Carbohydrate Binding Module Family 89

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• Authors: Mariana Abrahão Bueno de Morais and Gabriela Felix Persinoti
• Responsible Curator: Mario Murakami

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CAZy DB link

http://www.cazy.org/CBM89.html

Ligand specificities

CBM89 is a small family that has been identified in bacteria. The CBM89 interaction with beechwood xylan and rye arabinoxylan was assessed using affinity gel electrophoresis (AGE) Cabral202Cabral202. Although similar β-helix structural organization has been found in GH28, GH91, PL6, and CE8, it was not observed any catalytic activity of the isolated CapCBM89 in the tested substrates Cabral202Cabral202.

Structural Features

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• Fold: The 1.85 Å CBM89 solved structure (retrieved from capybara gut metagenome) Cabral202Cabral202 displays a parallel β-helix fold, consisting of 14 complete helical turns.

• Features of ligand binding: A Ca²⁺ was found in the structure, connecting the 11^th and 12^th turns (https://www.rcsb.org/structure/7JVI). The role of the ion seems to be only related to the domain stabilization, since a mutation in the Ca2+ binding site (D344L) affected the protein stability but not its capacity to bind to arabinoxylan/xylan Cabral202Cabral202. In CapCBM89, mutants Y62A and E82A impaired the capacity to bind to arabinoxylan/xylan, indicating the putative region for carbohydrate binding Cabral202Cabral202.

Functionalities

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• Functional role of CBM: In general, CBM89 might comprise approximately 600 to 1000 amino acids, which can be fused to GH domains. The CapCBM89 fused to a GH10 domain is inserted in a gene cluster targeting arabinoxylan Cabral202Cabral202. The cluster encodes the CapCBM89-GH10 and two exo-enzymes from GH43 and GH97 families <ref>Cabral2022<ref>. The GH10 domain is active on arabinoxylan and xylan, also suggesting that indeed the CapCBM89 might bind to these polysaccharides to assist GH10 catalysis in this case Cabral202Cabral202.
• Most Common Associated Modules: 1. Glycoside Hydrolases from family GH10.

Family Firsts

First Identified The first CBM89 to be identified was from a MAG of Bacteroidaceae bacterium from the capybara gut microbiome Cabral202Cabral202.

First Structural Characterization The first CBM89 structure is the PDB ID 7JVI https://www.rcsb.org/structure/7JVI, retrieved from the capybara gut microbiome Cabral202Cabral202.

References

1. pmid= 35110564