Carbohydrate Binding Module Family 60

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

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CAZy DB link

https://www.cazy.org/CBM60.html

Ligand specificities

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:

X14 displays a classical distorted β-jelly-roll fold consisting of eight β-strands in two antiparallel β-sheets, each of four strands. The edges of the protein structure comprise five and three loops respectively, and one α-helix completes the structure (Ala 75- Glu 76- Asn 77). On one edge, three loops (5, 7 and 8) form a deep and wide cleft (≈ 17.4 Å broad and 5.5 Å deep). This site is furnished by two exposed tryptophans, Trp 85 and Trp 98, and the side-chain of His 100. Although Trp 85 lies parallel with the protein surface, Trp 98 is twisted by approximatively 91° so that the two residues are perpendicular to each other. Trp 85 is surrounded by loops 5 and 7 which appear to be highly mobile, with poor side-chain density. However, a disulphide bond between Cys 90 and Cys 101 runs across the cleft. As a result of space group constraints, the entrance to the cleft is partially occupied by the C-terminal His6-tag of a symmetry-related molecule. One calcium ion is found in the contact zone between two symmetry-related molecules, involving the main-chain carbonyl oxygen of the His 118 of the His6-tag of one molecule and the following residues of the other molecule: the main-chain O of His 100 (loop 8), OD1 of Asp 55, OD2 of Asp 60 and the O of Arg 59 (loop 5). Coordination is completed with a water molecule.

• Type: Include here Type A, B, or C and properties
• Features of ligand binding:

The ligand binding sites in CBMs that display a -sandwich fold comprise, typically, the concave surface presented by one of the-sheets, or at the end of the elliptical protein, within the loops connecting these two structural elements

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. The Biochemist, vol. 30, no. 4., pp. 26-32. Download PDF version.

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 |