Carbohydrate Binding Module Family 20

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• Author: ^^^Marie Sofie Møller^^^
• Responsible Curators: ^^^Birte Svensson^^^ and ^^^Stephan Janecek^^^

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CAZy DB link

https://www.cazy.org/CBM20.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: Structural fold (beta trefoil, beta sandwich, etc.)
• Type: Include here Type A, B, or C and properties
• Features of ligand binding: At least one but more typically two binding sites have been found in modules having the CBM20 complexed with bound carbohydrate. Such complexes have been studied for modules originating from several amylolytic enzymes, e.g. GH13_2 CGTase from Bacillus circulans [7], GH14 β-amylase from Bacillus cereus [8] and GH15 glucoamylase from Aspergillus niger [9], as well as the human glucan phosphatase laforin [10]. 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: The enzymes, of which the CBM20 module constitutes a domain, have predominantly specificities from the ɑ-amylase family GH13 or enzymes from families GH70 and GH77, but can also belong to families GH14 β-amylases and GH15 glucoamylases [11]. Among other CAZy GH families, the CBM20 is found associated with enzymes from other CAZy families GH57, GH119 and the auxiliary activities family AA13. Furthermore, CBM20 modules have been recognised in enzymes of which the catalytic domain is not classified in CAZy. Examples are phosphoglucan, water dikinase, glycerophosphodiester phosphodiesterase-5, laforin, and genethonin-1 [12]. The modules of family CBM20 have commonly been found in a single copy and usually appear without SBDs from other CBM families within the same protein, although co-occurence has been observed with CBM25, CBM34, and CBM48 [12].
• 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 CBM20 was recognised in the early 1980s the C-termini of glucoamylases from Aspergillus awamori [13] and Aspergillus niger [14, 15, 16].

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 |
7. Penninga D, van der Veen BA, Knegtel RM, van Hijum SA, Rozeboom HJ, Kalk KH, Dijkstra BW, and Dijkhuizen L. (1996). The raw starch binding domain of cyclodextrin glycosyltransferase from Bacillus circulans strain 251. J Biol Chem. 1996;271(51):32777-84. DOI:10.1074/jbc.271.51.32777 |
8. Mikami B, Adachi M, Kage T, Sarikaya E, Nanmori T, Shinke R, and Utsumi S. (1999). Structure of raw starch-digesting Bacillus cereus beta-amylase complexed with maltose. Biochemistry. 1999;38(22):7050-61. DOI:10.1021/bi9829377 |
9. Sorimachi K, Le Gal-Coëffet MF, Williamson G, Archer DB, and Williamson MP. (1997). Solution structure of the granular starch binding domain of Aspergillus niger glucoamylase bound to beta-cyclodextrin. Structure. 1997;5(5):647-61. DOI:10.1016/s0969-2126(97)00220-7 |
10. Raththagala M, Brewer MK, Parker MW, Sherwood AR, Wong BK, Hsu S, Bridges TM, Paasch BC, Hellman LM, Husodo S, Meekins DA, Taylor AO, Turner BD, Auger KD, Dukhande VV, Chakravarthy S, Sanz P, Woods VL Jr, Li S, Vander Kooi CW, and Gentry MS. (2015). Structural mechanism of laforin function in glycogen dephosphorylation and lafora disease. Mol Cell. 2015;57(2):261-72. DOI:10.1016/j.molcel.2014.11.020 |
11. Janeček Š, Svensson B, and MacGregor EA. (2011). Structural and evolutionary aspects of two families of non-catalytic domains present in starch and glycogen binding proteins from microbes, plants and animals. Enzyme Microb Technol. 2011;49(5):429-40. DOI:10.1016/j.enzmictec.2011.07.002 |
12. Janeček Š, Mareček F, MacGregor EA, and Svensson B. (2019). Starch-binding domains as CBM families-history, occurrence, structure, function and evolution. Biotechnol Adv. 2019;37(8):107451. DOI:10.1016/j.biotechadv.2019.107451 |

13. Hayashida, S., Kunisaki, S., Nakao, M. and Flor, P.Q. (1982) Evidence for raw starch-affinity site on Aspergillus awamori glucoamylase I. Agric. Biol. Chem., vol. 46, pp. 83-89.

14. Svensson, B., Pedersen, T.G., Svendsen, I., Sakai, T. and Ottesen, M. (1982) Characterization of two forms of glucoamylase from Aspergillus niger. Carlsb. Res. Commun. vol. 47, pp. 55-69.

15. Svensson, B., Larsen, K., Svendsen, I., and Boel, E. (1983) The complete amino acid sequence of the glycoprotein, glucoamylase G1, from Aspergillus niger. Carlsb. Res. Commun. vol. 48, pp. 529-544.

16. Boel E, Hjort I, Svensson B, Norris F, Norris KE, and Fiil NP. (1984). Glucoamylases G1 and G2 from Aspergillus niger are synthesized from two different but closely related mRNAs. EMBO J. 1984;3(5):1097-102. DOI:10.1002/j.1460-2075.1984.tb01935.x |