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

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 a, b, and g, referring to the subdomain in 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

1. Fujimoto Z (2013). Structure and function of carbohydrate-binding module families 13 and 42 of glycoside hydrolases, comprising a β-trefoil fold. Biosci Biotechnol Biochem. 2013;77(7):1363-71. DOI:10.1271/bbb.130183 |
2. Cui X, Jiang Y, Chang L, Meng L, Yu J, Wang C, and Jiang X. (2018). Heterologous expression of an agarase gene in Bacillus subtilis, and characterization of the agarase. Int J Biol Macromol. 2018;120(Pt A):657-664. DOI:10.1016/j.ijbiomac.2018.07.118 |
3. Ichinose H, Kuno A, Kotake T, Yoshida M, Sakka K, Hirabayashi J, Tsumuraya Y, and Kaneko S. (2006). Characterization of an exo-beta-1,3-galactanase from Clostridium thermocellum. Appl Environ Microbiol. 2006;72(5):3515-23. DOI:10.1128/AEM.72.5.3515-3523.2006 |
4. Jiang D, Fan J, Wang X, Zhao Y, Huang B, Liu J, and Zhang XC. (2012). Crystal structure of 1,3Gal43A, an exo-β-1,3-galactanase from Clostridium thermocellum. J Struct Biol. 2012;180(3):447-57. DOI:10.1016/j.jsb.2012.08.005 |
5. Notenboom V, Boraston AB, Williams SJ, Kilburn DG, and Rose DR. (2002). High-resolution crystal structures of the lectin-like xylan binding domain from Streptomyces lividans xylanase 10A with bound substrates reveal a novel mode of xylan binding. Biochemistry. 2002;41(13):4246-54. DOI:10.1021/bi015865j |
6. Garrido MM, Piccinni FE, Landoni M, Peña MJ, Topalian J, Couto A, Wirth SA, Urbanowicz BR, and Campos E. (2022). Insights into the xylan degradation system of Cellulomonas sp. B6: biochemical characterization of rCsXyn10A and rCsAbf62A. Appl Microbiol Biotechnol. 2022;106(13-16):5035-5049. DOI:10.1007/s00253-022-12061-3 |
7. Hagiwara Y, Okeda T, Okuda K, Yatsunami R, and Nakamura S. (2022). Characterization of a xylanase belonging to the glycoside hydrolase family 5 subfamily 35 from Paenibacillus sp. H2C. Biosci Biotechnol Biochem. 2022;87(1):54-62. DOI:10.1093/bbb/zbac175 |
8. Schärpf M, Connelly GP, Lee GM, Boraston AB, Warren RA, and McIntosh LP. (2002). Site-specific characterization of the association of xylooligosaccharides with the CBM13 lectin-like xylan binding domain from Streptomyces lividans xylanase 10A by NMR spectroscopy. Biochemistry. 2002;41(13):4255-63. DOI:10.1021/bi015866b |
9. Fujimoto Z, Kaneko S, Kuno A, Kobayashi H, Kusakabe I, and Mizuno H. (2004). Crystal structures of decorated xylooligosaccharides bound to a family 10 xylanase from Streptomyces olivaceoviridis E-86. J Biol Chem. 2004;279(10):9606-14. DOI:10.1074/jbc.M312293200 |
10. Tamashiro T, Tanabe Y, Ikura T, Ito N, and Oda M. (2012). Critical roles of Asp270 and Trp273 in the α-repeat of the carbohydrate-binding module of endo-1,3-β-glucanase for laminarin-binding avidity. Glycoconj J. 2012;29(1):77-85. DOI:10.1007/s10719-011-9366-x |
11. Lian MQ, Furusawa G, and Teh AH. (2024). Trigalacturonate-producing pectate lyase PelQ1 from Saccharobesus litoralis with unique exolytic activity. Carbohydr Res. 2024;536:109045. DOI:10.1016/j.carres.2024.109045 |
12. Fujita A, Kawashima A, Noguchi Y, Hirose S, Kitagawa N, Watanabe H, Mori T, Nishimoto T, Aga H, Ushio S, and Yamamoto K. (2021). Cloning of the cycloisomaltotetraose-forming enzymes using whole genome sequence analyses of Agreia sp. D1110 and Microbacterium trichothecenolyticum D2006. Biosci Biotechnol Biochem. 2021;86(1):68-77. DOI:10.1093/bbb/zbab181 |