Carbohydrate Deacetylase Unique to Gut Microbe Bacteroides Reveals Atypical Structure

Schwartz, Lilith A.; Norman, Jordan O.; Hasan, Sharika; Adamek, Olive E.; Dzuong, Elisa; Lowenstein, Jasmine C.; Yost, Olivia G.; Sankaran, Banumathi; McLaughlin, Krystle J.

doi:10.1021/acs.biochem.4c00519

Title: Carbohydrate Deacetylase Unique to Gut Microbe Bacteroides Reveals Atypical Structure

Journal Article · 11 December 2024 · Biochemistry

DOI: https://doi.org/10.1021/acs.biochem.4c00519 · OSTI ID:2497298

^[1]; Norman, Jordan O. ^[1]; Hasan, Sharika ^[1]; Adamek, Olive E. ^[1]; Dzuong, Elisa ^[1]; Lowenstein, Jasmine C. ^[1]; Yost, Olivia G. ^[1]; Sankaran, Banumathi ^[2];

^[1]

Vassar College, Poughkeepsie, NY (United States)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Bacteroides are often the most abundant, commensal species in the gut microbiome of industrialized human populations. One of the most commonly detected species is Bacteroides ovatus. It has been linked to benefits like the suppression of intestinal inflammation but is also correlated with some autoimmune disorders, for example irritable bowel disorder (IBD). Bacterial cell surface carbohydrates, like capsular polysaccharides (CPS), may play a role in modulating these varied host interactions. Recent studies have begun to explore the diversity of CPS loci in Bacteroides; however, there is still much unknown. Here, we present structural and functional characterization of a putative polysaccharide deacetylase from Bacteroides ovatus (BoPDA) encoded in a CPS biosynthetic locus. We solved four high resolution crystal structures (1.36-1.56 Å) of the enzyme bound to divalent cations Co²⁺, Ni²⁺, Cu²⁺, or Zn²⁺ and performed carbohydrate binding and deacetylase activity assays. Structural analysis of BoPDA revealed an atypical domain architecture that is unique to this enzyme, with a carbohydrate esterase 4 (CE4) superfamily catalytic domain inserted into a carbohydrate binding module (CBM). Additionally, BoPDA lacks the canonical CE4 His-His-Asp metal binding motif and our structures show it utilizes a noncanonical His-Asp dyad to bind metal ions. BoPDA is the first protein involved in CPS biosynthesis from B. ovatus to be characterized, furthering our understanding of significant biosynthetic processes in this medically relevant gut microbe.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: National Institutes of Health (NIH); Research Corporation for Science Advancement (RCSA); USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2497298

Journal Information:: Biochemistry, Journal Name: Biochemistry Journal Issue: 1 Vol. 64; ISSN 0006-2960

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

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