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

This module was originally identified as a non-catalytic xylan-binding domain in GH54 α-L-arabinofuranosidase from Trichoderma reesei PC-3-7 [1]. In 2004, it was found to be a CBM specific for an L-arabinofuranosyl group because L-arabinofuranose molecules were bound to a non-catalytic domain of GH54 α-L-arabinofuranosidase B from Aspergillus kawachii (AkAbfB) [2]. CBM42 members have multivalent (usually divalent or trivalent) binding ability to non-reducing end L-arabinofuranosyl residues, which are present in plant polysaccharides (hemicelluloses) such as arabinoxylan, arabinan, and arabinogalactan. Most of CBM42s are associated with α-L-arabinofuranosidases from fungi (GH54) or bacteria (GH43).

Structural Features

Figure 1: CBM42 of α-L-arabinofuranosidase B from A. kawachii in complex with α-L-arabinofuranosyl-α-1,2-xylobiose (2D44). The α-domain is non-functional.

• Fold: CBM42s have a β-trefoil fold that is similar to CBM13 and R(ricin)-type lectins (Figure 1). The module has 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 [3].
• Features of ligand binding: The binding sites are located at side pockets 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 two aromatic residues (tyrosine, tryptophan, or phenylalanine) stacking to the furanose sugar (Figure 1). They are D425, H416, Y417 and Y456 in the β-subdomain of AkAbfB and are conserved in functional CBM42 subdomains.
• Available structures: Several crystal structures including complex structures with compounds containing an L-arabinofuranosyl group are available. For example, AkAbfB (α-subdomain is non-functional) 1wd3 1wd4 [2], 2d43 2d44 [3]; Exo-1,5-α-L-arabinofuranosidase from Sreptomyces avermitilis (all subdomains are functional)3akf 3akg 3akh 3aki [4]; CBM42A in Cthe_0015 from Clostridium thermocellum (β-subdomain is non-functional) 3KMV [5].

Functionalities

• Functional role of CBM: CBM42s are thought to target catalytic modules (usually α-L-arabinofuranosidases) to hemicelluloses that have L-arabinofuranosyl termini or branches. Mutations at the binding sites of CBM42 significantly reduced the catalytic activity toward natural polysaccharides in these enzymes, whereas the activity toward p-nitrophenyl α-L-arabinofuranoside was not affected [3, 5].
• Most Common Associated Modules: α-L-Arabinofuranosidases or exo-arabinanases of GH2, GH43, GH54, GH93, or non-classified GHs [5]. A survey using the GH-CBM tool shows that CBM42s are also associated with GH16 or GH30.
• Binding affinities: As a typical exo-type (Type C) CBM, the CBM42 in AkAbfB shows relatively low binding affinities to L-arabinofuranose-containing oligosaccharides with K_a values of 1~5 ×10³ M^-1. [3].
• Novel Applications: A CBM42 was used to create a chimeric enzyme with a feruloyl esterase [6].

Family Firsts

First Identified

The L-arabinofuranose-binding function of CBM42 was first suggested by crystallography of α-L-arabinofuranosidase B from Aspergillus kawachii (AkAbfB) [2].

First Structural Characterization

The first structure of CBM42 was revealed in 2004 in the x-ray crystal structure of AkAbfB in complex with arabinose as a full-length structure with a catalytic GH54 domain 1wd4 [2].

References

1. Nogawa M, Yatsui K, Tomioka A, Okada H, and Morikawa Y. (1999). An alpha-L-arabinofuranosidase from Trichoderma reesei containing a noncatalytic xylan-binding domain. Appl Environ Microbiol. 1999;65(9):3964-8. DOI:10.1128/AEM.65.9.3964-3968.1999 |
2. 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 |
3. 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 |
4. Fujimoto Z, Ichinose H, Maehara T, Honda M, Kitaoka M, and Kaneko S. (2010). Crystal structure of an Exo-1,5-{alpha}-L-arabinofuranosidase from Streptomyces avermitilis provides insights into the mechanism of substrate discrimination between exo- and endo-type enzymes in glycoside hydrolase family 43. J Biol Chem. 2010;285(44):34134-43. DOI:10.1074/jbc.M110.164251 |
5. Ribeiro T, Santos-Silva T, Alves VD, Dias FM, Luís AS, Prates JA, Ferreira LM, Romão MJ, and Fontes CM. (2010). Family 42 carbohydrate-binding modules display multiple arabinoxylan-binding interfaces presenting different ligand affinities. Biochim Biophys Acta. 2010;1804(10):2054-62. DOI:10.1016/j.bbapap.2010.07.006 |
6. Koseki T, Mochizuki K, Kisara H, Miyanaga A, Fushinobu S, Murayama T, and Shiono Y. (2010). Characterization of a chimeric enzyme comprising feruloyl esterase and family 42 carbohydrate-binding module. Appl Microbiol Biotechnol. 2010;86(1):155-61. DOI:10.1007/s00253-009-2224-0 |