Carbohydrate Binding Module Family 50

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• Author: Takayuki Ohnuma and Toki Taira
• Responsible Curator: Takayuki Ohnuma

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CAZy DB link

https://www.cazy.org/CBM50.html

Ligand specificities

CBM50 members are also known as LysM domains. They bind to the N-acetylglucosamine residues in bacterial peptidoglycans and in chitin. For example CBM50 of Lactococcus lactis N-acetylglucosaminidase AcmA was shown to bind to the glycan chain of bacterial peptidoglycans, a β-1,4 linked heteropolymer of alternating N-acetylglucosamine (GlcNAc) and N-acetylmuramic acid (MurNAc) [1]. A CBM50 module from Pteris ryukyuensis chitinase-A (PrChi-A) was demonstrated to bind to chitin, a β-1,4-linked homopolymer of GlcNAc [2]. From isothermal titration calorimetry, the CBM50 module from PrChi-A was found to bind to (GlcNAc)_n (n=4,5) with the binding stoichiometry of 1:1, whereas no significant binding heat was observed for the binding to (GlcNAc)₂ [3]. The binding site of the CBM50 module can accommodate at least three saccharide units.

Structural Features

CBM50 modules are about 50 amino acids long. The three-dimensional structures of several CBM50 modules attached to carbohydrate-active enzymes have been deposited in the Protein Data Bank (example PDB entries: 1e0g [4], 2mkx and 4pxv). The CBM50 modules have a βααβ fold with the two helices packing against one side of the two-stranded antiparallel β-sheet. Although no crystal structure of the CBM50 module in complex with the ligand has been determined yet, Ohnuma et al. first identified the chitin oligosaccharide binding site of the CBM50 module from PrChi-A based on the NMR titration experiments [3]. The chitin oligosaccharide binding site was estimated to be located in a shallow groove formed by the N-terminal part of helix 1, the loop between strand 1 and helix 1, the C-terminal part of helix 2, and the loop between helix 2 and strand 2.

Functionalities

CBM50 modules are generally found in bacterial lysins including muramidase [5], N-acetylglucosaminidase [1], γ-D-glutamate-meso-diaminopimelate muropeptidase [6] and N-acetylmuramoyl-L-alanine amidase [7]. The CBM50 modules in lysins are shown to bind to bacterial peptidoglycan and involved in cell division by localizing these enzymes to the divisional site [8]. CBM50 modules were also found in family GH18 chitinases [2, 9], and contribute to the antifungal activity of the enzymes through their binding ability to chitinous component of the fungal cell wall. CBM50 modules are found not only in carbohydrate-active enzymes but also in LysM-containing plant cell surface receptors for chitin oligosaccharides and their derivatives [10, 11] and fungal effectors [12]. The receptor proteins are involved in plant-microbe interactions upon symbiosis or infection.

Family Firsts

First Identified

CBM50s are also known as LysM domains. The LysM domain was first identified in lysozyme from Bacillus phage f29 [13]. LysM domains were first classified as a CBM in 2008 after demonstrating chitin oligosaccharide binding by an N-terminal LysM domain from Pteris ryukyuensis chitinase-A [3].

First Structural Characterization

The first three-dimensional structure of CBM50 module was determined for the LysM domain from E. coli membrane-bond lytic murein transglycosylase D (MltD) (PDB entry: 1e0g) by NMR spectroscopy [4].

