9D5T | pdb_00009d5t

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 
    0.201 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.175 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Carbohydrate Deacetylase Unique to Gut Microbe Bacteroides Reveals Atypical Structure.

Schwartz, L.A.Norman, J.O.Hasan, S.Adamek, O.E.Dzuong, E.Lowenstein, J.C.Yost, O.G.Sankaran, B.McLaughlin, K.J.

(2025) Biochemistry 64: 180-191

  • DOI: https://doi.org/10.1021/acs.biochem.4c00519
  • Primary Citation of Related Structures:  
    9D44, 9D4I, 9D5T, 9D60

  • PubMed Abstract: 

    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 ( Bo 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 2+ , Ni 2+ , Cu 2+ , or Zn 2+ and performed carbohydrate binding and deacetylase activity assays. Structural analysis of Bo 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, Bo 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. Bo PDA 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.


  • Organizational Affiliation
    • Department of Chemistry, Vassar College, 124 Raymond Ave, Poughkeepsie, New York 12604, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phage tail component domain protein480Bacteroides ovatus ATCC 8483Mutation(s): 0 
Gene Names: BACOVA_03992
UniProt
Find proteins for A0AAN3A5R0 (Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / BCRC 10623 / CCUG 4943 / NCTC 11153))
Explore A0AAN3A5R0 
Go to UniProtKB:  A0AAN3A5R0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAN3A5R0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free:  0.201 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.175 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.764α = 90
b = 73.183β = 90
c = 95.41γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30 GM124169-01

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Database references