6T5O

Bacteroides salyersiae GH164 beta-mannosidase

This is a non-PDB format compatible entry.

Summary for 6T5O

• Entry DOI: 10.2210/pdb6t5o/pdb
• Descriptor: Glyco_hydro_42M domain-containing protein, 1,2-ETHANEDIOL, S,R MESO-TARTARIC ACID, ... (8 entities in total)
• Functional Keywords: beta-mannosidase glycoside hydrolase, hydrolase
• Biological source: Bacteroides salyersiae
• Total number of polymer chains: 6
• Total formula weight: 462981.27

Authors

Armstrong, Z.,Davies, G. (deposition date: 2019-10-16, release date: 2020-01-01, Last modification date: 2024-05-15)

Primary citation

Armstrong, Z.,Davies, G.J.
Structure and function ofBs164 beta-mannosidase fromBacteroides salyersiaethe founding member of glycoside hydrolase family GH164.
J.Biol.Chem., 295:4316-4326, 2020

PubMed Abstract: Recent work exploring protein sequence space has revealed a new glycoside hydrolase (GH) family (GH164) of putative mannosidases. GH164 genes are present in several commensal bacteria, implicating these genes in the degradation of dietary glycans. However, little is known about the structure, mechanism of action, and substrate specificity of these enzymes. Herein we report the biochemical characterization and crystal structures of the founding member of this family (164) from the human gut symbiont Previous reports of this enzyme indicated that it has α-mannosidase activity, however, we conclusively show that it cleaves only β-mannose linkages. Using NMR spectroscopy, detailed enzyme kinetics of WT and mutant 164, and multiangle light scattering we found that it is a trimeric retaining β-mannosidase, that is susceptible to several known mannosidase inhibitors. X-ray crystallography revealed the structure of 164, the first known structure of a GH164, at 1.91 Å resolution. 164 is composed of three domains: a (β/α) barrel, a trimerization domain, and a β-sandwich domain, representing a previously unobserved structural-fold for β-mannosidases. Structures of 164 at 1.80-2.55 Å resolution in complex with the inhibitors noeuromycin, mannoimidazole, or 2,4-dinitrophenol 2-deoxy-2-fluoro-mannoside reveal the residues essential for specificity and catalysis including the catalytic nucleophile (Glu-297) and acid/base residue (Glu-160). These findings further our knowledge of the mechanisms commensal microbes use for nutrient acquisition.

PubMed: 31871050
DOI: 10.1074/jbc.RA119.011591

Experimental method

X-RAY DIFFRACTION (1.91 Å)