Carbohydrate Binding Module Family 13

This page is currently under construction. This means that the Responsible Curator has deemed that the page's content is not quite up to CAZypedia's standards for full public consumption. All information should be considered to be under revision and may be subject to major changes.

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

---

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 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 α site seemingly being the strongest [8, 9]. Avid binding has been demonstrated for laminarin, by a CBM13 domain found in a β-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 (Figure 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

Carbohydrate Binding Module family 13 has a rich history. The earliest known examples were biochemically characterised prior to their annotation as CBM13 domains. These were shown to be xylan binders increasing substrate affinity of industrial xylan-degrading enzymes [13], yet they often proved to be non-essential in xylan hydrolysing [14] and wood pulp bleaching applications [15, 16].

Bioinformatic analysis has revealed a strong cooccurrence of CBM13 and GH43 modules, with subfamily GH43_7 enzymes apparently all containing a CBM13 domain [17]. In that enzyme subfamily, the α-L-arabinofuranosidase AbfB from Streptomyces lividans carries a xylan-binding CBM13 domain [18], as does an endo-β-1,4-xylanase from Bacteroides intestinalis [19]. CBM13 domains are also abundant in β-agarases, found in enzyme families GH16, GH39, GH50, GH86, and GH118 [20].

Diverse other examples have shown that a CBM13 domain binding to the substrate of an appended glycoside hydrolase module does lead to activity potentiation through enhanced substrate proximity effects, such as in a GH16 agarase from Gilvimarinus agarilyticus JEA5 [21] and a GH5_35 xylanase from Paenibacillus sp. H2C [7]. The enzyme endo-β-agarase I from Microbulbifer thermotolerans JAMB-A94 was engineered by fusing the GH16 catalytic module to a CBM13 domain derived from the agarolytic marine bacterium Catenovulum agarivorans [22], leading to a substantial increase in agar binding and hydrolysis in the fusion enzyme [23].

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

Error fetching PMID 23832347:
Error fetching PMID 30059737:
Error fetching PMID 16672498:
Error fetching PMID 22960181:
Error fetching PMID 11914070:
Error fetching PMID 35799069:
Error fetching PMID 36352459:
Error fetching PMID 11914071:
Error fetching PMID 14670957:
Error fetching PMID 22198269:
Error fetching PMID 38340525:
Error fetching PMID 34661636:
Error fetching PMID 8161173:
Error fetching PMID 7717975:
Error fetching PMID 9572948:
Error fetching PMID 15650852:
Error fetching PMID 26729713:
Error fetching PMID 9148759:
Error fetching PMID 33469030:
Error fetching PMID 30333947:
Error fetching PMID 29551022:
Error fetching PMID 36352459:
Error fetching PMID 24824021:
Error fetching PMID 27702474: