Atypical Structure Revealed In Carbohydrate Deacetylase Unique to Bacteroides

TL;DR

Researchers discovered a unique enzyme in Bacteroides ovatus that could influence gut health and autoimmune disorders.

Contribution

The study reveals the first structural and functional analysis of a carbohydrate deacetylase from Bacteroides ovatus.

Findings

BoPDA has an atypical domain architecture with a CE4 NodB homology domain inserted into a CBM.

BoPDA uses a non-canonical His-Asp dyad instead of the typical CE4 metal binding motif.

The enzyme's structure and function were characterized through crystallography and biochemical assays.

Abstract

Bacteroides ovatus is one of the most commonly found Bacteroides species in the human gut and has been linked to benefits like the suppression of intestinal inflammation. Conversely, increased populations of B. ovatus is correlated with several autoimmune disorders, including irritable bowel disorder (IBD). Bacterial cell surface carbohydrates such as capsular polysaccharides (CPS) may play a role in these host-microbe interactions as they have known immunomodulatory effects such as polysaccharide A (PSA) from B. fragilis. Despite their importance, few enzymes encoded in CPS biosynthetic loci have been studied. We report structural characterization of a putative polysaccharide deacetylase from Bacteroides ovatus (BoPDA) encoded in a CPS biosynthetic locus. Four high resolution crystal structures (1.36 Å – 1.56 Å) of the enzyme bound to divalent cations Co2+, Ni2+, Cu2+ or Zn2+ revealed an atypical domain architecture that is unique to this enzyme. BoPDA has a carbohydrate esterase 4 (CE4) superfamily catalytic NodB homology domain inserted into a carbohydrate binding module (CBM). BoPDA also lacks the canonical CE4 His-His-Asp metal binding motif, instead using a non-canonical His-Asp dyad. We also performed carbohydrate binding and deacetylase activity assays to probe the function of the enzyme. Our work furthers understanding of this medically relevant microbe, as BoPDA represents the first protein involved in CPS biosynthesis from B. ovatus to be characterized.