7P26

Sulfated host glycan recognition by carbohydrate sulfatases of the human gut microbiota (BT4631_S1_15)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.123 

Starting Model: experimental
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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. [email protected].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative arylsulfataseA [auth AAA]517Bacteroides thetaiotaomicron VPI-5482Mutation(s): 0 
Gene Names: BT_4631
UniProt
Find proteins for Q89YV0 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50))
Explore Q89YV0 
Go to UniProtKB:  Q89YV0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ89YV0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
15P
Query on 15P

Download Ideal Coordinates CCD File 
B [auth AAA]POLYETHYLENE GLYCOL (N=34)
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
P4K
Query on P4K

Download Ideal Coordinates CCD File 
C [auth AAA]polyethylene glycol
C30 H62 O15
WWPGFZAAWXFBTF-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth AAA]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth AAA],
F [auth AAA]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.139 
  • R-Value Work: 0.123 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.924α = 90
b = 109.572β = 90
c = 117.531γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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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