Carbohydrate Binding Module Family 86

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• Author: Maria Louise Leth
• Responsible Curator: Maher Abou Hachem

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CAZy DB link

https://www.cazy.org/CBM86.html

Ligand specificities

Figure 1 A) Domain organization of the xylanase RiXyn10A from R. intestinalis. Grey module: signal peptide, light green module: BIG2, bacterial immunoglobulin-like domain group 2, dark green domain: LBR, Listeria-Bacteriodes repeat domain, and AA: amino acids. B) Architecture of the shallow binding site. C) Crystal structure of RiCBM86 (PDB: 6SGF) with the four visible xylosyl residues of the xylohexaose ligand. The aromatic residues and the residues contributing to direct hydrogen bonding are shown as sticks in green.

The CBM86 family was first described in 2018. The founding member, RiCBM86, was identified in a modular GH10 xylanase from the human gut bacteria Roseburia intestinalis L1-82 [1]. Members of CBM86 are approximately 138 residues and are found exclusively at the N-termini of GH10 xylananses. The interaction of CBM86 to xylo-oligosaccharides was determined by surface plasmon resonance and isothermal titration, resulting in highest affinity with xylohexaose (K_D=479 µM), followed by xylopentaose (K_D=490 µM), xylotetraose (K_D=998 µM), and xylotriose (K_D=1900 µM) [1]. The preference of CBM86 to xylan was determined by affinity electrophoresis, revealing that wheat arabinoxylan is preferred (K_D=0.02 mg ml^-1) compared to birch glucuronoxylan (K_D=0.6 mg ml^-1) [1]. The preference for arabinosyl substitutions rather than glucuronosyl was confirmed with NMR spectroscopy for both polymeric xylan and xylo-oligosaccharides [2].

Structural Features

The first crystal structure from family CBM86 in complex with xylohexaose was determined at a resolution of 1.8 Å in 2019 (PDB: 6SGF) [2]. The structure is a β-sandwich fold consisting of two sheets formed by 11 antiparallel β-stands and two helical turns connected by loops. The ligand-binding site shows clear density for four xylosyl residues and features an open and shallow surface with the ligand bound in a typical helical conformation (3-fold symmetry). The aromatic residues Y62 and Y110 make aromatic stacking interactions with the ligand. Mutational analysis of these aromatic residues confirmed that they are crucial for binding to xylan [1]. W42 contributes in addition to affinity, but to a lesser extent. The binding site is also consistent with NMR data showing that residues observed in the crystal structure undergo large chemical shift changes upon xylan binding [1]. RiCBM86 only recognizes a single xylosyl residue with direct hydrogen bonds consistent with the relatively low-affinity for xylohexaose, which is atypical amongst xylan binding type-B CBMs that display more extensive hydrogen bonding patterns to their ligand (e.g., CBM15) [3] or employ Ca²⁺ to mediate ligand binding (e.g., CBM36) [4].

Functionalities

Members of family CBM86 are exclusively located in the N-terminal of GH10 xylanases from the Clostridiales order of Firmicutes, where it is often associated with additional CBM modules from family 9 and 22. It recognizes both xylan and xylo-oligosaccharides[1, 2]. The truncation of this module from RiXyn10A resulted in about two fold higher K_m and a similar increase in k_cat, suggesting that this module contributes to xylan affinity and xylan capture [1].

Family Firsts

First Identified

Family CBM86 was first identified as part of the modular xylanase RiXyn10A from R. intestinalis L1-82 [1].

First Structural Characterization

The first crystal structure of the family CBM86 is RiCBM86 (PDB: 6SGF) originating from RiXyn10A [2]. The structure was determined in the presence of the ligand xylohexaose.

References

1. Leth ML, Ejby M, Workman C, Ewald DA, Pedersen SS, Sternberg C, Bahl MI, Licht TR, Aachmann FL, Westereng B, and Abou Hachem M. (2018). Differential bacterial capture and transport preferences facilitate co-growth on dietary xylan in the human gut. Nat Microbiol. 2018;3(5):570-580. DOI:10.1038/s41564-018-0132-8 |
2. Leth ML, Ejby M, Madland E, Kitaoku Y, Slotboom DJ, Guskov A, Aachmann FL, and Abou Hachem M. (2020). Molecular insight into a new low-affinity xylan binding module from the xylanolytic gut symbiont Roseburia intestinalis. FEBS J. 2020;287(10):2105-2117. DOI:10.1111/febs.15117 |
3. Szabo L, Jamal S, Xie H, Charnock SJ, Bolam DN, Gilbert HJ, and Davies GJ. (2001). Structure of a family 15 carbohydrate-binding module in complex with xylopentaose. Evidence that xylan binds in an approximate 3-fold helical conformation. J Biol Chem. 2001;276(52):49061-5. DOI:10.1074/jbc.M109558200 |
4. Jamal-Talabani S, Boraston AB, Turkenburg JP, Tarbouriech N, Ducros VM, and Davies GJ. (2004). Ab initio structure determination and functional characterization of CBM36; a new family of calcium-dependent carbohydrate binding modules. Structure. 2004;12(7):1177-87. DOI:10.1016/j.str.2004.04.022 |