Carbohydrate Binding Module Family 13

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• Author: Lauren McKee and Scott Mazurkewich
• Responsible Curator: Lauren McKee

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CAZy DB link

https://www.cazy.org/CBM13.html

File:CBM13overview.png

Figure 1. Structure of the CBM13 domain in the multidomain protein Xyn10A from Streptomyces olivaceoviridis E-86. The enzymes (A) StGE2 from Thermothelomyces thermophila (PDB ID 4G4J), (B) OtCE15A from Opitutus terrae (PDB ID 6GS0), and (C) TtCE15A from Teredinibacter turnerae (PDB ID 6HSW) are shown in cartoon representation. The catalytic triad in each enzyme is shown as sticks and the methyl ester of 4-O-methyl glucuronoate first observed in StGE2 is shown in all structures as green sticks. While all CE15 members contain the alpha/beta hydrolase fold, the most prominent difference across the CE15 family observed to-date are the presence, absence, or variety of inserted regions that protrude and build-up ridges around the active site (the differently colored regions in the OtCE15A and TtCE15A). The extent to which these regions affect the enzyme’s substrate specificity has yet to be fully elucidated.

Ligand specificities

The first identified CBM13 domains were in plant lectins like ricin and agglutinin, and were found to bind galactose residues [1]. The domains were later found to be common within many CAZymes, especially glycoside hydrolases and glycosyltransferases. Binding to galactose, lactose, and agar is common in the family [2], and binding to galacto-oligsaccharides of various different linkages has been observed [3, 4]. Some structural studies have shown the CBM13 binding sites can accommodate either the non-reducing end galactose or the reducing end glucose in lactose, showing remarkable plasticity in binding preference [5].

There are also many examples of xylan-binding CBM13 domains [6, 7]. Here there is evidence of mid-chain binding to longer oligosaccharides, and that xylopentaose can bind to two binding sites simultaneously, wrapping about the CBM13 domain to do so [5]. Multiple binding sites are often functional within CBM13 domains, with the alpha site seemingly the strongest [8, 9]. Avid binding has been demonstrated for laminarin, by a CBM13 domain found in a b-1,3-glucanase [10]. More recently, binding to alginate has also been demonstrated [11] and a CBM13 domain was identified in a cycloisomaltotetraose enzyme [12].

Structural Features

CBM13 proteins are Type C domains, comprising 3 internal subdomains (α, β, and γ), each approximately 40 residues in length, which fold in similar ways around a pseudo-3-fold axis, giving rise to a β-trefoil tertiary structure (Fig. 1), as is also common for plant lectins. The ligand binding site in each subdomain is found in a surface exposed pocket, where binding is principally facilitated by tyrosine and aspartate residues found conserved within each subdomain. The binding sites are designated as α, β, and γ, referring to the subdomain from which they are found. The same naming system has been used for the other multivalent β-trefoil members families CBM42 and CBM92, which share the same modular structure as CBM13 domains.

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

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