5NOA

Polysaccharide Lyase BACCELL_00875

Summary for 5NOA

• Entry DOI: 10.2210/pdb5noa/pdb
• Descriptor: Family 88 glycosyl hydrolase (2 entities in total)
• Functional Keywords: human gut microbiota, polysaccharide lyase, bacteroides thetaiotaomicron, gum arabic, hydrolase
• Biological source: Bacteroides thetaiotaomicron
• Total number of polymer chains: 1
• Total formula weight: 43673.03

Authors

Cartmell, A.,Munoz-Munoz, J.,Terrapon, N.,Basle, A.,Henrissat, B.,Gilbert, H.J. (deposition date: 2017-04-11, release date: 2017-06-28, Last modification date: 2024-01-17)

Primary citation

Munoz-Munoz, J.,Cartmell, A.,Terrapon, N.,Basle, A.,Henrissat, B.,Gilbert, H.J.
An evolutionarily distinct family of polysaccharide lyases removes rhamnose capping of complex arabinogalactan proteins.
J. Biol. Chem., 292:13271-13283, 2017

PubMed 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 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 , 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) 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.

PubMed: 28637865
DOI: 10.1074/jbc.M117.794578

Experimental method

X-RAY DIFFRACTION (1.26 Å)