Carbohydrate Binding Module Family 32

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• Author: ^^^Elizabeth Ficko-Blean^^^
• Responsible Curator: ^^^Al Boraston^^^

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CAZy DB link

https://www.cazy.org/CBM32.html

Ligand specificities

In 1994 the first CBM32 structure and canonical ligand specificity for D-galactose were determined from a fungal galactose oxidase[1]

A CBM32 from a multi-modular sialidase produced by Micromonospora viridifaciens has galactose and lactose binding specificity [2, 3].

A CBM32 from a Cellvibrio mixtus family 16 glycoside hydrolase binds laminarin and pustulan [4]

A CBM32 from a Clostridium thermocellum mannanase has demonstrated binding on the non-reducing end of β-mannans and β-1,4-linked mannooligosaccharides[5]

A periplasmic CBM32 from Yersinia enterolitica binds polygalaturonic acid components of pectin [6].

The Clostridium perfringens CBM32s have been well studied and many of their ligand specificities determined as follows: D-galactose, N-acetyl-D-galactosamine[7, 8, 9], D-galactose-β-1,4-N-acetyl-D-glucosamine (LacNAc), L-fucose-α-1,2-D-galactose-β-1,4-N-acetyl-D-glucosamine (type II blood group H-trisaccharide) [9] N-acetyl-D-glucosamine, N-acetyl-D-glucosamine-β-1,3-N-acetyl-D-galactosamine, N-acetyl-D-glucosamine-β-1,2-D-mannose, N-acetyl-D-glucosamine-β-1,3-D-mannose (non-biological) [10], N-acetyl-D-glucosamine-α-1,4-D-galactose[8]

Some members of the family 32 CBMs have demonstrated a degree of promiscuity in their binding, these include CpCBM32-2 from the NagH enzyme and CpCBM32C from the NagJ enzyme, both produced by Clostridium perfringens[9, 10].

Please see these references for an essential introduction to the CAZy classification system: [11, 12]. CBMs, in particular, have been extensively reviewed [13, 14, 15, 16].

Structural Features

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

• Fold: beta sandwich
• Type: This family falls into the Type C category of lectin-like CBMs[17]. Typically members of the CBM32 family show fairly weak binding (K_as in the mM^-1 and low μM^-1 range).

• Features of ligand binding: The binding site is located at the terminal loop region within the CBM32 family. The binding sites are surface located and in some cases quite shallow and designed to bind monosaccharides or short oligosaccharides. Variability within the apical loop region within the family confers the different ligand specificities. In most cases the CBM32 family interacts with the non-reducing end of the sugars, however, this is not always the case as demonstrated by the CBM32 from Y. enterocolitica which binds polygalacturonic polymers[6]. important residues for binding (W, Y, F, subsites), 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: CBM32s are often, but not always, appended to carbohydrate active enzymes. The types of catalytic modules that the CBM32 members are associated with vary widely and include sialidases, β-N-acetylglucosaminidases, α-N-acetylglucosaminidases, and mannanases (to name a few). There are now examples of CBM32s that are independant of a catalytic module. In enteric bacteria the CBM32 motif may occur more than once in the same enzyme and they may or may not share the same ligand specifities suggesting the possibility of heterogenic multivalent binding. Other modules that may be associated in the same enzymes are different families of CBMs, FNIII domains, and cohesin and dockerin domains.
• 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. Ito N, Phillips SE, Yadav KD, and Knowles PF. (1994). Crystal structure of a free radical enzyme, galactose oxidase. J Mol Biol. 1994;238(5):794-814. DOI:10.1006/jmbi.1994.1335 |
2. Gaskell A, Crennell S, and Taylor G. (1995). The three domains of a bacterial sialidase: a beta-propeller, an immunoglobulin module and a galactose-binding jelly-roll. Structure. 1995;3(11):1197-205. DOI:10.1016/s0969-2126(01)00255-6 |
3. Newstead SL, Watson JN, Bennet AJ, and Taylor G. (2005). Galactose recognition by the carbohydrate-binding module of a bacterial sialidase. Acta Crystallogr D Biol Crystallogr. 2005;61(Pt 11):1483-91. DOI:10.1107/S0907444905026132 |
4. Centeno MS, Goyal A, Prates JA, Ferreira LM, Gilbert HJ, and Fontes CM. (2006). Novel modular enzymes encoded by a cellulase gene cluster in Cellvibrio mixtus. FEMS Microbiol Lett. 2006;265(1):26-34. DOI:10.1111/j.1574-6968.2006.00464.x |
5. Mizutani K, Fernandes VO, Karita S, Luís AS, Sakka M, Kimura T, Jackson A, Zhang X, Fontes CM, Gilbert HJ, and Sakka K. (2012). Influence of a mannan binding family 32 carbohydrate binding module on the activity of the appended mannanase. Appl Environ Microbiol. 2012;78(14):4781-7. DOI:10.1128/AEM.07457-11 |
6. Abbott DW, Hrynuik S, and Boraston AB. (2007). Identification and characterization of a novel periplasmic polygalacturonic acid binding protein from Yersinia enterolitica. J Mol Biol. 2007;367(4):1023-33. DOI:10.1016/j.jmb.2007.01.030 |
7. Boraston AB, Ficko-Blean E, and Healey M. (2007). Carbohydrate recognition by a large sialidase toxin from Clostridium perfringens. Biochemistry. 2007;46(40):11352-60. DOI:10.1021/bi701317g |
8. Ficko-Blean E, Stuart CP, Suits MD, Cid M, Tessier M, Woods RJ, and Boraston AB. (2012). Carbohydrate recognition by an architecturally complex α-N-acetylglucosaminidase from Clostridium perfringens. PLoS One. 2012;7(3):e33524. DOI:10.1371/journal.pone.0033524 |
9. Ficko-Blean E and Boraston AB. (2006). The interaction of a carbohydrate-binding module from a Clostridium perfringens N-acetyl-beta-hexosaminidase with its carbohydrate receptor. J Biol Chem. 2006;281(49):37748-57. DOI:10.1074/jbc.M606126200 |
10. Ficko-Blean E and Boraston AB. (2009). N-acetylglucosamine recognition by a family 32 carbohydrate-binding module from Clostridium perfringens NagH. J Mol Biol. 2009;390(2):208-20. DOI:10.1016/j.jmb.2009.04.066 |

11. 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

12. 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 |
13. 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 |
14. 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 |
15. 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 |
16. 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 |
17. Boraston AB, Notenboom V, Warren RA, Kilburn DG, Rose DR, and Davies G. (2003). Structure and ligand binding of carbohydrate-binding module CsCBM6-3 reveals similarities with fucose-specific lectins and "galactose-binding" domains. J Mol Biol. 2003;327(3):659-69. DOI:10.1016/s0022-2836(03)00152-9 |