8AXS | pdb_00008axs

Sialidases and Fucosidases of Akkermansia muciniphila are key for rapid growth on colonic mucin and nutrient sharing amongst mucin-associated human gut microbiota


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.188 (Depositor), 0.194 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 8AXS

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Sialidases and fucosidases of Akkermansia muciniphila are crucial for growth on mucin and nutrient sharing with mucus-associated gut bacteria.

Shuoker, B.Pichler, M.J.Jin, C.Sakanaka, H.Wu, H.Gascuena, A.M.Liu, J.Nielsen, T.S.Holgersson, J.Nordberg Karlsson, E.Juge, N.Meier, S.Morth, J.P.Karlsson, N.G.Abou Hachem, M.

(2023) Nat Commun 14: 1833-1833

  • DOI: https://doi.org/10.1038/s41467-023-37533-6
  • Primary Citation Related Structures: 
    8AXI, 8AXS, 8AXT, 8AYR

  • PubMed Abstract: 

    The mucolytic human gut microbiota specialist Akkermansia muciniphila is proposed to boost mucin-secretion by the host, thereby being a key player in mucus turnover. Mucin glycan utilization requires the removal of protective caps, notably fucose and sialic acid, but the enzymatic details of this process remain largely unknown. Here, we describe the specificities of ten A. muciniphila glycoside hydrolases, which collectively remove all known sialyl and fucosyl mucin caps including those on double-sulfated epitopes. Structural analyses revealed an unprecedented fucosidase modular arrangement and explained the sialyl T-antigen specificity of a sialidase of a previously unknown family. Cell-attached sialidases and fucosidases displayed mucin-binding and their inhibition abolished growth of A. muciniphila on mucin. Remarkably, neither the sialic acid nor fucose contributed to A. muciniphila growth, but instead promoted butyrate production by co-cultured Clostridia. This study brings unprecedented mechanistic insight into the initiation of mucin O-glycan degradation by A. muciniphila and nutrient sharing between mucus-associated bacteria.


  • Organizational Affiliation
    • Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, 2800, Denmark.

Macromolecule Content 

  • Total Structure Weight: 130.62 kDa 
  • Atom Count: 10,740 
  • Modeled Residue Count: 1,145 
  • Deposited Residue Count: 1,154 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Exo-alpha-sialidase578Akkermansia muciniphilaMutation(s): 0 
Gene Names: HXS70_08015
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Exo-alpha-sialidase576Akkermansia muciniphilaMutation(s): 0 
Gene Names: HXS70_08015

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SLB
(Subject of Investigation/LOI)

Query on SLB



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
M [auth B]
N-acetyl-beta-neuraminic acid
C11 H19 N O9
SQVRNKJHWKZAKO-PFQGKNLYSA-N
DAN

Query on DAN



Download:Ideal Coordinates CCD File
N [auth B]2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
C11 H17 N O8
JINJZWSZQKHCIP-UFGQHTETSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
L [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
IMD

Query on IMD



Download:Ideal Coordinates CCD File
E [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A]
G [auth A]
H [auth A]
O [auth B]
P [auth B]
F [auth A],
G [auth A],
H [auth A],
O [auth B],
P [auth B],
Q [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
K [auth A],
T [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
R [auth B],
S [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.188 (Depositor), 0.194 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.07α = 90
b = 51.78β = 93.07
c = 118.44γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
xia2data reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danish Council for Independent ResearchDenmark1026-00386B
Other governmentIraq--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-01
    Type: Initial release
  • Version 1.1: 2023-04-19
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection
  • Version 1.3: 2024-05-01
    Changes: Refinement description