9D4I

Crystal structure of Ni(II)-bound polysaccharide deacetylase from Bacteroides ovatus

Summary for 9D4I

• Entry DOI: 10.2210/pdb9d4i/pdb
• Related: 9D44 9D5T 9D60
• Descriptor: Phage tail component domain protein, GLYCEROL, NICKEL (II) ION, ... (4 entities in total)
• Functional Keywords: esterase, hydrolase
• Biological source: Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / BCRC 10623 / CCUG 4943 / NCTC 11153)
• Total number of polymer chains: 1
• Total formula weight: 56029.10

Authors

Dzuong, E.,McLaughlin, K.J. (deposition date: 2024-08-12, release date: 2024-12-25, Last modification date: 2025-01-22)

Primary citation

Schwartz, L.A.,Norman, J.O.,Hasan, S.,Adamek, O.E.,Dzuong, E.,Lowenstein, J.C.,Yost, O.G.,Sankaran, B.,McLaughlin, K.J.
Carbohydrate Deacetylase Unique to Gut Microbe Bacteroides Reveals Atypical Structure.
Biochemistry, 64:180-191, 2025

PubMed Abstract: are often the most abundant, commensal species in the gut microbiome of industrialized human populations. One of the most commonly detected species is . 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 ; however, there is still much unknown. Here, we present structural and functional characterization of a putative polysaccharide deacetylase from (PDA) 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 Co, Ni, Cu, or Zn and performed carbohydrate binding and deacetylase activity assays. Structural analysis of PDA 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, PDA 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. PDA is the first protein involved in CPS biosynthesis from to be characterized, furthering our understanding of significant biosynthetic processes in this medically relevant gut microbe.

PubMed: 39663570
DOI: 10.1021/acs.biochem.4c00519

Experimental method

X-RAY DIFFRACTION (1.48 Å)