Carbohydrate Binding Module Family 42

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• Author: ^^^Shinya Fushinobu^^^
• Responsible Curator: ^^^Shinya Fushinobu^^^

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CAZy DB link

https://www.cazy.org/CBM42.html

Ligand specificities

CBM42 members have multivalent (usually divalent or trivalent) binding ability to non-reducing end L-arabinofuranosyl residues [1] which are present in plant polysaccharides such as arabinoxylan, arabinan, and arabinogalactan.

Structural Features

• Fold: CBM42s have a β-trefoil fold that is similar to CBM13 and R(ricin)-type lectins. The module display a sequential 3-fold internal repeat of approximately 45 amino acid residues comprising three subdomains. The three subdomains are denoted as α, β, and γ. Each subdomain contains a discrete ligand binding site, but one of the three subdomains sometimes loses its function due to mutations at critical residues for ligand binding.
• Type: CBM42s are typical Type C CBMs that bind termini of glycans with pocket-type binding sites for short oligosaccharides. The binding pockets are small but can accommodate the branched side chain L-arabinofuranosyl moiety attached to the xylan backbone of arabinoxylans [2].
• Features of ligand binding: The binding sites are located at side of the triangular structure of the β-trefoil fold. Residues important for the binding to a non-reducing end L-arabinofuranosyl group are as follows: an aspartate forming hydrogen bonds to the O2 and O3 hydroxyls, a histidine forming a hydrogen bond to the O5 hydroxyl, and a tyrosine stacking to the furanose ring. They are D425, H416, and Y456 in α-L-arabinofuranosidase B from Aspergillus kawachii (AkAbfB) and are conserved in functional CBM42 subdomains.
• Available structures: AkAbfB, whose α-subdomain is non-functional, in complex with arabinose [1]

Describe CBM binding pocket location (Side or apex) important residues for binding (W, Y, F, subsites), interact with reducing end, non-reducing end, planar surface or within polysaccharide chains. Include examples pdb codes. Metal ion dependent. Etc.

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. Miyanaga A, Koseki T, Matsuzawa H, Wakagi T, Shoun H, and Fushinobu S. (2004). Crystal structure of a family 54 alpha-L-arabinofuranosidase reveals a novel carbohydrate-binding module that can bind arabinose. J Biol Chem. 2004;279(43):44907-14. DOI:10.1074/jbc.M405390200 |
2. Miyanaga A, Koseki T, Miwa Y, Mese Y, Nakamura S, Kuno A, Hirabayashi J, Matsuzawa H, Wakagi T, Shoun H, and Fushinobu S. (2006). The family 42 carbohydrate-binding module of family 54 alpha-L-arabinofuranosidase specifically binds the arabinofuranose side chain of hemicellulose. Biochem J. 2006;399(3):503-11. DOI:10.1042/BJ20060567 |