7ZVO

Structure of CBM BT0996-C from Bacteroides thetaiotaomicron

Summary for 7ZVO

• Entry DOI: 10.2210/pdb7zvo/pdb
• Descriptor: Beta-galactosidase, (4S)-2-METHYL-2,4-PENTANEDIOL, SERINE, ... (8 entities in total)
• Functional Keywords: cbm, carbohydrate-binding module, carbohydrate, rhamnogalacturonan ii, bacterial, microbiome, human gut, sugar binding protein
• Biological source: Bacteroides thetaiotaomicron VPI-5482
• Total number of polymer chains: 1
• Total formula weight: 16415.75

Authors

Trovao, F.,Pinheiro, B.A.,Correia, V.G.,Palma, A.S.,Carvalho, A.L. (deposition date: 2022-05-16, release date: 2023-02-08, Last modification date: 2024-05-01)

Primary citation

Trovao, F.,Correia, V.G.,Lourenco, F.M.,Ribeiro, D.O.,Carvalho, A.L.,Palma, A.S.,Pinheiro, B.A.
The structure of a Bacteroides thetaiotaomicron carbohydrate-binding module provides new insight into the recognition of complex pectic polysaccharides by the human microbiome.
J Struct Biol X, 7:100084-100084, 2023

PubMed Abstract: The  has developed a consortium of enzymes capable of overcoming steric constraints and degrading, in a sequential manner, the complex rhamnogalacturonan II (RG-II) polysaccharide. BT0996 protein acts in the initial stages of the RG-II depolymerisation, where its two catalytic modules remove the terminal monosaccharides from RG-II side chains A and B. BT0996 is modular and has three putative carbohydrate-binding modules (CBMs) for which the roles in the RG-II degradation are unknown. Here, we present the characterisation of the module at the C-terminal domain, which we designated BT0996-C. The high-resolution structure obtained by X-ray crystallography reveals that the protein displays a typical β-sandwich fold with structural similarity to CBMs assigned to families 6 and 35. The distinctive features are: 1) the presence of several charged residues at the BT0996-C surface creating a large, broad positive lysine-rich patch that encompasses the putative binding site; and 2) the absence of the highly conserved binding-site signatures observed in CBMs from families 6 and 35, such as region A tryptophan and region C asparagine. These findings hint at a binding mode of BT0996-C not yet observed in its homologues. In line with this, carbohydrate microarrays and microscale thermophoresis show the ability of BT0996-C to bind α1-4-linked polygalacturonic acid, and that electrostatic interactions are essential for the recognition of the anionic polysaccharide. The results support the hypothesis that BT0996-C may have evolved to potentiate the action of BT0996 catalytic modules on the complex structure of RG-II by binding to the polygalacturonic acid backbone sequence.

PubMed: 36660365
DOI: 10.1016/j.yjsbx.2022.100084

Experimental method

X-RAY DIFFRACTION (1.65 Å)