Carbohydrate Binding Module Family 58

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• Author: ^^^Nicole Koropatkin^^^
• Responsible Curator: ^^^Nicole Koropatkin^^^

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CAZy DB link

http://www.cazy.org/CBM58.html

Ligand specificities

Only a single CBM58 family member has been characterized, the founding member from in the neopullulanase SusG of the human gut symbiont Bacteroides thetaiotaomicron [1]. The crystal structure of SusG featuring CBM58 revealed binding to maltoheptaose as well as acarbose. Isothermal titration calorimetry as well as affinity PAGE demonstrates that the CBM58 of SusG binds maltoheptaose, α-cyclodextrin and amylopectin. Based upon these data as reported by Koropatkin[1], the CBM58 family is believed to bind exclusively to α1,4-linked glucan structures in starch, with no apparent recognition or affinity for regions displaying α1,6- branching.

Structural Features

The crystal structure of CBM58 from SusG of B. thetaiotaomicron displays a canonical β-sandwich fold, with a single binding site accomodated by the loops connecting β3 and β4, connecting β6 and β7, and β7 and β8 [1]. These loops fold over one of the β-sheets. Because CBM58 recognizes internal regions of the polypeptide chain, it can be classified as a type B CBM [2]. Like many starch-specific CBMs [3], the helical α -glucan at CBM58 in SusG is cradled by aromatic stacking interactions with two aromatic residues, W287 and W299, as well as hydrogen bonding interactions with K304, N330 and Y260 that aid in positioning the adjacent glucose residues stacking with the two tryptophans [1].

A unique facet of the CBM58 of SusG is its position in the middle of the polypeptide chain, occupying residues 216-335 of the protein. This domain is inserted between α3 and β3 of the catalytic domain the, and essentially expands the typically small B domain of GH13 enzymes. In SusG, two short linker sequences from residues 212-217 and 334-338 span about 12Å between the A domain and the CBM58 have B-factors and an amino acid sequence imply this domain is held in a fixed position, without inherent flexibility. There are only 14 other members of the CBM58 family, and they all reside within the Bacteroidetes phylum and include similar GH13 enzymes from isolates of Alistipes finegoldii, Alistipes shahii, Bacteroides dorei, Bacteroides eggerthii, and Bacteroides vulgatus. A sequence alignment of all 15 GH13 enzymes possessing a CBM58 reveals that the location of this domain is invariant as an extension of the B domain.

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. Koropatkin NM and Smith TJ. (2010). SusG: a unique cell-membrane-associated alpha-amylase from a prominent human gut symbiont targets complex starch molecules. Structure. 2010;18(2):200-15. DOI:10.1016/j.str.2009.12.010 |
2. Gilbert HJ, Knox JP, and Boraston AB. (2013). Advances in understanding the molecular basis of plant cell wall polysaccharide recognition by carbohydrate-binding modules. Curr Opin Struct Biol. 2013;23(5):669-77. DOI:10.1016/j.sbi.2013.05.005 |
3. Machovic M and Janecek S. (2006). Starch-binding domains in the post-genome era. Cell Mol Life Sci. 2006;63(23):2710-24. DOI:10.1007/s00018-006-6246-9 |

4. 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.

5. 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 |
6. 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 |
7. 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 |
8. 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 |