6VHO

Glycoside hydrolase family 16 endo-glucanase from Bacteroides ovatus in complex with G4G4G3G-NHCOCH2Br

This is a non-PDB format compatible entry.

Summary for 6VHO

• Entry DOI: 10.2210/pdb6vho/pdb
• Descriptor: Glycosyl hydrolase family 16, beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-N-acetyl-beta-D-glucopyranosylamine (3 entities in total)
• Functional Keywords: inhibitor, glucanase, hydrolase
• Biological source: Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153)
• Total number of polymer chains: 2
• Total formula weight: 61849.45

Authors

Tamura, K.,Brumer, H.,van Petegem, F. (deposition date: 2020-01-10, release date: 2021-01-13, Last modification date: 2023-10-11)

Primary citation

Jain, N.,Tamura, K.,Dejean, G.,Van Petegem, F.,Brumer, H.
Orthogonal Active-Site Labels for Mixed-Linkage endo-beta-Glucanases.
Acs Chem.Biol., 16:1968-1984, 2021

PubMed Abstract: Small molecule irreversible inhibitors are valuable tools for determining catalytically important active-site residues and revealing key details of the specificity, structure, and function of glycoside hydrolases (GHs). β-glucans that contain backbone β(1,3) linkages are widespread in nature, e.g., mixed-linkage β(1,3)/β(1,4)-glucans in the cell walls of higher plants and β(1,3)glucans in yeasts and algae. Commensurate with this ubiquity, a large diversity of mixed-linkage endoglucanases (MLGases, EC 3.2.1.73) and endo-β(1,3)-glucanases (laminarinases, EC 3.2.1.39 and EC 3.2.1.6) have evolved to specifically hydrolyze these polysaccharides, respectively, in environmental niches including the human gut. To facilitate biochemical and structural analysis of these GHs, with a focus on MLGases, we present here the facile chemo-enzymatic synthesis of a library of active-site-directed enzyme inhibitors based on mixed-linkage oligosaccharide scaffolds and -bromoacetylglycosylamine or 2-fluoro-2-deoxyglycoside warheads. The effectiveness and irreversibility of these inhibitors were tested with exemplar MLGases and an endo-β(1,3)-glucanase. Notably, determination of inhibitor-bound crystal structures of a human-gut microbial MLGase from Glycoside Hydrolase Family 16 revealed the orthogonal labeling of the nucleophile and catalytic acid/base residues with homologous 2-fluoro-2-deoxyglycoside and -bromoacetylglycosylamine inhibitors, respectively. We anticipate that the selectivity of these inhibitors will continue to enable the structural and mechanistic analyses of β-glucanases from diverse sources and protein families.

PubMed: 33988963
DOI: 10.1021/acschembio.1c00063

Experimental method

X-RAY DIFFRACTION (2.148 Å)