382

2. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, and Henrissat B. (2009). The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2009;37(Database issue):D233-8. DOI:10.1093/nar/gkn663 |
3. Boraston AB, Bolam DN, Gilbert HJ, and Davies GJ. (2004). Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem J. 2004;382(Pt 3):769-81. DOI:10.1042/BJ20040892 |
4. Hashimoto H (2006). Recent structural studies of carbohydrate-binding modules. Cell Mol Life Sci. 2006;63(24):2954-67. DOI:10.1007/s00018-006-6195-3 |
5. Shoseyov O, Shani Z, and Levy I. (2006). Carbohydrate binding modules: biochemical properties and novel applications. Microbiol Mol Biol Rev. 2006;70(2):283-95. DOI:10.1128/MMBR.00028-05 |
6. Guillén D, Sánchez S, and Rodríguez-Sanoja R. (2010). Carbohydrate-binding domains: multiplicity of biological roles. Appl Microbiol Biotechnol. 2010;85(5):1241-9. DOI:10.1007/s00253-009-2331-y |