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. a) The overall structure with the subdomains distinctly coloured and its ligand binding tyrosine and aspartate residues of each subdomain shown as sticks (PDB accession https://www.rcsb.org/3d-view/1xyf 1XYF). b) The binding site found in the α-subdomain of the CBM13 domain in complex with 2³-4-O-methyl-α-D-glucuronosyl-xylotriose (MeGlcUA-X3, PDB accession 1V6X). c) Overlay of the subdomains showing sequence conservation within the binding sites. Single letter residue codes are coloured based on the subdomains shown in panel a) and are labelled for subdomains ⍺/β/γ, in that order.

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

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First Structural Characterization

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References

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