8PVS

Targeting extended blood antigens by Akkermansia muciniphila enzymes unveils a missing link for generating universal donor blood


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Akkermansia muciniphila exoglycosidases target extended blood group antigens to generate ABO-universal blood.

Jensen, M.Stenfelt, L.Ricci Hagman, J.Pichler, M.J.Weikum, J.Nielsen, T.S.Hult, A.Morth, J.P.Olsson, M.L.Abou Hachem, M.

(2024) Nat Microbiol 9: 1176-1188

  • DOI: https://doi.org/10.1038/s41564-024-01663-4
  • Primary Citation of Related Structures:  
    8PVS, 8PXT, 8PXU, 8PXV

  • PubMed Abstract: 

    Matching donor and recipient blood groups based on red blood cell (RBC) surface ABO glycans and antibodies in plasma is crucial to avoid potentially fatal reactions during transfusions. Enzymatic conversion of RBC glycans to the universal group O is an attractive solution to simplify blood logistics and prevent ABO-mismatched transfusions. The gut symbiont Akkermansia muciniphila can degrade mucin O-glycans including ABO epitopes. Here we biochemically evaluated 23 Akkermansia glycosyl hydrolases and identified exoglycosidase combinations which efficiently transformed both A and B antigens and four of their carbohydrate extensions. Enzymatic removal of canonical and extended ABO antigens on RBCs significantly improved compatibility with group O plasmas, compared to conversion of A or B antigens alone. Finally, structural analyses of two B-converting enzymes identified a previously unknown putative carbohydrate-binding module. This study demonstrates the potential utility of mucin-degrading gut bacteria as valuable sources of enzymes for production of universal blood for transfusions.


  • Organizational Affiliation

    Department of Biotechnology & Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Alpha-1,3-galactosidase B
A, B
731Akkermansia muciniphilaMutation(s): 0 
Gene Names: glaBAmuc_0480
EC: 3.2.1 (PDB Primary Data), 3.2.1.22 (PDB Primary Data)
UniProt
Find proteins for B2UNU8 (Akkermansia muciniphila (strain ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP 107961 / Muc))
Explore B2UNU8 
Go to UniProtKB:  B2UNU8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2UNU8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GLA (Subject of Investigation/LOI)
Query on GLA

Download Ideal Coordinates CCD File 
C [auth A],
M [auth B]
alpha-D-galactopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PHYPRBDBSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
N [auth B],
O [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT
Query on FMT

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
P [auth B]
Q [auth B]
E [auth A],
F [auth A],
G [auth A],
P [auth B],
Q [auth B],
R [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
S [auth B],
T [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth A],
K [auth A],
L [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.171 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.527α = 90
b = 134.035β = 90
c = 215.346γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
xia2data reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danmarks Frie Forskningsfond | Teknologi og ProduktionDenmark0136-00086A

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-28
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Database references
  • Version 1.2: 2024-05-15
    Changes: Database references
  • Version 1.3: 2024-05-22
    Changes: Database references