An evolutionarily distinct family of polysaccharide lyases removes rhamnose capping of complex arabinogalactan proteins



Munoz-Munoz, Jose, Cartmell, Alan ORCID: 0000-0002-5512-249X, Terrapon, Nicolas, Basle, Arnaud, Henrissat, Bernard and Gilbert, Harry J
(2017) An evolutionarily distinct family of polysaccharide lyases removes rhamnose capping of complex arabinogalactan proteins. Journal of Biological Chemistry, 292 (32). 13271 - 13283.

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Abstract

The human gut microbiota utilizes complex carbohydrates as major nutrients. The requirement for efficient glycan degrading systems exerts a major selection pressure on this microbial community. Thus, we propose that this microbial ecosystem represents a substantial resource for discovering novel carbohydrate active enzymes. To test this hypothesis we screened the potential enzymatic functions of hypothetical proteins encoded by genes of Bacteroides thetaiotaomicron that were up-regulated by arabinogalactan proteins or AGPs. Although AGPs are ubiquitous in plants, there is a paucity of information on their detailed structure, the function of these glycans in planta, and the mechanisms by which they are depolymerized in microbial ecosystems. Here we have discovered a new polysaccharide lyase family that is specific for the L-rhamnose-α1,4-D-glucuronic acid linkage that caps the side chains of complex AGPs. The reaction product generated by the lyase, Δ4,5-unsaturated uronic acid, is removed from AGP by a glycoside hydrolase located in family GH105, producing the final product 4-deoxy-β-L-threo-hex-4-enepyranosyl-uronic acid. The crystal structure of a member of the novel lyase family revealed a catalytic domain that displays an (α/α)6 barrel-fold. In the center of the barrel is a deep pocket, which, based on mutagenesis data and amino acid conservation, comprises the active site of the lyase. A tyrosine is the proposed catalytic base in the β-elimination reaction. This study illustrates how highly complex glycans can be used as a scaffold to discover new enzyme families within microbial ecosystems where carbohydrate metabolism is a major evolutionary driver.

Item Type: Article
Uncontrolled Keywords: carbohydrate processing, glycobiology, glycoside hydrolase, microbiome, X-ray crystallography
Depositing User: Symplectic Admin
Date Deposited: 10 Sep 2019 15:50
Last Modified: 12 Jan 2021 04:10
DOI: 10.1074/jbc.M117.794578
Open Access URL: http://www.jbc.org/content/292/32/13271.full.pdf
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3054143