References

1. Steen A, Buist G, Leenhouts KJ, El Khattabi M, Grijpstra F, Zomer AL, Venema G, Kuipers OP, and Kok J. (2003). Cell wall attachment of a widely distributed peptidoglycan binding domain is hindered by cell wall constituents. J Biol Chem. 2003;278(26):23874-81. DOI:10.1074/jbc.M211055200 |
2. Onaga S and Taira T. (2008). A new type of plant chitinase containing LysM domains from a fern (Pteris ryukyuensis): roles of LysM domains in chitin binding and antifungal activity. Glycobiology. 2008;18(5):414-23. DOI:10.1093/glycob/cwn018 |
3. Ohnuma T, Onaga S, Murata K, Taira T, and Katoh E. (2008). LysM domains from Pteris ryukyuensis chitinase-A: a stability study and characterization of the chitin-binding site. J Biol Chem. 2008;283(8):5178-87. DOI:10.1074/jbc.M707156200 |
4. Bateman A and Bycroft M. (2000). The structure of a LysM domain from E. coli membrane-bound lytic murein transglycosylase D (MltD). J Mol Biol. 2000;299(4):1113-9. DOI:10.1006/jmbi.2000.3778 |
5. Chu CP, Kariyama R, Daneo-Moore L, and Shockman GD. (1992). Cloning and sequence analysis of the muramidase-2 gene from Enterococcus hirae. J Bacteriol. 1992;174(5):1619-25. DOI:10.1128/jb.174.5.1619-1625.1992 |
6. Margot P, Pagni M, and Karamata D. (1999). Bacillus subtilis 168 gene lytF encodes a gamma-D-glutamate-meso-diaminopimelate muropeptidase expressed by the alternative vegetative sigma factor, sigmaD. Microbiology (Reading). 1999;145 ( Pt 1):57-65. DOI:10.1099/13500872-145-1-57 |
7. Kajimura J, Fujiwara T, Yamada S, Suzawa Y, Nishida T, Oyamada Y, Hayashi I, Yamagishi J, Komatsuzawa H, and Sugai M. (2005). Identification and molecular characterization of an N-acetylmuramyl-L-alanine amidase Sle1 involved in cell separation of Staphylococcus aureus. Mol Microbiol. 2005;58(4):1087-101. DOI:10.1111/j.1365-2958.2005.04881.x |
8. Visweswaran GR, Steen A, Leenhouts K, Szeliga M, Ruban B, Hesseling-Meinders A, Dijkstra BW, Kuipers OP, Kok J, and Buist G. (2013). AcmD, a homolog of the major autolysin AcmA of Lactococcus lactis, binds to the cell wall and contributes to cell separation and autolysis. PLoS One. 2013;8(8):e72167. DOI:10.1371/journal.pone.0072167 |
9. Gruber S, Vaaje-Kolstad G, Matarese F, López-Mondéjar R, Kubicek CP, and Seidl-Seiboth V. (2011). Analysis of subgroup C of fungal chitinases containing chitin-binding and LysM modules in the mycoparasite Trichoderma atroviride. Glycobiology. 2011;21(1):122-33. DOI:10.1093/glycob/cwq142 |
10. Kaku H, Nishizawa Y, Ishii-Minami N, Akimoto-Tomiyama C, Dohmae N, Takio K, Minami E, and Shibuya N. (2006). Plant cells recognize chitin fragments for defense signaling through a plasma membrane receptor. Proc Natl Acad Sci U S A. 2006;103(29):11086-91. DOI:10.1073/pnas.0508882103 |
11. Limpens E, Franken C, Smit P, Willemse J, Bisseling T, and Geurts R. (2003). LysM domain receptor kinases regulating rhizobial Nod factor-induced infection. Science. 2003;302(5645):630-3. DOI:10.1126/science.1090074 |
12. Bolton MD, van Esse HP, Vossen JH, de Jonge R, Stergiopoulos I, Stulemeijer IJ, van den Berg GC, Borrás-Hidalgo O, Dekker HL, de Koster CG, de Wit PJ, Joosten MH, and Thomma BP. (2008). The novel Cladosporium fulvum lysin motif effector Ecp6 is a virulence factor with orthologues in other fungal species. Mol Microbiol. 2008;69(1):119-36. DOI:10.1111/j.1365-2958.2008.06270.x |
13. Garvey KJ, Saedi MS, and Ito J. (1986). Nucleotide sequence of Bacillus phage phi 29 genes 14 and 15: homology of gene 15 with other phage lysozymes. Nucleic Acids Res. 1986;14(24):10001-8. DOI:10.1093/nar/14.24.10001 |