7OZA

Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT3796_S1_16)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.141 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Sulfated glycan recognition by carbohydrate sulfatases of the human gut microbiota.

Luis, A.S.Basle, A.Byrne, D.P.Wright, G.S.A.London, J.A.Jin, C.Karlsson, N.G.Hansson, G.C.Eyers, P.A.Czjzek, M.Barbeyron, T.Yates, E.A.Martens, E.C.Cartmell, A.

(2022) Nat Chem Biol 18: 841-849

  • DOI: https://doi.org/10.1038/s41589-022-01039-x
  • Primary Citation of Related Structures:  
    7OZ8, 7OZ9, 7OZA, 7OZC, 7OZE, 7P24, 7P26

  • PubMed Abstract: 

    Sulfated glycans are ubiquitous nutrient sources for microbial communities that have coevolved with eukaryotic hosts. Bacteria metabolize sulfated glycans by deploying carbohydrate sulfatases that remove sulfate esters. Despite the biological importance of sulfatases, the mechanisms underlying their ability to recognize their glycan substrate remain poorly understood. Here, we use structural biology to determine how sulfatases from the human gut microbiota recognize sulfated glycans. We reveal seven new carbohydrate sulfatase structures spanning four S1 sulfatase subfamilies. Structures of S1_16 and S1_46 represent novel structures of these subfamilies. Structures of S1_11 and S1_15 demonstrate how non-conserved regions of the protein drive specificity toward related but distinct glycan targets. Collectively, these data reveal that carbohydrate sulfatases are highly selective for the glycan component of their substrate. These data provide new approaches for probing sulfated glycan metabolism while revealing the roles carbohydrate sulfatases play in host glycan catabolism.


  • Organizational Affiliation

    Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA. ana.luis@medkem.gu.se.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative secreted sulfatase ydeNA [auth AAA],
B [auth CCC]
522Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Gene Names: BT_3796
UniProt
Find proteins for Q8A171 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q8A171 
Go to UniProtKB:  Q8A171
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8A171
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
15P
Query on 15P

Download Ideal Coordinates CCD File 
G [auth CCC]POLYETHYLENE GLYCOL (N=34)
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
P6G
Query on P6G

Download Ideal Coordinates CCD File 
C [auth AAA]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
G4S (Subject of Investigation/LOI)
Query on G4S

Download Ideal Coordinates CCD File 
D [auth AAA],
I [auth CCC]
4-O-sulfo-beta-D-galactopyranose
C6 H12 O9 S
LOTQRUGOUKUSEY-DGPNFKTASA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
F [auth CCC],
H [auth CCC]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth AAA],
J [auth CCC]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
K [auth CCC]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.141 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.18α = 90
b = 88.95β = 112.05
c = 87.91γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2022-06-29 
  • Deposition Author(s): Cartmell, A.

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-29
    Type: Initial release
  • Version 1.1: 2022-08-10
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description