Carbohydrate Binding Module Family 16

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• Author: Maria Matard-Mann
• Responsible Curator: ^^^Elizabeth Ficko-Blean^^^

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CAZy DB link

https://www.cazy.org/CBM16.html

Ligand specificities

Family 16 CBMs are found essentially in bacteria (only 4 are in archaea compared to 494 bacteria inventoried in CAZY). They are also found associated with catalytic modules belonging mainly to 4 families of CAZymes: GH5 mannanase [1, 2], GH16 kappa carrageenase [3, 4, 5], GH18 chitinase [6] and PL18 alginate lyase [7, 8]. Binding to glucomannan and kappa-carrageenan has been demonstrated. CBM16 binding to glucomannan (mixed β-1,4-linked polymer contains both glucose and mannose) has been studied by mean of ITC analysis and crystallography of complex with pentomannan and pentoglucan [1, 2]. Conversely, binding to kappa-carrageenan has been shown by a double-blind approach on polysaccharide microarray [5].

Structural Features

CBM16 is a type B CBM family, with a characteristic concave cleft, allowing the binding of substrate longer than triose. The ligand binding cleft shows some promiscuity as it can accommodate both pentoses (glucose and mannose), but only in the context of planar polymer like β-1,4-glucans, and not helical β-1,3-glucans [1]. The crystallographic structure determination of both CBM of Caldanaerobius polysaccharolyticus (formerly Thermoanaerobacterium polysaccharolyticum) ManA revealed the importance of two aromatic residues in the binding cleft, as long as two stretches of polar residues on both sides of the cleft [1]. Study of affinity of targeted mutant for the predicted key resides confirmed the importance of two tryptophanes (Trp-20 and Trp-125), and two glutamines (Gln-81 and Gln-93) [2].

Based on sequence similarity and conservation of secondary structure element, it has been proposed that along with the CBM-4, 17, 22 and 27 families, they form a superfamily [9].

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

In the Man5A of Caldanaerobius polysaccharolyticus, the deletion of its both CBM16 severely impaired the ability of the catalytic module (GH5) to bind cellulose [10].

In the case of CgkA from Zobellia galactanivorans, the presence of the CBM16 is not required for the enzymatic activity on kappa-carrageenan, but has been shown to take part in the processive mechanism of the catalytic module (GH16) [4].

Even if frequently found within the gene coding for alginate lyase from family PL18, it is absent in the mature form of the enzyme, and no role in alginate degradation has been found up to now [8]. A chaperon function of this N-terminal module has been proposed after observation that its deletion hindered the correct folding and activity of the catalytic module [7].

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

[11, 12]: two CBM16 tandem associated, in C-terminal side of the Man5A GH5

First Structural Characterization

[13, 14]

References

15. 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 |

16. 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.

17. 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 |
18. 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 |
19. 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 |
20. 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 |
21. Armenta S, Moreno-Mendieta S, Sánchez-Cuapio Z, Sánchez S, and Rodríguez-Sanoja R. (2017). Advances in molecular engineering of carbohydrate-binding modules. Proteins. 2017;85(9):1602-1617. DOI:10.1002/prot.25327 |