7P26 | pdb_00007p26

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

• PDB DOI: https://doi.org/10.2210/pdb7P26/pdb

• Classification: HYDROLASE
• Organism(s): Bacteroides thetaiotaomicron VPI-5482
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2021-07-04 Released: 2022-06-29 
• Deposition Author(s): Cartmell, A.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.139 (Depositor), 0.139 (DCC) 
• R-Value Work: 
  0.123 (Depositor), 0.123 (DCC) 

Starting Model: experimental

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

• PubMed: 35710619 
• DOI: https://doi.org/10.1038/s41589-022-01039-x
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA. [e-mail].
Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden. [e-mail].
Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, UK.
Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden.
Faculty of Health Sciences, Department of Life Sciences and Health, Pharmacy, Oslo Metropolitan University, Oslo, Norway.
Sorbonne Université, Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS, Roscoff, France.
Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 59.53 kDa 
• Atom Count: 4,704 
• Modeled Residue Count: 484 
• Deposited Residue Count: 517 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative arylsulfatase	A [auth AAA]	517	Bacteroides thetaiotaomicron VPI-5482	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
15P	B [auth AAA]	POLYETHYLENE GLYCOL (N=34) C69 H140 O35 VUYXVWGKCKTUMF-UHFFFAOYSA-N
P4K	C [auth AAA]	polyethylene glycol C30 H62 O15 WWPGFZAAWXFBTF-UHFFFAOYSA-N
CA	D [auth AAA]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	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 (Depositor), 0.139 (DCC) 
• R-Value Work:  0.123 (Depositor), 0.123 (DCC) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.924	α = 90
b = 109.572	β = 90
c = 117.531	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

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

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• 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