8PXV | pdb_00008pxv

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: 2.50 Å
  • R-Value Free: 
    0.212 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8PXV

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 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.

Macromolecule Content 

  • Total Structure Weight: 220.73 kDa 
  • Atom Count: 15,590 
  • Modeled Residue Count: 1,912 
  • Deposited Residue Count: 1,965 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-N-acetylhexosaminidase
A, B, C
655Akkermansia muciniphilaMutation(s): 0 
Gene Names: Amuc_0369
EC: 3.2.1.52
UniProt
Find proteins for B2UN02 (Akkermansia muciniphila (strain ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP 107961 / Muc))
Explore B2UN02 
Go to UniProtKB:  B2UN02
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2UN02
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranoseD [auth E],
E [auth F]
2N/A
Glycosylation Resources
GlyTouCan: G84224TW
GlyCosmos: G84224TW
GlyGen: G84224TW

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.212 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.181 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.26α = 90
b = 170.42β = 90
c = 171.94γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
xia2data reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Independent Research Fund Denmark - Technology and Production SciencesDenmark0136-00086A

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