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 that this domain binds to maltoheptaose as well as acarbose. Isothermal titration calorimetry with maltoheptaose and α-cyclodextrin as well as isotherm depletion assays with insoluble cornstarch further confirmed that CBM58 is a starch-specific CBM. 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, 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 that stack with the 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, and essentially expands the typically small B domain of GH13 enzymes. In SusG, two short linker sequences from residues 212-217 and 334-338, spanning 12Å between the A domain and CBM58, have B-factors and an amino acid sequence that imply this domain is held in a fixed position, without inherent flexibility [1]. There are only 14 other members of the CBM58 family, and they all reside within the Bacteroidetes phylum. This includes 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. The majority of these CBM58 containing proteins are expressed within canonical polysaccharide utilization loci of the Bacteroidetes that also encode homologs of the TonB-dependent transporter SusC and a homolog of the starch-binding protein SusD.

Functionalities

CBM58 is only found within GH13 enzymes, and the conserved placement of the domain within the B. thetaiotaomicron SusG and like enzymes is somewhat unique as it interrupts the fold of the catalytic domain. In the structure of SusG, the starch-binding face of CBM58 is located 45Å away and on the opposite face of the protein from the catalytic cleft [1]. A mutant enzyme of SusG in which the CBM58 has been deleted retains catalytic activity against small substrates such as PNP-maltohexaose similar to the wild-type enzyme [1]. The CBM-less SusG enzyme is 2-3 fold more active on autoclaved soluble starch such as maize amylopectin, but only retains ~30% of the wild-type activity on insoluble corn starch [1]. B. thetaiotaomicron expressing only an allele for the CBM-less SusG grow the same as wild-type cells on autoclaved soluble starches [4].

While the CBM58 of SusG has not been used in any novel applications, this CBM was replaced with the Halo-tag® protein for single-molecule fluorescence imaging of the SusG protein in live B. thetaiotaomicron cultured on glucose and starch [5].

Family Firsts

First Identified

The CBM58 domain was identified during the biochemical and structural characterization of SusG from B. thetaiotaomicron.

First Structural Characterization

The crystal structure of the GH13 enzyme SusG with maltoheptaose revealed an extended B domain, CBM58, that recognizes starch and maltooligosaccharides.

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. Cameron EA, Kwiatkowski KJ, Lee BH, Hamaker BR, Koropatkin NM, and Martens EC. (2014). Multifunctional nutrient-binding proteins adapt human symbiotic bacteria for glycan competition in the gut by separately promoting enhanced sensing and catalysis. mBio. 2014;5(5):e01441-14. DOI:10.1128/mBio.01441-14 |
6. Karunatilaka KS, Cameron EA, Martens EC, Koropatkin NM, and Biteen JS. (2014). Superresolution imaging captures carbohydrate utilization dynamics in human gut symbionts. mBio. 2014;5(6):e02172. DOI:10.1128/mBio.02172-14 |