Structural insights into a family 39 glycoside hydrolase from the gut symbiont Bacteroides cellulosilyticus WH2

J Struct Biol. 2017 Mar;197(3):227-235. doi: 10.1016/j.jsb.2016.11.004. Epub 2016 Nov 24.


Bacteria from the human gut are equipped with an arsenal of carbohydrate-active enzymes that degrade dietary and host-derived glycans. In this study, we present the 2.5Å resolution crystal structure of a member (GH39wh2) from the human gut bacteria Bacteroides cellulosilyticus WH2 representative of a new subgroup within family GH39. Together with 6 other GHs, GH39wh2 belongs to a polysaccharide utilization locus (PUL) that could be involved in detecting, binding and hydrolysing a specific carbohydrate species from the intestinal tract. GH39wh2 shares a similar architecture as other members of family GH39 dominated by a typical (β/α)8-barrel fold harboring the catalytic residues and decorated by β-sandwich accessory domains. The GH39wh2 structure unveils an atypical shallow groove rather than a deep pocket due to drastic rearrangements in surface loops surrounding the catalytic interface. These structural adaptations seem to favour recognition of large branched substrates and may explain the lack of activity of GH39wh2 toward small xylose-based and other typical substrates from GH39 members, emphasizing the molecular diversity within the GH39 family. A phylogenetic analysis of the entire GH39 family assigns GH39wh2 as a new subgroup, consistent with the extensive remodelling of the active site region that may confer new substrate specificity toward a complex glycan chain.

Keywords: Bacteroides; Endoglycosidase; Glycoside hydrolase 39; Phylogeny.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteroides / enzymology*
  • Catalytic Domain
  • Computational Biology
  • Crystallography, X-Ray
  • Gastrointestinal Microbiome
  • Glycoside Hydrolases / chemistry*
  • Glycoside Hydrolases / classification
  • Glycoside Hydrolases / metabolism*
  • Phylogeny
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Substrate Specificity


  • Glycoside Hydrolases