Carbohydrate Binding Module Family 91

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• Author: Daichi Ito
• Responsible Curator: Elizabeth Ficko-Blean

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CAZy DB link

https://www.cazy.org/CBM91.html

Ligand specificities

PxCBM91 from Paenibacillus xynaniclasticus bound to oat spelt xylan with K_a value of 2.0×10^-5 M^-1, and bound birchwood xylan [1]. It did not bind to lichenan or the cellulosic substrates carboxymethyl-cellulose or ball-milled cellulose [1]. Therefore, PxCBM91 can recognize and bind to insoluble xylan [1].

Structural Features

Figure 1. The structure of PxXyl43A and PxCBM91 [2]. The structure prediction by Alpha Fold 2 of PxCBM91 (red). This CBM91 is appended to the catalytic domain of PxXyl43A (green).

Alpha Fold 2 structural analysis of PxCBM91 exhibited a β-sandwich fold consisted of 12 β-strands and two opposing antiparallel beta sheets [2]. The concave surface and loops around it connecting the β-strands possess several hydrophobic amino acid residues, the surface is expected to be the binding site[2].

Functionalities

Paenibacillus xylaniclastuicus was isolated from an anaerobic digester fed with pineapple waste and grows with xylose as sole carbon source [3, 4]. P. xylaniclastuicus likely degrades xylosic substrates efficiently because it has a lot of genes encoding xylolytic enzymes. Xylosidases, like PxXyl43A, which produces xylose from xylan and xylooligosaccharides is one of the vital enzymes. Therefore, the appended PxCBM91 contributes to producing the carbon sources for the growth of this xylolytic bacteria.

CBM91 are often connected to β-xylosidases belonging to glycoside hydrolase family 43 (GH43) (see CBM91 page of the CAZy Database). CBM91 binding to the substrates would place the catalytic domain in the vicinity of substrates in which substrate concentration is high. These enzymes would utilize CBM91 as a tool for efficient saccharification in combination with other xylanases which release xylobiose and/or xylo-oligosaccharides from insoluble substrates.

Family Firsts

First Identified

Xylan binding was first identified in PxCBM91 from PxXyl43A of Paenibacillus xynaniclasticus strain TW1 [1].

First Structural Characterization

β-D-xylosidase, a family 43 glycoside hydrolase from Clostridium acetobutylicum ATCC 824 (Released: 2005-01-25) PDB ID 1Y7B [5].

References

1. Ito D, Nakano E, Karita S, Umekawa M, Ratanakhanokchai K, and Tachaapaikoon C. (2022). Characterization of a GH Family 43 β-Xylosidase Having a Novel Carbohydrate-binding Module from Paenibacillus xylaniclasticus Strain TW1. J Appl Glycosci (1999). 2022;69(3):65-71. DOI:10.5458/jag.jag.JAG-2022_0001 |

2. Ito, D., 2023. Characterization of plant cell wall degrading enzymes from Paenibacillus sp., 2023, Mie University, Ph. D. thesis. https://dl.ndl.go.jp/pid/12910195/1/1

3. C. Tachaapaikoon, S. Tanasupawat, P. Pason, S. Sornyotha, R. Waeonukul, K.L. Kyu and K. Ratanakhanockchai: Paenibacillus xylaniclasticus sp. nov., a xylanolytic-cellulolytic bacterium isolated from sludge in an anaerobic digester. J.Microbiol., 50, 394–400 (2012) DOI:10.1007/s12275-012-1480-3

4. K. Ratanakhanockchai, C. Tachaapaikoon, K.L. Kyu and P. Pason: A novel multienzyme complex from a newly isolated facultative anaerobic bacterium, Paenibacillus sp. TW1. Act. Biol. Hung., 63, 288–300 (2012) DOI:10.1556/ABiol.63.2012.2.10

5. Teplyakov, A., Fedorov, E., Gilliland, G.L., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)